subject:(tRNA)

1. 前田, 雄翔. 塩基配列情報に基づいたtRNA共起解析 : tRNA architecture analysis based on nucleotide sequences; エンキハイレツジョウホウニモトズイタ tRNA キョウキカイセキ.

Degree: Nara Institute of Science and Technology / 奈良先端科学技術大学院大学

URL: http://hdl.handle.net/10061/5200

Subjects/Keywords: tRNA

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APA (6^th Edition):

前田, �. (n.d.). 塩基配列情報に基づいたtRNA共起解析 : tRNA architecture analysis based on nucleotide sequences; エンキハイレツジョウホウニモトズイタ tRNA キョウキカイセキ. (Thesis). Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Retrieved from http://hdl.handle.net/10061/5200

Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

前田, 雄翔. “塩基配列情報に基づいたtRNA共起解析 : tRNA architecture analysis based on nucleotide sequences; エンキハイレツジョウホウニモトズイタ tRNA キョウキカイセキ.” Thesis, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Accessed January 15, 2021. http://hdl.handle.net/10061/5200.

Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

前田, 雄翔. “塩基配列情報に基づいたtRNA共起解析 : tRNA architecture analysis based on nucleotide sequences; エンキハイレツジョウホウニモトズイタ tRNA キョウキカイセキ.” Web. 15 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
No year of publication.

Vancouver:

前田 �. 塩基配列情報に基づいたtRNA共起解析 : tRNA architecture analysis based on nucleotide sequences; エンキハイレツジョウホウニモトズイタ tRNA キョウキカイセキ. [Internet] [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; [cited 2021 Jan 15]. Available from: http://hdl.handle.net/10061/5200.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.

Council of Science Editors:

前田 �. 塩基配列情報に基づいたtRNA共起解析 : tRNA architecture analysis based on nucleotide sequences; エンキハイレツジョウホウニモトズイタ tRNA キョウキカイセキ. [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; Available from: http://hdl.handle.net/10061/5200

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.

University of Illinois – Chicago

2. Holman, Kaitlyn M. The mechanism of substrate recognition by promiscuous aminoacyl-tRNA synthetases.

Degree: 2016, University of Illinois – Chicago

URL: http://hdl.handle.net/10027/20259

► Faithful translation of the genetic information, imprinted in the mRNA, into a functional protein is a fundamental biological process. Aminoacyl-tRNA synthetases (aaRSs) are ancient enzymes… (more)

▼ Faithful translation of the genetic information, imprinted in the mRNA, into a functional protein is a fundamental biological process. Aminoacyl-tRNA synthetases (aaRSs) are ancient enzymes that ensure fidelity of gene translation by coupling every proteinogenic amino acid with the cognate transfer RNA (tRNA). Whereas selection of the amino acid is dictated by the architecture of the aminoacylation site, recognition of tRNA requires specific interactions between the aaRS and several structural motifs in the tRNA. Because of these features it was presumed that aaRSs are highly specific and cannot act on tRNAs with different structures and anticodon sequences. This also served as a basis for the proposal that the genetic code is universal and that perhaps arose as the result of the “frozen accident”. However, in the yeast mitochondria the CUN box codes for threonine instead of the canonical leucine, whereas the opal stop codon is recoded into a signal for selenocysteine incorporation in all domains of life. The main goal of this doctoral thesis is to explain at the structural level how these genetic code reassignment events are promoted. These mechanisms are of particular interest since they alter the interpretation of the genetic code and thus facilitate its evolution. Our results show that the leucine-to-threonine recoding in the yeast mitochondria is promoted by a promiscuous ThrRS (MST1) and a non-canonical tRNA1Thr that harbors enlarged anticodon loop and anticodon sequence complementary to the CUN codon box. We show that MST1 employs distinct mechanisms for binding to tRNA1Thr and tRNA2Thr, that pre-transfer editing is utilized for selection against serine, and that unique properties of the anticodon-binding domain are perhaps important for binding to distinct isoacceptor tRNAs. On the other hand, recoding of the opal stop codon is facilitated by promiscuous SerRS that acts on both tRNASer and tRNASec. In contrast to MST1, human SerRS does not bind anticodon loops of either tRNA. Further, our results show that SerRS binds both tRNAs with similar binding affinities, yet utilizes tRNASer as a superior substrate presumably because of its canonical fold. Hence, MST1 and SerRS use completely different strategies for promoting recoding of particular codons. Advisors/Committee Members: Simonovic, Miljan (advisor), Caffrey, Michael (committee member), Colley, Karen (committee member), Lavie, Arnon (committee member), Volz, Karl (committee member), Mankin, Alexander (committee member).

Subjects/Keywords: aminoacyl-tRNA synthetases; codon reassignment events; tRNA

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APA (6^th Edition):

Holman, K. M. (2016). The mechanism of substrate recognition by promiscuous aminoacyl-tRNA synthetases. (Thesis). University of Illinois – Chicago. Retrieved from http://hdl.handle.net/10027/20259

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Holman, Kaitlyn M. “The mechanism of substrate recognition by promiscuous aminoacyl-tRNA synthetases.” 2016. Thesis, University of Illinois – Chicago. Accessed January 15, 2021. http://hdl.handle.net/10027/20259.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Holman, Kaitlyn M. “The mechanism of substrate recognition by promiscuous aminoacyl-tRNA synthetases.” 2016. Web. 15 Jan 2021.

Vancouver:

Holman KM. The mechanism of substrate recognition by promiscuous aminoacyl-tRNA synthetases. [Internet] [Thesis]. University of Illinois – Chicago; 2016. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/10027/20259.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Holman KM. The mechanism of substrate recognition by promiscuous aminoacyl-tRNA synthetases. [Thesis]. University of Illinois – Chicago; 2016. Available from: http://hdl.handle.net/10027/20259

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Western Ontario

3. Zhu, Yanrui. Determining Whether the Nature of the Amino Acid Substitution or the Extent of Mistranslation Affects the Impact of Mistranslating tRNAs in Saccharomyces cerevisiae.

Degree: 2020, University of Western Ontario

URL: https://ir.lib.uwo.ca/etd/6982

► Mistranslation occurs when an mRNA sequence is improperly decoded. Mistranslation can destabilize the proteome thus having a detrimental impact on the cell. tRNA variants with… (more)

Subjects/Keywords: Mistranslation; tRNA; tRNA variants; proteotoxic stress; Biochemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zhu, Y. (2020). Determining Whether the Nature of the Amino Acid Substitution or the Extent of Mistranslation Affects the Impact of Mistranslating tRNAs in Saccharomyces cerevisiae. (Thesis). University of Western Ontario. Retrieved from https://ir.lib.uwo.ca/etd/6982

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zhu, Yanrui. “Determining Whether the Nature of the Amino Acid Substitution or the Extent of Mistranslation Affects the Impact of Mistranslating tRNAs in Saccharomyces cerevisiae.” 2020. Thesis, University of Western Ontario. Accessed January 15, 2021. https://ir.lib.uwo.ca/etd/6982.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zhu, Yanrui. “Determining Whether the Nature of the Amino Acid Substitution or the Extent of Mistranslation Affects the Impact of Mistranslating tRNAs in Saccharomyces cerevisiae.” 2020. Web. 15 Jan 2021.

Vancouver:

Zhu Y. Determining Whether the Nature of the Amino Acid Substitution or the Extent of Mistranslation Affects the Impact of Mistranslating tRNAs in Saccharomyces cerevisiae. [Internet] [Thesis]. University of Western Ontario; 2020. [cited 2021 Jan 15]. Available from: https://ir.lib.uwo.ca/etd/6982.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zhu Y. Determining Whether the Nature of the Amino Acid Substitution or the Extent of Mistranslation Affects the Impact of Mistranslating tRNAs in Saccharomyces cerevisiae. [Thesis]. University of Western Ontario; 2020. Available from: https://ir.lib.uwo.ca/etd/6982

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Rochester

4. Payea, Matthew John. Characterization of tRNA Quality Control Pathways in Yeast.

Degree: PhD, 2020, University of Rochester

URL: http://hdl.handle.net/1802/36077

► Fully mature tRNAs are critical for translation, and defects in tRNA modification, processing, and stability can cause neurological and mitochondrial diseases. In the yeast Saccharomyces… (more)

▼ Fully mature tRNAs are critical for translation, and defects in tRNA modification, processing, and stability can cause neurological and mitochondrial diseases. In the yeast Saccharomyces cerevisiae, the integrity of pre-tRNA and mature tRNAs are monitored by the nuclear surveillance pathway and the rapid tRNA decay (RTD) pathway respectively. The RTD pathway operates through two 5'–3' exonucleases, Rat1 and Xrn1, which act to degrade tRNAs with a tertiary structure more vulnerable to 5' attack through either hypomodification or destabilizing mutations. Previous work on the RTD pathway indicated that tRNA variants in the acceptor stem and T-stem were degraded because of instability in the acceptor/T-stem coaxial stack of the tertiary structure. However, this understanding of the RTD pathway could only describe a limited set of substrates, and could not accurately predict non-substrates. Here I will describe my results characterizing substrate specificity of the RTD pathway and the identification of a potentially new tRNA decay pathway that targets destabilized pre-tRNA. I will present the results of a high-throughput in vivo screen that was used to identify the effects of variants on the function and RTD susceptibility of the SUP4oc suppressor tRNA. From this screen, we discovered that tRNAs are highly resistant to mutations but are also broadly susceptible to the RTD pathway, as destabilizing mutations in every region of the tRNA were able to provoke RTD. Variants with mutations in the anticodon stem were particularly surprising, since destabilization of the anticodon stem would not be expected to contribute to 5'–3' exonuclease susceptibility. I will also present results showing that RTD susceptibility and temperature sensitivity are linked. We analyzed our SUP4oc variant library for function at 37 °C and 28 °C, and found that a majority of variants are temperature sensitive. This temperature sensitivity is due to degradation by the RTD pathway in a majority of these variants since tRNA function is improved when RTD is inhibited. I will then describe results indicating that the SUP4oc anticodon stem variants identified in our high-throughput screen are degraded as both pre-tRNA and mature tRNA, and that the pre-tRNA degradation occurs by a yet unknown mechanism. I will present evidence that anticodon stem variants accumulate dramatic amounts of pre-tRNA, in some cases rivaling the amounts measured for the endogenous tRNATyr, and that this pre-tRNA is increased in a strain where 5'–3' exonucleases are inhibited, thus implying it is decayed. I will provide evidence that indicates the pre-tRNA degradation of anticodon stem variants is not mediated by either the RTD pathway or the nuclear surveillance pathway, but instead by a previously unknown mechanism of pre-tRNA decay. I will then present a model for the decay of pre-tRNA called Opportunistic Decay in which tRNA decay is determined by tRNA instability and tRNA availability, both of which are necessary. Furthermore, I will show that this model can be…

Subjects/Keywords: RNA Quality control; Rapid tRNA decay; tRNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Payea, M. J. (2020). Characterization of tRNA Quality Control Pathways in Yeast. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/36077

Chicago Manual of Style (16^th Edition):

Payea, Matthew John. “Characterization of tRNA Quality Control Pathways in Yeast.” 2020. Doctoral Dissertation, University of Rochester. Accessed January 15, 2021. http://hdl.handle.net/1802/36077.

MLA Handbook (7^th Edition):

Payea, Matthew John. “Characterization of tRNA Quality Control Pathways in Yeast.” 2020. Web. 15 Jan 2021.

Vancouver:

Payea MJ. Characterization of tRNA Quality Control Pathways in Yeast. [Internet] [Doctoral dissertation]. University of Rochester; 2020. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/1802/36077.

Council of Science Editors:

Payea MJ. Characterization of tRNA Quality Control Pathways in Yeast. [Doctoral Dissertation]. University of Rochester; 2020. Available from: http://hdl.handle.net/1802/36077

University of Alberta

5. Clelland, Brett William. Studies on the control of tRNA transcription by the replication stress checkpoint.

Degree: PhD, Department of Biochemistry, 2011, University of Alberta

URL: https://era.library.ualberta.ca/files/j6731377h

► RNA polymerase III (RNAPIII) pre-initiation complexes at tRNA genes naturally cause replication fork pausing in the yeast Saccharomyces cerevisiae, and interference with replication is known… (more)

▼ RNA polymerase III (RNAPIII) pre-initiation complexes at tRNA genes naturally cause replication fork pausing in the yeast Saccharomyces cerevisiae, and interference with replication is known to have deleterious effects on genome stability. It follows that repression of tRNA gene transcription could be advantageous to minimize replication perturbation. Consistent with this idea, our lab has previously reported that the replication stress checkpoint inhibits tRNA gene transcription. Here, I describe how repression by checkpoint signalling, induced by treatment with the replication inhibitor hydroxyurea (HU), is associated with RNAPIII pre-initiation complex disassembly at tRNA genes. In addition, I show that active checkpoint signals likely impinge on Maf1, a key negative regulator of RNAPIII transcription, to signal to tRNA genes during HU exposure. Next, I report that checkpoint signalling affects the protein complex assemblage at tRNA genes during normal proliferation. Inactivation of the replication stress checkpoint, which is associated with an induction of tRNA gene transcription, results in greater RNAPIII occupancy at tRNA genes and a decrease in condensin association, condensin being an important tDNA localized complex that is vital for maintenance of genome integrity. Next, I extended these results by monitoring replication in cells with elevated tRNA gene transcription using cross-linking of replication proteins as proxy for replication fork movement. Despite the fact that tRNA gene transcription interferes with replication, by this method I detected no greater fork pausing at tRNA genes in strains with elevated transcription. These data are discussed in the context of current controversy in the literature about this type of replication perturbation. One possibility is that in cells unable to repress transcription, replication interference promotes greater genome instability in a way that does not include amplified fork pausing. Altogether, the results presented here are in harmony with the idea that the replication stress checkpoint functions to disassemble RNAPIII transcriptional machinery, likely to maintain genome stability. Lastly, I present preliminary data that identifies potential cell division cycle links to tRNA transcription. We propose a possible new pathway that restrains tRNA gene transcription involving Cdc28, the main cyclin-dependent kinase in yeast.

Subjects/Keywords: transcription; tRNA; replication

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Clelland, B. W. (2011). Studies on the control of tRNA transcription by the replication stress checkpoint. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/j6731377h

Chicago Manual of Style (16^th Edition):

Clelland, Brett William. “Studies on the control of tRNA transcription by the replication stress checkpoint.” 2011. Doctoral Dissertation, University of Alberta. Accessed January 15, 2021. https://era.library.ualberta.ca/files/j6731377h.

MLA Handbook (7^th Edition):

Clelland, Brett William. “Studies on the control of tRNA transcription by the replication stress checkpoint.” 2011. Web. 15 Jan 2021.

Vancouver:

Clelland BW. Studies on the control of tRNA transcription by the replication stress checkpoint. [Internet] [Doctoral dissertation]. University of Alberta; 2011. [cited 2021 Jan 15]. Available from: https://era.library.ualberta.ca/files/j6731377h.

Council of Science Editors:

Clelland BW. Studies on the control of tRNA transcription by the replication stress checkpoint. [Doctoral Dissertation]. University of Alberta; 2011. Available from: https://era.library.ualberta.ca/files/j6731377h

University of Toronto

6. Her, Sohyoung. Lanthanum-mediated Biomimetic Aminoacylation.

Degree: 2012, University of Toronto

URL: http://hdl.handle.net/1807/42391

►

Methods are being developed to produce “designer proteins” from unnatural amino acids that are added into specific locations by the ribosome using an altered mRNA.… (more)

Subjects/Keywords: tRNA; aminoacylation; 0490

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Her, S. (2012). Lanthanum-mediated Biomimetic Aminoacylation. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/42391

Chicago Manual of Style (16^th Edition):

Her, Sohyoung. “Lanthanum-mediated Biomimetic Aminoacylation.” 2012. Masters Thesis, University of Toronto. Accessed January 15, 2021. http://hdl.handle.net/1807/42391.

MLA Handbook (7^th Edition):

Her, Sohyoung. “Lanthanum-mediated Biomimetic Aminoacylation.” 2012. Web. 15 Jan 2021.

Vancouver:

Her S. Lanthanum-mediated Biomimetic Aminoacylation. [Internet] [Masters thesis]. University of Toronto; 2012. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/1807/42391.

Council of Science Editors:

Her S. Lanthanum-mediated Biomimetic Aminoacylation. [Masters Thesis]. University of Toronto; 2012. Available from: http://hdl.handle.net/1807/42391

University of California – Santa Cruz

7. Lin, Brian Y. Practical Tools for Exploring tRNA Conservation.

Degree: Bioinformatics, 2018, University of California – Santa Cruz

URL: http://www.escholarship.org/uc/item/3hn1q3rb

► Transfer RNAs (tRNAs) are universal to living organisms, and are involved in a variety of noncanonical functions. Systematically identifying atypical tRNAs is of considerable biological… (more)

Subjects/Keywords: Bioinformatics; Biology; tRNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Lin, B. Y. (2018). Practical Tools for Exploring tRNA Conservation. (Thesis). University of California – Santa Cruz. Retrieved from http://www.escholarship.org/uc/item/3hn1q3rb

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Lin, Brian Y. “Practical Tools for Exploring tRNA Conservation.” 2018. Thesis, University of California – Santa Cruz. Accessed January 15, 2021. http://www.escholarship.org/uc/item/3hn1q3rb.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Lin, Brian Y. “Practical Tools for Exploring tRNA Conservation.” 2018. Web. 15 Jan 2021.

Vancouver:

Lin BY. Practical Tools for Exploring tRNA Conservation. [Internet] [Thesis]. University of California – Santa Cruz; 2018. [cited 2021 Jan 15]. Available from: http://www.escholarship.org/uc/item/3hn1q3rb.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Lin BY. Practical Tools for Exploring tRNA Conservation. [Thesis]. University of California – Santa Cruz; 2018. Available from: http://www.escholarship.org/uc/item/3hn1q3rb

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universitat de Valencia

8. Martínez Zamora, Ana. Caracterización funcional de GTPBP3: una proteína G implicada en la modificación de tRNAs mitocondriales.

Degree: 2015, Universitat de Valencia

URL: http://hdl.handle.net/10550/47796

► Determinadas enfermedades mitocondriales, como MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes), MERRF (myoclonus epilepsy associated with ragged-red-fibers), cardiomiopatía hipertrófica y acidosis láctica dependiente… (more)

▼ Determinadas enfermedades mitocondriales, como MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes), MERRF (myoclonus epilepsy associated with ragged-red-fibers), cardiomiopatía hipertrófica y acidosis láctica dependiente de GTPBP3, cardiomiopatía hipertrófica infantil y acidosis láctica dependiente de MTO1 y fallo hepático infantil agudo dependiente de TRMU, están asociadas con una disfunción severa del sistema de fosforilación oxidativa (OXPHOS) que, se cree, podría ser resultado de defectos en la modificación postranscripcional de la uridina localizada en la posición de tambaleo (U34) de ciertos tRNAs mitocondriales (mt-tRNAs) y, por consiguiente, de un mal funcionamiento de la traducción mitocondrial. A partir de la alta conservación evolutiva del proceso de modificación de la U34 se ha sugerido que las proteínas humanas TRMU, GTPBP3 y MTO1 desempeñan las mismas funciones que sus homólogas en levaduras y bacterias. GTPBP3 y MTO1 se encargarían de introducir el grupo taurinometil en la posición 5 de la U34 en los mt-tRNAs Leu, Lys, Glu, Gln y Trp, mientras que, TRMU introduce el grupo tiol en la posición 2 de la U34 de los mt-tRNAs Lys, Glu y Gln. En humanos, mutaciones en GTPBP3 causan cardiomiopatía hipertrófica y acidosis láctica, y han sido asociadas con defecto en la traducción mitocondrial, aunque el mecanismo patogénico no está claro. En esta tesis utilizamos un sistema modelo donde GTPBP3 se encuentra silenciado establemente (células shGTPBP3) para conseguir una caracterización más profunda del fenotipo conferido por la deficiencia de GTPBP3 y poder estudiar el mecanismo molecular subyacente. Usando un ensayo de sensibilidad a la digestión por angiogenina de los mt-tRNAs, que validamos con tRNAs de Escherichia coli, demostramos experimentalmente por primera vez que la falta de GTPBP3 está asociada con hipomodificación del mt-tRNA, puesto que los mt-tRNAs de las células silenciadas para GTPBP3 son más sensibles a la digestión con angiogenina que los de las células control. A pesar de que el efecto del silenciamiento estable de GTPBP3 sobre la síntesis mitocondrial de proteínas global es bastante suave, observamos una disminución del 50% en los niveles estacionarios y actividad del Complejo I del sistema OXPHOS, así como en los niveles de ATP celular en las células shGTPBP3 respecto a las células control. Llamativamente, la actividad ATPasa del Complejo V se encuentra incrementada un 40% en las células shGTPBP3, sugiriendo que la mitocondria consume ATP para mantener el potencial de membrana mitocondrial. Además, las células shGTPBP3 exhiben una capacidad antioxidante aumentada y un incremento de casi dos veces en los niveles de la proteína desacoplante UCP2. Los datos obtenidos indican que el silenciamiento estable de GTPBP3 inicia una señalización retrógrada dependiente de AMPK que disminuye los niveles de mRNA de los factores de ensamblaje del Complejo I NDUFAF3 y NDUFAF4 y la expresión (a nivel de mRNA y de proteína) del transportador del piruvato (MPC), mientras que… Advisors/Committee Members: Armengod González, María Eugenia (advisor).

Subjects/Keywords: tRNA mitocondrial; gtpbp3; oxphos; trna mitocondrial; modificación trna; metabolismo mitocondrial

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Martínez Zamora, A. (2015). Caracterización funcional de GTPBP3: una proteína G implicada en la modificación de tRNAs mitocondriales. (Doctoral Dissertation). Universitat de Valencia. Retrieved from http://hdl.handle.net/10550/47796

Chicago Manual of Style (16^th Edition):

Martínez Zamora, Ana. “Caracterización funcional de GTPBP3: una proteína G implicada en la modificación de tRNAs mitocondriales. ” 2015. Doctoral Dissertation, Universitat de Valencia. Accessed January 15, 2021. http://hdl.handle.net/10550/47796.

MLA Handbook (7^th Edition):

Martínez Zamora, Ana. “Caracterización funcional de GTPBP3: una proteína G implicada en la modificación de tRNAs mitocondriales. ” 2015. Web. 15 Jan 2021.

Vancouver:

Martínez Zamora A. Caracterización funcional de GTPBP3: una proteína G implicada en la modificación de tRNAs mitocondriales. [Internet] [Doctoral dissertation]. Universitat de Valencia; 2015. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/10550/47796.

Council of Science Editors:

Martínez Zamora A. Caracterización funcional de GTPBP3: una proteína G implicada en la modificación de tRNAs mitocondriales. [Doctoral Dissertation]. Universitat de Valencia; 2015. Available from: http://hdl.handle.net/10550/47796

Uniwersytet im. Adama Mickiewicza w Poznaniu

9. Plewka, Patrycja. Transkrypty genów tRNA i tRNA-podobnych i pochodzące z nich małe RNA u Arabidopsis thaliana .

Degree: 2019, Uniwersytet im. Adama Mickiewicza w Poznaniu

URL: http://hdl.handle.net/10593/25156

► Transportowe RNA (tRNA) odgrywają kluczową rolę w dekodowaniu informacji genetycznej zawartej w sekwencji zasad DNA. Poza genami kodującymi klasyczne cząsteczki tRNA, zidentyfikowano także szeroką gamę… (more)

Subjects/Keywords: Arabidopsis thaliana; tRNA; sekwencje tRNA-podobne; tRNA-like sequences; fragmenty pochodzące od tRNA (tRF); tRNA-derived fragments (tRF)

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APA (6^th Edition):

Plewka, P. (2019). Transkrypty genów tRNA i tRNA-podobnych i pochodzące z nich małe RNA u Arabidopsis thaliana . (Doctoral Dissertation). Uniwersytet im. Adama Mickiewicza w Poznaniu. Retrieved from http://hdl.handle.net/10593/25156

Chicago Manual of Style (16^th Edition):

Plewka, Patrycja. “Transkrypty genów tRNA i tRNA-podobnych i pochodzące z nich małe RNA u Arabidopsis thaliana .” 2019. Doctoral Dissertation, Uniwersytet im. Adama Mickiewicza w Poznaniu. Accessed January 15, 2021. http://hdl.handle.net/10593/25156.

MLA Handbook (7^th Edition):

Plewka, Patrycja. “Transkrypty genów tRNA i tRNA-podobnych i pochodzące z nich małe RNA u Arabidopsis thaliana .” 2019. Web. 15 Jan 2021.

Vancouver:

Plewka P. Transkrypty genów tRNA i tRNA-podobnych i pochodzące z nich małe RNA u Arabidopsis thaliana . [Internet] [Doctoral dissertation]. Uniwersytet im. Adama Mickiewicza w Poznaniu; 2019. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/10593/25156.

Council of Science Editors:

Plewka P. Transkrypty genów tRNA i tRNA-podobnych i pochodzące z nich małe RNA u Arabidopsis thaliana . [Doctoral Dissertation]. Uniwersytet im. Adama Mickiewicza w Poznaniu; 2019. Available from: http://hdl.handle.net/10593/25156

Indian Institute of Science

10. Govindan, Ashwin. Alternate Fates of tRNAs in Initiation and Elongation.

Degree: PhD, Faculty of Science, 2018, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/4119

► Protein synthesis in all organisms utilizes a special tRNA called the initiator tRNA. Initiator tRNAs take part in the initiation step of protein synthesis by… (more)

▼ Protein synthesis in all organisms utilizes a special tRNA called the initiator tRNA. Initiator tRNAs take part in the initiation step of protein synthesis by their direct binding to the P‐site of the ribosome. The other tRNAs (elongator tRNAs) bind first to the A‐site of the ribosome and are subsequently translocated to the P‐site during elongation. The initiator tRNA possesses sequence and structural characteristics, which enable it to perform its unique function in protein synthesis. In addition to the highly conserved three consecutive G:C base pairs in the anticodon stem of the initiator tRNA which facilitate its P‐site binding, bacterial and organellar initiator tRNAs are also formylated by FMT (methionyl‐tRNAfMet formyltransferase) to enable their binding to initiation factor 2 (IF2), directing them specifically into initiation. Structure‐function studies of E. coli initiator tRNA in‐vivo using reporter constructs showed that formylation plays a crucial role in deciding the fate of the initiator tRNA in initiation. The tRNA mutants deficient in formylation take part in initiation and/or elongation. Protein factors like IF2, elongation factor Tu (EF‐Tu) and peptidyl‐tRNA hydrolase (Pth) also contribute to the fate of the tRNA in‐vivo. The current study aims to understand how the balance of protein factors and sequence elements present on a tRNA determine its participation at the steps of initiation and/or elongation using E. coli and M. smegmatis as model organisms. The findings of my research have been described in three distinct investigations as follows: PART‐I. Development of assay systems for amber codon decoding at the steps of initiation and elongation by tRNAfMet derivatives in mycobacteria The bulk of our understanding of the mechanism of protein synthesis in bacteria is derived from the studies in E. coli. The mechanism of translation in Gram positive bacteria remains a relatively less understood process. Gram positive bacteria possess significant differences in their translational apparatus as compared to the Gram negative organisms, and therefore present with interesting systems to understand the mechanism of translation. For example, Gram positive bacteria use an indirect pathway for synthesis of Gln‐tRNAGln and Asn‐tRNAAsn as opposed to direct synthesis of Gln‐tRNAGln by glutaminyl‐tRNA synthetase (GlnRS) in E. coli. We used M. smegmatis, a slow growing Gram positive bacterium, as the model organism to study translation. The understanding of protein synthesis in these bacteria has been limited by the lack of well characterized genetic systems. Using chloramphenicol acetyltransferase (CAT) reporters (having an amber codon as the start codon or as a codon at an internal position within the reading frame of the mRNA), we developed genetic systems where the amber codon is decoded by a mutant initiator tRNA (wherein the CAU anticodon was mutated to CUA with or without additional changes in the acceptor stem) either at the step of initiation or elongation in M. smegmatis, enabling us to… Advisors/Committee Members: Varshney, Umesh (advisor).

Subjects/Keywords: tRNA Structure; tRNA Function; tRNA Participation; Protein Synthesis; tRNAfMet; Microbiology and Cell Biology

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APA (6^th Edition):

Govindan, A. (2018). Alternate Fates of tRNAs in Initiation and Elongation. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/4119

Chicago Manual of Style (16^th Edition):

Govindan, Ashwin. “Alternate Fates of tRNAs in Initiation and Elongation.” 2018. Doctoral Dissertation, Indian Institute of Science. Accessed January 15, 2021. http://etd.iisc.ac.in/handle/2005/4119.

MLA Handbook (7^th Edition):

Govindan, Ashwin. “Alternate Fates of tRNAs in Initiation and Elongation.” 2018. Web. 15 Jan 2021.

Vancouver:

Govindan A. Alternate Fates of tRNAs in Initiation and Elongation. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2018. [cited 2021 Jan 15]. Available from: http://etd.iisc.ac.in/handle/2005/4119.

Council of Science Editors:

Govindan A. Alternate Fates of tRNAs in Initiation and Elongation. [Doctoral Dissertation]. Indian Institute of Science; 2018. Available from: http://etd.iisc.ac.in/handle/2005/4119

University of Arizona

11. McCarty, Reid Michael. Elucidation of the Biosynthetic Pathway for 7-Deazapurines .

Degree: 2011, University of Arizona

URL: http://hdl.handle.net/10150/204334

► Small molecules containing a 7-deazapurine moiety are ubiquitous in nature. They comprise a broad range of structurally diverse antibiotics produced by terrestrial and marine microorganisms… (more)

Subjects/Keywords: antibiotics; enzymology; natural products; tRNA

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APA (6^th Edition):

McCarty, R. M. (2011). Elucidation of the Biosynthetic Pathway for 7-Deazapurines . (Doctoral Dissertation). University of Arizona. Retrieved from http://hdl.handle.net/10150/204334

Chicago Manual of Style (16^th Edition):

McCarty, Reid Michael. “Elucidation of the Biosynthetic Pathway for 7-Deazapurines .” 2011. Doctoral Dissertation, University of Arizona. Accessed January 15, 2021. http://hdl.handle.net/10150/204334.

MLA Handbook (7^th Edition):

McCarty, Reid Michael. “Elucidation of the Biosynthetic Pathway for 7-Deazapurines .” 2011. Web. 15 Jan 2021.

Vancouver:

McCarty RM. Elucidation of the Biosynthetic Pathway for 7-Deazapurines . [Internet] [Doctoral dissertation]. University of Arizona; 2011. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/10150/204334.

Council of Science Editors:

McCarty RM. Elucidation of the Biosynthetic Pathway for 7-Deazapurines . [Doctoral Dissertation]. University of Arizona; 2011. Available from: http://hdl.handle.net/10150/204334

Universitat de Valencia

12. Garzón Garzón, María José. Caracterización bioquímica y funcional de MnmC, una proteína modificadora de tRNA de Escherichia coli .

Degree: 2015, Universitat de Valencia

URL: http://hdl.handle.net/10550/42615

► En esta tesis doctoral se ha pretendido conocer aspectos bioquímicos y funcionales de la proteína bifuncional MnmC, modificadora de la U34 en algunos tRNAs del… (more)

Subjects/Keywords: mnmc; trna; modificacion; coli

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APA (6^th Edition):

Garzón Garzón, M. J. (2015). Caracterización bioquímica y funcional de MnmC, una proteína modificadora de tRNA de Escherichia coli . (Doctoral Dissertation). Universitat de Valencia. Retrieved from http://hdl.handle.net/10550/42615

Chicago Manual of Style (16^th Edition):

Garzón Garzón, María José. “Caracterización bioquímica y funcional de MnmC, una proteína modificadora de tRNA de Escherichia coli .” 2015. Doctoral Dissertation, Universitat de Valencia. Accessed January 15, 2021. http://hdl.handle.net/10550/42615.

MLA Handbook (7^th Edition):

Garzón Garzón, María José. “Caracterización bioquímica y funcional de MnmC, una proteína modificadora de tRNA de Escherichia coli .” 2015. Web. 15 Jan 2021.

Vancouver:

Garzón Garzón MJ. Caracterización bioquímica y funcional de MnmC, una proteína modificadora de tRNA de Escherichia coli . [Internet] [Doctoral dissertation]. Universitat de Valencia; 2015. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/10550/42615.

Council of Science Editors:

Garzón Garzón MJ. Caracterización bioquímica y funcional de MnmC, una proteína modificadora de tRNA de Escherichia coli . [Doctoral Dissertation]. Universitat de Valencia; 2015. Available from: http://hdl.handle.net/10550/42615

University of Texas – Austin

13. -9732-4017. The codon usage of a influenza A virus gene originating from avian viruses adapts to the tRNA pools in interferon-induced human cells.

Degree: PhD, Cell and Molecular Biology, 2015, University of Texas – Austin

URL: http://hdl.handle.net/2152/63856

► Influenza A virus infection causes a highly contagious annual respiratory disease in humans as well as periodic pandemics with higher mortality rates. Due to the… (more)

▼ Influenza A virus infection causes a highly contagious annual respiratory disease in humans as well as periodic pandemics with higher mortality rates. Due to the segmented nature of influenza A virus’ negative-sense RNA genome, reassortment may occur between viruses infecting the same host cell, which generates new combinations of influenza A genomic segments within a single virion. Reassortment events between avian and human-infecting viruses have been a source of pandemic influenza A viruses in the past, and these lineages have stably switched to human hosts, causing seasonal epidemics in the human population. As different organisms display different patterns of synonymous codon usage, I expected that the codon usage of human-infecting avian origin influenza A viral genes would adapt over time to reflect codon usage found in humans. I found instead that the codon usage of the PB1 gene from the H3N2 lineage is adapting to be less like the presumed optimal codon usage as determined by CAI. Upon generating recombinant viruses displaying a PB1 codon usage more similar to modern viruses, there was no difference in growth in cell culture between viruses with early and modern patterns of codon usage. In interferon treated cells, however, viruses with a PB1 displaying modern codon usage patterns grew to a titer 10-fold higher than that of viruses with a PB1 with a codon usage similar to early viruses. This result implied that the codon usage of modern H3N2 PB1 genes is adaptive in interferon stimulated cells, but not in unstimulated cells, and that this adaptation may describe the differences in codon usage observed in PB1 across the H3N2 lineage. To test this hypothesis, I used TGIRT-seq to sequence the tRNA pools in both IFN-treated and untreated human A549 cells. In fact, my results show that over time, the codon usage of H3N2 PB1 proteins has been changing to more closely reflect the tRNA availability in IFN-treated cells. These results show that adaptation to the IFN- induced antiviral state has driven the changes in the codon usage of the PB1 protein of H3N2 viruses. Advisors/Committee Members: Krug, Robert M. (advisor), Wilke, C. (Claus) (advisor), Bull, James J (committee member), Sullivan, Christopher S (committee member), Dudley, Jaquelin P (committee member).

Subjects/Keywords: Influenza; Codon usage; tRNA; Interferon

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APA (6^th Edition):

-9732-4017. (2015). The codon usage of a influenza A virus gene originating from avian viruses adapts to the tRNA pools in interferon-induced human cells. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/63856

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

-9732-4017. “The codon usage of a influenza A virus gene originating from avian viruses adapts to the tRNA pools in interferon-induced human cells.” 2015. Doctoral Dissertation, University of Texas – Austin. Accessed January 15, 2021. http://hdl.handle.net/2152/63856.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

-9732-4017. “The codon usage of a influenza A virus gene originating from avian viruses adapts to the tRNA pools in interferon-induced human cells.” 2015. Web. 15 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

-9732-4017. The codon usage of a influenza A virus gene originating from avian viruses adapts to the tRNA pools in interferon-induced human cells. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2015. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/2152/63856.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

-9732-4017. The codon usage of a influenza A virus gene originating from avian viruses adapts to the tRNA pools in interferon-induced human cells. [Doctoral Dissertation]. University of Texas – Austin; 2015. Available from: http://hdl.handle.net/2152/63856

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

The Ohio State University

14. Wu, Jingyan. A Genome-wide Analysis to Identify and Characterize Novel Genes Involved in tRNA Biology in Saccharomyces cerevisiae.

Degree: PhD, Plant Cellular and Molecular Biology, 2015, The Ohio State University

URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1429197786

► Transfer ribonucleic acids (tRNAs) are essential molecules in all living cells, as they serve as the adapters that bring amino acids to ribosomes for protein… (more)

Subjects/Keywords: Genetics; Molecular Biology; Cellular Biology; tRNA biogenesis, tRNA subcellular dynamics, tRNA processing, tRNA intron turnover, Xrn1, Rlg1, Crm1

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Wu, J. (2015). A Genome-wide Analysis to Identify and Characterize Novel Genes Involved in tRNA Biology in Saccharomyces cerevisiae. (Doctoral Dissertation). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1429197786

Chicago Manual of Style (16^th Edition):

Wu, Jingyan. “A Genome-wide Analysis to Identify and Characterize Novel Genes Involved in tRNA Biology in Saccharomyces cerevisiae.” 2015. Doctoral Dissertation, The Ohio State University. Accessed January 15, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu1429197786.

MLA Handbook (7^th Edition):

Wu, Jingyan. “A Genome-wide Analysis to Identify and Characterize Novel Genes Involved in tRNA Biology in Saccharomyces cerevisiae.” 2015. Web. 15 Jan 2021.

Vancouver:

Wu J. A Genome-wide Analysis to Identify and Characterize Novel Genes Involved in tRNA Biology in Saccharomyces cerevisiae. [Internet] [Doctoral dissertation]. The Ohio State University; 2015. [cited 2021 Jan 15]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1429197786.

Council of Science Editors:

Wu J. A Genome-wide Analysis to Identify and Characterize Novel Genes Involved in tRNA Biology in Saccharomyces cerevisiae. [Doctoral Dissertation]. The Ohio State University; 2015. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1429197786

University of Cincinnati

15. Lobue, Peter. Towards the Parallel, Accurate, and High-throughput Mapping of RNA Modifications by Liquid Chromatography Tandem Mass Spectrometry.

Degree: PhD, Arts and Sciences: Chemistry, 2020, University of Cincinnati

URL: http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595005836099446

► Ribonucleic acids (RNA) play critical roles in regulating the flow of genetic information inside a cell. Ribonucleosides, the building blocks of RNA (adenosine - A,… (more)

▼ Ribonucleic acids (RNA) play critical roles in regulating the flow of genetic information inside a cell. Ribonucleosides, the building blocks of RNA (adenosine - A, guanosine - G, cytidine - C and uridine – U), store another layer of information in the form of post-transcriptional modifications (PTMs) in almost all types of RNA, including messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), long non-coding RNA (lncRNA), and micro RNA (miRNA). These nucleoside modifications do not change the amino acid sequence of the encoded protein, but can affect the stability, localization, translational accuracy and the function of RNA. More than 160 different kinds of chemically diverse PTMs have been reported in RNA, including those produced both enzymatically and synthetically.In addition to the previously stated roles of RNA modifications, the absence or presence of a modification (or set of modifications) may also play an important role in the development in human diseases. Transfer RNA (tRNA) is the most densely modified of class of RNAs, containing chemical modifications that range from simple base and ribose methylations, to more complex so-called “hyper-modifications” that result from multiple-step enzymatic transformations. Correlation between tRNA modification profiles and human diseases continues to emerge, with special focus recently on inherited disease caused by mitochondrial DNA mutations and altered modification profiles of mitochondrial tRNAs. Though mitochondrial abnormalities have been linked to prevalent central nervous system (CNS) disorders, very little is known about the modification profiles in normal cells (only 3 of the 22 normal human mt-tRNA sequences have been reported). Therefore, mapping the complete set of modifications in human mt-tRNA may provide important biomarkers and drug targets with the ultimate therapeutic goal of restoring normal CNS function. The most commonly understood tRNA mutation in mt-tRNA Leu (UUR) is known to lead to MELAS (Mitochondrial Encephalomyopathy, Lactic Acidosis and Stroke-like episodes), affecting at least 1 in 6000 individuals – for which there is currently no approved drug treatment.The most commonly applied RNA modification mapping approach involves isolation of the target RNA (e.g. mt-tRNA) and its subsequent enzymatic hydrolysis to generate oligonucleotides that are amenable to LC-MS/MS analysis. The sequence of the oligonucleotide including the potential modification will be deciphered from this tandem mass spectrum. Thus, the intact modified RNA sequence is reconstructed from the sequences of oligonucleotide digestion products in a bottom-up approach. Though this approach has shown its utility for over two decades, acquiring complete modification maps of mt-tRNA requires state-of-the-art analytical techniques like LC-MS/MS due to the challenges of isolating sufficiently pure amounts of sample and the complex mixture of oligonucleotide digestion products that must be separated and sequenced. Therefore, the goal of the research presented in this… Advisors/Committee Members: Limbach, Patrick (Committee Chair).

Subjects/Keywords: Chemistry; tRNA; RNA; chemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Lobue, P. (2020). Towards the Parallel, Accurate, and High-throughput Mapping of RNA Modifications by Liquid Chromatography Tandem Mass Spectrometry. (Doctoral Dissertation). University of Cincinnati. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595005836099446

Chicago Manual of Style (16^th Edition):

Lobue, Peter. “Towards the Parallel, Accurate, and High-throughput Mapping of RNA Modifications by Liquid Chromatography Tandem Mass Spectrometry.” 2020. Doctoral Dissertation, University of Cincinnati. Accessed January 15, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595005836099446.

MLA Handbook (7^th Edition):

Lobue, Peter. “Towards the Parallel, Accurate, and High-throughput Mapping of RNA Modifications by Liquid Chromatography Tandem Mass Spectrometry.” 2020. Web. 15 Jan 2021.

Vancouver:

Lobue P. Towards the Parallel, Accurate, and High-throughput Mapping of RNA Modifications by Liquid Chromatography Tandem Mass Spectrometry. [Internet] [Doctoral dissertation]. University of Cincinnati; 2020. [cited 2021 Jan 15]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595005836099446.

Council of Science Editors:

Lobue P. Towards the Parallel, Accurate, and High-throughput Mapping of RNA Modifications by Liquid Chromatography Tandem Mass Spectrometry. [Doctoral Dissertation]. University of Cincinnati; 2020. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595005836099446

16. Αποστολίδη, Μαρία. Μελέτες της λειτουργικής συμμετοχής της La πρωτεΐνης του Dictyostelium discoideum στην ωρίμανση πρόδρομων μορίων tRNA.

Degree: 2011, University of Patras

URL: http://hdl.handle.net/10889/5273

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Η La πρωτεΐνη περιγράφηκε για πρώτη φορά στον άνθρωπο ως αυτοαντιγόνο το οποίο αναγνωρίζεται από αντισώματα που είναι παρόντα στον ορό ασθενών που πάσχουν από… (more)

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Η La πρωτεΐνη περιγράφηκε για πρώτη φορά στον άνθρωπο ως αυτοαντιγόνο το οποίο αναγνωρίζεται από αντισώματα που είναι παρόντα στον ορό ασθενών που πάσχουν από συστηματικό ερυθηματώδη λύκο (systemic lupus erythematosus) και σύνδρομο Sjögren. Είναι γνωστό σήμερα ότι συμμετέχει ενεργά στη βιογένεση μικρών μορίων RNA, συμπεριλαμβανομένου της ιδιότητάς της να συνδέεται και να προστατεύει την 3’ ακόλουθη αλληλουχία των πρόδρομων tRNA μεταγράφων. Επιπλέον, έχει προταθεί ότι in vivo διευκολύνει την απομάκρυνση της 5’ οδηγού αλληλουχίας από την RNase P. Στην παρούσα μελέτη, πραγματοποιήθηκε μοριακή κλωνοποίηση της La πρωτεΐνης του D. discoideum (354aa, 40,3-kDa) και υπερέκφρασή της. Η ανασυνδυασμένη La-His6 απομονώθηκε σε δύο στάδια καθαρισμού και εξετάστηκε ως προς την ικανότητα δέσμευσής της σε μόρια tRNA με ανάλυση EMSA (Electrophoresis Mobility Shift Assay). Τα αποτελέσματα με τη δοκιμή του ομόλογου pre-tRNASer που φέρει 3’ ακόλουθη αλληλουχία ως προσδέτη σε σχέση με ένα pre- tRNASer στο οποίο απουσιάζει η αντίστοιχη αλληλουχία, έδειξε ότι η La πρωτεΐνη έχει προτίμηση για αυτούσια πρόδρομα tRNA. In silico ανάλυση της πρωτεΐνης, έδειξε ότι περιλαμβάνει μοτίβα χαρακτηριστικά για RNA πρόσδεση με υψηλή συντήρηση στο Ν-τελικό της άκρο. Η προσθήκη αυξανόμενων συγκεντρώσεων ανασυνδυασμένης πρωτεΐνης La αναστέλλει σε ένα ποσοστό 10% την ωρίμανση του tRNA από την ομόλογη RNase P. Επιπρόσθετα, πραγματοποιήθηκαν in vitro δοκιμές για τη μελέτη της ικανότητας της La να βοηθά στη σωστή αναδίπλωση και άλλων πρόδρομων μεταγράφων της RNA πολυμεράσης ΙΙΙ. Για το λόγο αυτό ελέγχθηκε η ικανότητα ωρίμανσης παρουσία της La και της RNA υπομονάδας της RNase P. Κάτω από ποικίλες συνθήκες δοκιμής η παρουσία της La δεν ευνόησε την ενεργότητα του ριβοενζύμου. Τέλος, φωσφορυλίωση της La πρωτεΐνης σε συγκεκριμένα αμινοξέα δεν έδειξε ενίσχυση της συγγένειας για το υπόστρωμα. Η La του D. discoideum, μπορεί να συνδέεται με αρκετά μεγάλη συγγένεια με το ομόλογό της υπόστρωμα (Kd = 4±1nM, συγκρίσιμη με αντίστοιχες τιμές ομόλογων πρωτεϊνών) χωρίς την απαίτηση του μοτίβου 3’UUU-OH, το οποίο φαίνεται να είναι απαραίτητο για La πρωτεΐνες από άλλους οργανισμούς (H. sapiens, S. pombe, S. cerevisiae, T. brucei). Το γεγονός αυτό εγείρει πολλά ερωτήματα για την εξελικτική προέλευση αυτής της πρωτεΐνης και για την εξακρίβωση του ρόλου της ως αυτοαντιγόνου στα νοσήματα που αναφέρθηκαν. Βιοχημικές και δομικές μελέτες βρίσκονται σε εξέλιξη για να απαντήσουν σε αυτά τα ερωτήματα.

The La protein was first described in humans as an autoantigen recognized by antibodies present in serum of patients suffering from systemic lupus erythematosus and Sjögren syndrome. It is known that it participates actively in the biogenesis of small RNA molecules, including the binding and protection of the 3' trailer sequence of the precursor tRNA. Furthermore, it has been suggested that it facilitates the RNase P to remove the 5' leader sequence in vivo. In this study, molecular cloning and overexpression of the La protein D. discoideum (354aa, 40,3-kDa) were realized. Recombinant…

Advisors/Committee Members: Σταθόπουλος, Κωνσταντίνος, Apostolidi, Maria, Δραϊνας, Διονύσιος, Μουζάκη, Αθανασία.

Subjects/Keywords: Πρωτεΐνη La; Βιογένεση μορίων tRNA; 572.884 5; La protein; tRNA biogenesis

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APA (6^th Edition):

Αποστολίδη, �. (2011). Μελέτες της λειτουργικής συμμετοχής της La πρωτεΐνης του Dictyostelium discoideum στην ωρίμανση πρόδρομων μορίων tRNA. (Masters Thesis). University of Patras. Retrieved from http://hdl.handle.net/10889/5273

Chicago Manual of Style (16^th Edition):

Αποστολίδη, Μαρία. “Μελέτες της λειτουργικής συμμετοχής της La πρωτεΐνης του Dictyostelium discoideum στην ωρίμανση πρόδρομων μορίων tRNA.” 2011. Masters Thesis, University of Patras. Accessed January 15, 2021. http://hdl.handle.net/10889/5273.

MLA Handbook (7^th Edition):

Αποστολίδη, Μαρία. “Μελέτες της λειτουργικής συμμετοχής της La πρωτεΐνης του Dictyostelium discoideum στην ωρίμανση πρόδρομων μορίων tRNA.” 2011. Web. 15 Jan 2021.

Vancouver:

Αποστολίδη �. Μελέτες της λειτουργικής συμμετοχής της La πρωτεΐνης του Dictyostelium discoideum στην ωρίμανση πρόδρομων μορίων tRNA. [Internet] [Masters thesis]. University of Patras; 2011. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/10889/5273.

Council of Science Editors:

Αποστολίδη �. Μελέτες της λειτουργικής συμμετοχής της La πρωτεΐνης του Dictyostelium discoideum στην ωρίμανση πρόδρομων μορίων tRNA. [Masters Thesis]. University of Patras; 2011. Available from: http://hdl.handle.net/10889/5273

17. 이, 순장. Expanding the genetic code of a mouse.

Degree: 2015, Ajou University

URL: http://repository.ajou.ac.kr/handle/201003/11813 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000020382

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Genetic code expansion has used the site-specific insertion of unnatural amino acids into proteins(Greiss and Chin, 2011). An aminoacyl-tRNA synthetase and a tRNA are used… (more)

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Genetic code expansion has used the site-specific insertion of unnatural amino acids into proteins(Greiss and Chin, 2011). An aminoacyl-tRNA synthetase and a tRNA are used to specifically insert the unnatural amino acid during mRNA translation, in response to an amber stop codon (UAG) placed at a user-defined site in a gene interest (Davis and Chin, 2012) In this study, I used Acetyllysine(AcK) as unnatural amino acids, N? -acetyl-lysyl-tRNA synthetase (AcKRS) as AcK-tRNA synthetase, pyrrolysyl-tRNA(PylT) as tRNA from Methanosarcina mazei (Mukai et al., 2008). Amber codon was inserted in GFP that is role of reporter gene. AcKRS aminoacylates PylT , and mRNA encoding the full-length GFP bearing an amber codon that directs amino acid incopration. I created AcKRS, GFP mouse, and generated immortalized MEF(mouse embryonic fibroblast). Immortalized MEF(AcKRS.GPF) was treated by AcK., but GFP signal was not detected. I thought that no dectable GFP signal was likely due to the three reasons : First, AcK did not internalize into the system. Second, AcK can be degraded by deacetylase. Third, mRNA was effected by NMD(nonsense-mediated mRNA decay) that can break mRNA containing amber condons. I find the reason that low GFP expression was due to the degradation of mRNA through NMD To investigate GFP signal in AcKRS.GFP mouse I did cryosection and observed by confocal microsope. Because NMD efficiency is various according to organs, I got GFP expression in stomach and muscle in AcKRS.GFP mouse.

I.INTRODUCTION 1 II.MATERIALS AND METHOD 3 A. Generation of transgenic mice 3 B. DNA extraction from mouse tail and genotyping PCR 3 C. Isolation of primary mouse embryo fibroblast and SV40 immortalization 3 D. siRNA Transfection 4 E. Cryosection / Confocal microscope 4 III.RESULTS 5 A. Generation of AcKRS.GFP mouse 5 B. Conformation of transgenic mouse 8 C. No dectectable GFP induced by AcK 9 D. Inhibition of Nonsense-mediated mRNA decay through UPF2 Knock down 12 E. Detection of GFP signal in AcKRS.GFP mouse by cryosection 15 IV.DISCUSSION 17 V. CONCLUSION 18 REFERENCES 19 국문요약 21

Master

Advisors/Committee Members: 대학원 의생명과학과, 201324380, 이, 순장.

Subjects/Keywords: aminoacyl-tRNA synthetase; Acetyllysine; pyrrolysyl-tRNA; nonsense-mediated mRNA decay

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

이, �. (2015). Expanding the genetic code of a mouse. (Thesis). Ajou University. Retrieved from http://repository.ajou.ac.kr/handle/201003/11813 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000020382

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

이, 순장. “Expanding the genetic code of a mouse.” 2015. Thesis, Ajou University. Accessed January 15, 2021. http://repository.ajou.ac.kr/handle/201003/11813 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000020382.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

이, 순장. “Expanding the genetic code of a mouse.” 2015. Web. 15 Jan 2021.

Vancouver:

이 �. Expanding the genetic code of a mouse. [Internet] [Thesis]. Ajou University; 2015. [cited 2021 Jan 15]. Available from: http://repository.ajou.ac.kr/handle/201003/11813 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000020382.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

이 �. Expanding the genetic code of a mouse. [Thesis]. Ajou University; 2015. Available from: http://repository.ajou.ac.kr/handle/201003/11813 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000020382

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas – Austin

18. Lamech, Lilian Tawsein M. Mitochondrial tyrosyl-tRNA synthetases : evolving a function beyond translation.

Degree: PhD, Microbiology, 2014, University of Texas – Austin

URL: http://hdl.handle.net/2152/31554

► Pezizomycotina mitochondrial tyrosyl-tRNA synthetases (mtTyrRS) are bifunctional, with the ability to splice group I introns in addition to catalyzing aminoacylation. Work done with the Neurospora… (more)

▼ Pezizomycotina mitochondrial tyrosyl-tRNA synthetases (mtTyrRS) are bifunctional, with the ability to splice group I introns in addition to catalyzing aminoacylation. Work done with the Neurospora crassa mtTyrRS (CYT-18 protein) showed that it promotes splicing by binding and stabilizing the conserved catalytically active structure of the intron RNA. To interact with intron RNA, Pezizomycotina mtTyrRSs evolved a new intron-binding surface via structural adaptations on the side of the catalytic domain opposite that which binds tRNA[superscript Tyr]. To examine the variability of these adaptations and intron-binding surface differences between Pezizomycotina mtTyrRSs, I solved the structures of C-terminally truncated C. posadasii and A. nidulans mtTyrRSs. Comparison of these structures to CYT-18 revealed differences in some of the Pezizomycotina specific adaptations that are important for stabilizing key tertiary interactions required for group I intron folding. These studies highlight variations that likely affect intron-RNA binding and potentially splicing and also help define regions for therapeutic intervention. While my and previous studies have provided information on the N-terminal adaptations and intron-binding interactions, little information is available about the Cterminal domain (CTD) interactions. I conducted small angle X-ray scattering (SAXS), binding and splicing assays to further elucidate the domain arrangements of full length CYT-18 and contributions of the CTDs to splicing. My results suggest a model in which free CYT-18 exists in an extended conformation in solution, and upon binding intron RNA, forms a compact structure with both CTDs clamping down onto the RNA. These studies also revealed that the mtTyrRS CTDs have high non-specific binding affinity, which may have facilitated the evolution of the RNA splicing activity in Pezizomycotina mtTyrRSs. Finally, to further investigate the evolution of splicing activity by Pezizomycotina mtTyrRSs, which likely occurred during or after its divergence from Saccharomycotina, I studied bioinformatically reconstructed ancestral mtTyrRSs from the two fungal subphylums. These studies suggest that the common ancestor of the two subphylums may have been capable of non-specifically binding nucleic acid. My research suggests an evolutionary scenario in which an initial non-specific interaction between a self-splicing intron and an ancestral mtTyrRS led to the dependence of the intron on the mtTyrRS for splicing. Advisors/Committee Members: Lambowitz, Alan (advisor), Russell, Rick (committee member), Johnson, Arlen (committee member), Keatinge-Clay, Adrian T (committee member), Stevens, Scott (committee member), Herrin, David L (committee member).

Subjects/Keywords: TRNA; Tyrosyl-tRNA synthetase; CYT-18; MtTyrRS; SAXS; X-ray crystallography

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APA (6^th Edition):

Lamech, L. T. M. (2014). Mitochondrial tyrosyl-tRNA synthetases : evolving a function beyond translation. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/31554

Chicago Manual of Style (16^th Edition):

Lamech, Lilian Tawsein M. “Mitochondrial tyrosyl-tRNA synthetases : evolving a function beyond translation.” 2014. Doctoral Dissertation, University of Texas – Austin. Accessed January 15, 2021. http://hdl.handle.net/2152/31554.

MLA Handbook (7^th Edition):

Lamech, Lilian Tawsein M. “Mitochondrial tyrosyl-tRNA synthetases : evolving a function beyond translation.” 2014. Web. 15 Jan 2021.

Vancouver:

Lamech LTM. Mitochondrial tyrosyl-tRNA synthetases : evolving a function beyond translation. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2014. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/2152/31554.

Council of Science Editors:

Lamech LTM. Mitochondrial tyrosyl-tRNA synthetases : evolving a function beyond translation. [Doctoral Dissertation]. University of Texas – Austin; 2014. Available from: http://hdl.handle.net/2152/31554

The Ohio State University

19. Vargas-Rodriguez, Oscar E. Characterization of Fidelity Mechanisms in Protein Translation.

Degree: PhD, Chemistry, 2014, The Ohio State University

URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1397685427

► Decoding of the genetic information is established by aminoacyl-tRNA synthetases (ARSs), which are responsible for pairing amino acids with tRNA adaptors carrying nucleotide triplets matching… (more)

▼ Decoding of the genetic information is established by aminoacyl-tRNA synthetases (ARSs), which are responsible for pairing amino acids with tRNA adaptors carrying nucleotide triplets matching the corresponding codon on the messenger RNA. The accuracy in amino acid selection by ARSs is challenged by the structural similarities shared by some genetically encoded amino acids, which leads to the formation of mis-matched aminoacyl-tRNA (aa-tRNA) pairs. Accumulation of such aa-tRNA species results in mis-incorporation of amino acids into protein sequences, which may induce protein misfolding and aggregation leading to a myriad of cellular phenotypes including apoptosis and neurodegeneration. Thus, some synthetases have adopted alternative catalytic functions to prevent mistranslation. In most bacterial prolyl-tRNA synthetases (ProRSs), which mischarge Cys and Ala onto tRNAPro, an editing domain (INS) functions to deacylate Ala-tRNAPro. In contrast, a dedicated trans-acting editing enzyme, known as YbaK, homologous to INS, is responsible for the hydrolysis of Cys-tRNAPro. However, in approximately 30% of bacteria, ProRSs lack an INS domain, and instead many of these organisms encode a single-domain INS-like protein known as ProXp-ala, which deacylates Ala-tRNAPro in trans. INS, YbaK, and ProXp-ala are part of a larger family of deacylases known as the INS superfamily that also includes three proteins of unknown function: ProXp-x, ProXp-y, and ProXp-z. In this work, we used biochemical approaches to investigate the function of the INS superfamily in the fidelity of protein translation. We first analyzed the distribution of INS and INS-like domains to establish the phylogenetic relationship between the six families. This study revealed the species-specific distribution of these proteins, which are proposed to be involved in preventing mistranslation. We focused on Caulobacter crescentus, which encodes a ProRS with a truncated INS domain that lacks catalytic activity, as well as YbaK and ProXp-ala. The in vitro characterization of these three enzymes highlighted the diversity of approaches used to prevent protein mistranslation and revealed a novel triple-sieve mechanism of editing that relies exclusively on trans-acting enzymes. Furthermore, investigation of the tRNA specificity of INS, YbaK, and ProXp-ala showed three distinct strategies for tRNA recognition. Whereas YbaK lacks inherent tRNA specificity, ProXp-ala and INS require tRNAPro acceptor stem elements G72/A73 and anticodon bases G35/G36, respectively. Furthermore, we show that evolutionary changes of the tRNAPro operational code acted as a selective pressure on ProXp-ala, which allowed co-adaptation of human ProXp-ala to recognize cytosolic tRNAPro. Finally, we investigated ProXp-z activity and showed that although this enzyme is homologous to INS, its catalytic activity is unrelated to ProRS aminoacylation errors. Using in vitro deacylation assays with a series of aa-tRNA substrates, we determined that ProXp-z is a dual specific deacylase that preferentially… Advisors/Committee Members: Musier-Forsyth, Karin (Advisor).

Subjects/Keywords: Biochemistry; Chemistry; Aminoacyl-tRNA synthetases; tRNA; translation; editing; proofreading

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Vargas-Rodriguez, O. E. (2014). Characterization of Fidelity Mechanisms in Protein Translation. (Doctoral Dissertation). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1397685427

Chicago Manual of Style (16^th Edition):

Vargas-Rodriguez, Oscar E. “Characterization of Fidelity Mechanisms in Protein Translation.” 2014. Doctoral Dissertation, The Ohio State University. Accessed January 15, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu1397685427.

MLA Handbook (7^th Edition):

Vargas-Rodriguez, Oscar E. “Characterization of Fidelity Mechanisms in Protein Translation.” 2014. Web. 15 Jan 2021.

Vancouver:

Vargas-Rodriguez OE. Characterization of Fidelity Mechanisms in Protein Translation. [Internet] [Doctoral dissertation]. The Ohio State University; 2014. [cited 2021 Jan 15]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1397685427.

Council of Science Editors:

Vargas-Rodriguez OE. Characterization of Fidelity Mechanisms in Protein Translation. [Doctoral Dissertation]. The Ohio State University; 2014. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1397685427

University of Guelph

20. Pierce, Jacqueline. Regulation of nuclear tRNA export in response to nutrient stress is not evolutionarily conserved and requires the TORC1 and PKA signaling pathways in Saccharomyces cerevisiae.

Degree: PhD, Department of Molecular and Cellular Biology, 2013, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/5335

► Saccharomyces cerevisiae are unicellular organisms that are highly adaptable to acute changes in nutrient availability. The two main signaling pathways that allow S. cerevisiae to… (more)

▼ Saccharomyces cerevisiae are unicellular organisms that are highly adaptable to acute changes in nutrient availability. The two main signaling pathways that allow S. cerevisiae to sense and respond to changes in glucose availability in the environment are the conserved cAMP/PKA and AMPK/Snf1 kinase-dependent pathways. The conserved TORC1 pathway is primarily responsible for allowing cells to respond to the availability of nitrogen. Studies have shown that S. cerevisiae, but not mammalian and plant cells, regulate nuclear tRNA trafficking in response to nutrient stress. Here, we show that the yeast species of the Saccharomyces genus, but not Schizosaccharomyces pombe and Kluyveromyces lactis specifically regulate nuclear tRNA export in response to nutrient stress, providing further evidence that regulation of nuclear tRNA export in response to nutrient availability is not evolutionarily conserved. We also established that amino acid and nitrogen starvation affects nuclear export of a subset of tRNAs in S. cerevisiae. Inhibition of TORC1 signaling by rapamycin treatment, which simulates nitrogen starvation, also affects nuclear export of the same subset of tRNAs, suggesting that the TORC1 signaling pathway plays a role in regulating nuclear export of the tRNAs in response to nitrogen level. Regulation of nuclear export of these tRNAs by nitrogen deprivation is most likely due to an effect on the function of the nuclear tRNA export receptors, as overexpression of the tRNA export receptor, Los1p, restores export of the tRNAs during nitrogen starvation. These findings suggest that the TORC1 signaling pathway may, in part, regulate nuclear export of the tRNAs by affecting the function of the tRNA export receptors. In contrast to amino acid and nitrogen starvation, glucose depletion affects nuclear export of all tRNA species in S. cerevisiae. Evidence obtained suggests that nuclear retention of tRNA in cells deprived of glucose is due to a block in nuclear re-import of the nuclear tRNA export receptors. Retention of the receptors in the cytoplasm is not caused by activation of Snf1p, but by the inactivation of PKA during glucose deprivation. Furthermore, regulation of nuclear re-import of the receptors is not due to phosphorylation of the tRNA export receptors by PKA. However, PKA phosphorylates known components of the tRNA export machinery. A model that is consistent with the data is that PKA and an unknown mechanism regulate the activity of these components or an unidentified protein(s) to control nuclear re-import of the receptors in response to glucose availability. Advisors/Committee Members: van der Merwe, George (advisor).

Subjects/Keywords: PKA; Snf1p; TORC1; Yeast; Nuclear tRNA export receptors; Nuclear-cytoplasmic tRNA trafficking; Nutrient stress; Regulation of nuclear tRNA export

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APA (6^th Edition):

Pierce, J. (2013). Regulation of nuclear tRNA export in response to nutrient stress is not evolutionarily conserved and requires the TORC1 and PKA signaling pathways in Saccharomyces cerevisiae. (Doctoral Dissertation). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/5335

Chicago Manual of Style (16^th Edition):

Pierce, Jacqueline. “Regulation of nuclear tRNA export in response to nutrient stress is not evolutionarily conserved and requires the TORC1 and PKA signaling pathways in Saccharomyces cerevisiae.” 2013. Doctoral Dissertation, University of Guelph. Accessed January 15, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/5335.

MLA Handbook (7^th Edition):

Pierce, Jacqueline. “Regulation of nuclear tRNA export in response to nutrient stress is not evolutionarily conserved and requires the TORC1 and PKA signaling pathways in Saccharomyces cerevisiae.” 2013. Web. 15 Jan 2021.

Vancouver:

Pierce J. Regulation of nuclear tRNA export in response to nutrient stress is not evolutionarily conserved and requires the TORC1 and PKA signaling pathways in Saccharomyces cerevisiae. [Internet] [Doctoral dissertation]. University of Guelph; 2013. [cited 2021 Jan 15]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/5335.

Council of Science Editors:

Pierce J. Regulation of nuclear tRNA export in response to nutrient stress is not evolutionarily conserved and requires the TORC1 and PKA signaling pathways in Saccharomyces cerevisiae. [Doctoral Dissertation]. University of Guelph; 2013. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/5335

University of Washington

21. Barros Alvarez, Ximena. Aminoacyl-tRNA Synthetases as Targets for Structure Guided Drug Design (SGDD) Against Pathogenic Protozoa and Bacteria.

Degree: PhD, 2018, University of Washington

URL: http://hdl.handle.net/1773/42206

► Tuberculosis (TB) and neglected tropical diseases (NTDs) caused by trypanosomatids are devastating diseases affecting millions of people around the globe. Mycobacterium tuberculosis causes TB, while… (more)

▼ Tuberculosis (TB) and neglected tropical diseases (NTDs) caused by trypanosomatids are devastating diseases affecting millions of people around the globe. Mycobacterium tuberculosis causes TB, while the trypanosomatids Trypanosoma brucei, Trypanosoma cruzi and parasites of the genus Leishmania, cause sleeping sickness (or human African trypanosomiasis (HAT)), Chagas disease (or American trypanosomiasis) and the leishmaniases in tropical and subtropical areas of the world. Visceral leishmaniasis (VL), the deadliest form of the disease, is caused by L. infantum and L. donovani. For some of these diseases there is no vaccine or cure. For others, vaccine protection and treatment efficiency are limited. In some cases, development of resistance to available drugs has made useless otherwise successful treatments. New drugs as well as new drug targets are desperately needed. The essential aminoacyl-tRNA synthetase (aaRS) enzymes provide the charged tRNAs required for protein synthesis. AaRS have been previously pursued as drug targets in bacteria and fungi and have been validated as drug targets in protozoa. The structural work presented as part of this dissertation has been part of collaborative structure guided drug design (SGDD) projects among various research groups, most of them within University of Washington, for the discovery and iterative optimization of inhibitors targeting aaRSs of parasitic protozoa and bacteria. The selection of methionyl-tRNA synthetase (MetRS) and tyrosyl-tRNA synthetase (TyrRS) as drug targets was done based on their predicted feasibility of developing selective inhibitors. Crystal structures of M. tuberculosis and T. brucei MetRS (MtubMetRS and TbruMetRS) and L. donovani TyrRS (LdonTyrRS) were solved in the presence of different compounds to assist in the iterative SGDD development of drugs against TB, HAT and VL, respectively. Structural information contributed in different stages in the SGDD process, from the description of new protein structures of the essential pathogenic aaRSs to the assistance in the optimization and design of novel inhibitors. In an example of early steps in the SGDD process, the crystal structure of MtubMetRS in complex with the catalytic intermediate Met-AMP was solved at 2.6 Å resolution. Differences with other MetRSs including the human counterparts were revealed and could potentially be useful in the chemotherapeutic development against TB. The use of nanobodies as crystallization chaperones and of the tyrosyl adenylate analog TyrSA was crucial for obtaining well diffracting crystals that lead to solving the crystal structure of LdonTyrRS at 2.75 Å resolution. The presence of an extra pocket (EP) was revealed that is not present in the human counterparts, but is shared with other pathogens, and could be exploited in seeking for a cure for VL and other infectious diseases. As an example of the value of the contribution of structural information in later stages in the SGDD process, a total of 57 crystal structures obtained upon soaking of TbruMetRS with multiple… Advisors/Committee Members: Hol, Wilhelmus G.J. (advisor).

Subjects/Keywords: Aminoacyl-tRNA synthetase; Methionyl-tRNA synthetase; Structure guided drug design; Trypanosomatids; Tuberculosis; Tyrosyl-tRNA synthetase; Biochemistry; Biological chemistry

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APA (6^th Edition):

Barros Alvarez, X. (2018). Aminoacyl-tRNA Synthetases as Targets for Structure Guided Drug Design (SGDD) Against Pathogenic Protozoa and Bacteria. (Doctoral Dissertation). University of Washington. Retrieved from http://hdl.handle.net/1773/42206

Chicago Manual of Style (16^th Edition):

Barros Alvarez, Ximena. “Aminoacyl-tRNA Synthetases as Targets for Structure Guided Drug Design (SGDD) Against Pathogenic Protozoa and Bacteria.” 2018. Doctoral Dissertation, University of Washington. Accessed January 15, 2021. http://hdl.handle.net/1773/42206.

MLA Handbook (7^th Edition):

Barros Alvarez, Ximena. “Aminoacyl-tRNA Synthetases as Targets for Structure Guided Drug Design (SGDD) Against Pathogenic Protozoa and Bacteria.” 2018. Web. 15 Jan 2021.

Vancouver:

Barros Alvarez X. Aminoacyl-tRNA Synthetases as Targets for Structure Guided Drug Design (SGDD) Against Pathogenic Protozoa and Bacteria. [Internet] [Doctoral dissertation]. University of Washington; 2018. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/1773/42206.

Council of Science Editors:

Barros Alvarez X. Aminoacyl-tRNA Synthetases as Targets for Structure Guided Drug Design (SGDD) Against Pathogenic Protozoa and Bacteria. [Doctoral Dissertation]. University of Washington; 2018. Available from: http://hdl.handle.net/1773/42206

University of Illinois – Urbana-Champaign

22. Sarkar, Jaya. CP1 domain of leucyl-tRNA synthetase: dissecting its dual roles in amino acid editing and RNA splicing.

Degree: PhD, 0318, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/32018

► The essential family of aminoacyl-tRNA synthetase (AARS) enzymes catalyzes the attachment of an amino acid to its cognate tRNA during ribosome-based translation of mRNA. Leucyl-tRNA… (more)

▼ The essential family of aminoacyl-tRNA synthetase (AARS) enzymes catalyzes the attachment of an amino acid to its cognate tRNA during ribosome-based translation of mRNA. Leucyl-tRNA synthetase (LeuRS) ensures fidelity in protein synthesis via proofreading or editing mechanisms. The editing that hydrolyzes noncognate amino acids mischarged onto tRNALeu is called post-transfer editing. The hydrolytic post-transfer editing active site is located in a discretely folded polypeptide insertion called connective polypeptide 1 (CP1) that is linked to the enzyme’s main body by two flexible β-strand linkers. Disruption of the CP1 domain-based editing function in LeuRS results in amino acid toxicities that compromise cell viability. A fluorescence-based in vivo assay was designed to quantify the effects of editing defects and hence assess the limits of mistranslation that can be borne by the cell. Sequence enabled reassembly of N and C-terminal fragments of the green fluorescence protein (GFP) were studied in vivo in the presence of editing defective LeuRS and noncognate amino acids. In the yeast cytoplasmic LeuRS (ycLeuRS), the conserved post-transfer editing pocket is the target binding site for a novel class of benzoxaborole-based antimicrobials that trap tRNALeu and halt protein synthesis. Resistance mutations (D487G and D487N) to the antimicrobial compound AN2690 lie outside the drug binding pocket and provided a unique opportunity to study editing mechanisms in the ycLeuRS. The Asp487 residue is located in a CP1 domain-based eukaryote-specific flexible insert called I4 that forms a ‘cap’ over the benzoxaborole-AMP adduct bound in the CP1 domain editing active site. Mutational and biochemical analysis at Asp487 identified a salt bridge between Asp487 and Arg316 in the hinge region of the I4 cap that is critical to tRNA deacylation. Thus, this electrostatic interaction stabilizes the cap during binding of the editing substrate for hydrolysis in the ycLeuRS. An alternative pre-transfer editing pathway has also been identified in LeuRS and cleaves the noncognate amino acid before it is transferred to tRNALeu, at the stage of aminoacyl-AMP. Co-existence of both pre- and post-transfer editing pathways was highlighted in the ycLeuRS, as has also been shown earlier for E. coli LeuRS. Detailed biochemical investigations on the editing activity of this enzyme revealed that ycLeuRS shifts between the two editing pathways and this shift is dictated by the chemical identity of the noncognate amino acid misactivated by the enzyme. While isoleucine is mainly cleared via the post-transfer editing route that targets Ile-tRNALeu, methionine is edited via the pre-transfer pathway by hydrolysis of methionyl-adenylate in ycLeuRS. The yeast mitochondrial LeuRS (ymLeuRS) was recruited to perform an alternate cellular role of mRNA splicing. Splicing-sensitive sites have been located within and and in close proximity to the CP1 domain. Remarkably, E. coli LeuRS supports splicing in vivo, although its CP1 domain appears to lack… Advisors/Committee Members: Martinis, Susan A. (advisor), Martinis, Susan A. (Committee Chair), Silverman, Scott K. (committee member), Kranz, David M. (committee member), Tajkhorshid, Emad (committee member).

Subjects/Keywords: Aminoacyl-tRNA synthetases (AARSs); Leucyl-tRNA synthetase (LeuRS); transfer ribonucleic acid (tRNA); splicing; amino acid editing; connective polypeptide-1 (CP1) domain

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sarkar, J. (2012). CP1 domain of leucyl-tRNA synthetase: dissecting its dual roles in amino acid editing and RNA splicing. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/32018

Chicago Manual of Style (16^th Edition):

Sarkar, Jaya. “CP1 domain of leucyl-tRNA synthetase: dissecting its dual roles in amino acid editing and RNA splicing.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed January 15, 2021. http://hdl.handle.net/2142/32018.

MLA Handbook (7^th Edition):

Sarkar, Jaya. “CP1 domain of leucyl-tRNA synthetase: dissecting its dual roles in amino acid editing and RNA splicing.” 2012. Web. 15 Jan 2021.

Vancouver:

Sarkar J. CP1 domain of leucyl-tRNA synthetase: dissecting its dual roles in amino acid editing and RNA splicing. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/2142/32018.

Council of Science Editors:

Sarkar J. CP1 domain of leucyl-tRNA synthetase: dissecting its dual roles in amino acid editing and RNA splicing. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/32018

Uniwersytet im. Adama Mickiewicza w Poznaniu

23. Thompson, Agnieszka. Biogeneza i funkcja cząsteczek pochodzących z tRNA Arabidopsis thaliana .

Degree: 2018, Uniwersytet im. Adama Mickiewicza w Poznaniu

URL: http://hdl.handle.net/10593/23958

► Celem niniejszej pracy jest identyfikacja cząsteczek tRF Arabidopsis thaliana, stworzenie bazy danych tych fragmentów oraz rozpoznanie enzymów i czynników odpowiadających za ich powstawanie, wraz z… (more)

Subjects/Keywords: tRNA; tRNA-derived fragments; małe RNA; tRFs; fragmenty tRNA; small RNAs; modyfikacje; modifications; sekwencje docelowe; target sequences

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APA (6^th Edition):

Thompson, A. (2018). Biogeneza i funkcja cząsteczek pochodzących z tRNA Arabidopsis thaliana . (Doctoral Dissertation). Uniwersytet im. Adama Mickiewicza w Poznaniu. Retrieved from http://hdl.handle.net/10593/23958

Chicago Manual of Style (16^th Edition):

Thompson, Agnieszka. “Biogeneza i funkcja cząsteczek pochodzących z tRNA Arabidopsis thaliana .” 2018. Doctoral Dissertation, Uniwersytet im. Adama Mickiewicza w Poznaniu. Accessed January 15, 2021. http://hdl.handle.net/10593/23958.

MLA Handbook (7^th Edition):

Thompson, Agnieszka. “Biogeneza i funkcja cząsteczek pochodzących z tRNA Arabidopsis thaliana .” 2018. Web. 15 Jan 2021.

Vancouver:

Thompson A. Biogeneza i funkcja cząsteczek pochodzących z tRNA Arabidopsis thaliana . [Internet] [Doctoral dissertation]. Uniwersytet im. Adama Mickiewicza w Poznaniu; 2018. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/10593/23958.

Council of Science Editors:

Thompson A. Biogeneza i funkcja cząsteczek pochodzących z tRNA Arabidopsis thaliana . [Doctoral Dissertation]. Uniwersytet im. Adama Mickiewicza w Poznaniu; 2018. Available from: http://hdl.handle.net/10593/23958

The Ohio State University

24. Levengood, Jeffrey D. Biochemical properties of class I LYSYL-tRNA synthetase.

Degree: PhD, Biochemistry, 2007, The Ohio State University

URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1166509612

► The family of aminoacyl-tRNA synthetases (aaRSs) performs the essential cellular function of charging tRNA molecules with their cognate amino acids. This enzyme family can be… (more)

▼ The family of aminoacyl-tRNA synthetases (aaRSs) performs the essential cellular function of charging tRNA molecules with their cognate amino acids. This enzyme family can be divided into two unrelated classes with each evolving from different origins. Lysyl-tRNA synthetase (LysRS) is the only synthetase known to have a form in each class. Steady-state kinetics were used to study the mechanisms which LysRS1 employs to recognize its substrates. The binding of lysine was analyzed by studying the ability of several lysine analogues to inhibit the aminoacylation reaction. It was found that the R-group plays a critical role in discrimination rather than the functional groups at the á-carbon. Within the R-group, the size of the chain was a very important point for discrimination. The binding of tRNALys was examined using both LysRS, mutated based on the modeled tRNALys bound to LysRS1, and tRNALys with mutant anticodons. Analysis of the bound tRNALys revealed that LysRS is able to specifically recognize the bases at anticodon positions 35 and 36, but not 34. The experiments with variant enzymes in relation to the model revealed LysRS1 likely uses a variety of bonds to recognize the anticodon. Aromatic residues form non-specific stacking interactions with the bases, charged and polar residues form specific hydrogen bonds with the bases, and other charged residues form non-specific electrostatic interactions with the phosphate backbone of the anticodon stem. Comparison of the mechanisms for substrate recognition between LysRS1 and LysRS2 revealed differences in the recognition of substrates that could be the cause for the divergence of the two enzymes. The two LysRSs were shown to have different patterns of inhibition to naturally occurring lysine analogues that had consequences for growth in vivo. With the tRNALys anticodon binding, it was found anticodon binding is much more important for binding with LysRS2 than LysRS1. This could have had consequences with the divergence of other synthetases that must recognize similar anticodons. The presence of LysRS1 may have allowed these other synthetases to put more emphasis on the anticodon in recognition of their cognate tRNA. Advisors/Committee Members: Ibba, Michael (Advisor).

Subjects/Keywords: tRNA; aminoacyl-tRNA synthetase; lysyl-tRNA synthetase

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APA (6^th Edition):

Levengood, J. D. (2007). Biochemical properties of class I LYSYL-tRNA synthetase. (Doctoral Dissertation). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1166509612

Chicago Manual of Style (16^th Edition):

Levengood, Jeffrey D. “Biochemical properties of class I LYSYL-tRNA synthetase.” 2007. Doctoral Dissertation, The Ohio State University. Accessed January 15, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu1166509612.

MLA Handbook (7^th Edition):

Levengood, Jeffrey D. “Biochemical properties of class I LYSYL-tRNA synthetase.” 2007. Web. 15 Jan 2021.

Vancouver:

Levengood JD. Biochemical properties of class I LYSYL-tRNA synthetase. [Internet] [Doctoral dissertation]. The Ohio State University; 2007. [cited 2021 Jan 15]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1166509612.

Council of Science Editors:

Levengood JD. Biochemical properties of class I LYSYL-tRNA synthetase. [Doctoral Dissertation]. The Ohio State University; 2007. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1166509612

University of Rochester

25. Whipple, Joseph M. Defining the Substrate Specificity Determinants for the Yeast Rapid tRNA Decay Pathway and the Identification of Factors that Mediate Degradation.

Degree: PhD, 2011, University of Rochester

URL: http://hdl.handle.net/1802/17698

► tRNAs are a highly stable and highly modified class of noncoding RNAs that are exquisitely adapted to mediate protein synthesis. A diverse array of posttranscriptional… (more)

▼ tRNAs are a highly stable and highly modified class of noncoding RNAs that are exquisitely adapted to mediate protein synthesis. A diverse array of posttranscriptional modifications aid tRNAs in fulfilling the requirements imposed by translation through contributions to tRNA function and stability. A dramatic demonstration of the important role of modifications came from previous work in this lab, which uncovered a previously unknown rapid tRNA decay (RTD) pathway in yeast that specifically deacylated and degraded mature tRNAVal(AAC)lacking 7- methyguanosine (TRM8) and 5-metylcytidine (TRM4), resulting in a temperature sensitive growth phenotype. This study demonstrates that RTD is carried out by the 5’-3’ exonucleases Xrn1 and Rat1, is mediated by Met22, and is a general surveillance mechanism acting on different tRNA species. Furthermore, RTD is shown to be governed primarily by the stability of the acceptor and T-stems of the tRNA, which limits the accessibility of the 5’ end to 5’-3’ exonucleases, and is not necessarily dependent on modification status. Modifications modulate degradation by stabilizing the tertiary structure of the tRNA, which indirectly enhances the stability of secondary structures including the acceptor and T-stems. Consistent with this mode of substrate selectivity, purified Xrn1 is shown to preferentially degrade tRNAs with acceptor and T-stems that are weakened by mutations or by the absence of critical modifications. Thus, the RTD pathway imposes an additional evolutionary constraint on tRNA stability. Genetic evidence suggests that RTD may involve the fundamental biological processes of translation and transcription. Screening of suppressors that rescue the temperature sensitive growth phenotype of a trm8- trm4- mutant reveals that BUD27 and RPO31 are additional mediators of RTD. Mutations in BUD27 or RPO31 restore growth to a trm8- trm4- mutant up to 35°C and suppress degradation and deacylation of tRNAVal(AAC). Deletion of the Bud27 domain required for its function in translation initiation suppresses temperature sensitive growth of a trm8- trm4- mutant, suggesting the function of Bud27 in translation is also linked to its function in RTD. The involvement of Rpo31 in RTD indicates a role for transcription in this pathway, although preliminary results suggest suppression is not due to increased tRNA transcription.

Subjects/Keywords: S. Cerevisiae; Xrnl; Rat1; Met22; tRNA; Turnover

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Whipple, J. M. (2011). Defining the Substrate Specificity Determinants for the Yeast Rapid tRNA Decay Pathway and the Identification of Factors that Mediate Degradation. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/17698

Chicago Manual of Style (16^th Edition):

Whipple, Joseph M. “Defining the Substrate Specificity Determinants for the Yeast Rapid tRNA Decay Pathway and the Identification of Factors that Mediate Degradation.” 2011. Doctoral Dissertation, University of Rochester. Accessed January 15, 2021. http://hdl.handle.net/1802/17698.

MLA Handbook (7^th Edition):

Whipple, Joseph M. “Defining the Substrate Specificity Determinants for the Yeast Rapid tRNA Decay Pathway and the Identification of Factors that Mediate Degradation.” 2011. Web. 15 Jan 2021.

Vancouver:

Whipple JM. Defining the Substrate Specificity Determinants for the Yeast Rapid tRNA Decay Pathway and the Identification of Factors that Mediate Degradation. [Internet] [Doctoral dissertation]. University of Rochester; 2011. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/1802/17698.

Council of Science Editors:

Whipple JM. Defining the Substrate Specificity Determinants for the Yeast Rapid tRNA Decay Pathway and the Identification of Factors that Mediate Degradation. [Doctoral Dissertation]. University of Rochester; 2011. Available from: http://hdl.handle.net/1802/17698

University of Rochester

26. Walling, Lauren R. Specificity Determinants of Homologous VapBC Toxin-Antitoxin Systems.

Degree: PhD, 2020, University of Rochester

URL: http://hdl.handle.net/1802/35510

► Type II toxin-antitoxin (TA) systems are ubiquitous in bacteria and archaea, where they play a pivotal role in the establishment and maintenance of dormancy. Under… (more)

▼ Type II toxin-antitoxin (TA) systems are ubiquitous in bacteria and archaea, where they play a pivotal role in the establishment and maintenance of dormancy. Under normal growth conditions, the protein antitoxin neutralizes the toxin. However, under conditions of stress, such as nutrient starvation or treatment with antibiotics, the antitoxin is degraded by cellular proteases, freeing the toxin, which arrests bacterial growth. TA systems are of particular concern in pathogenic organisms such as nontypeable Haemophilus influenzae (NTHi), as they may elicit dormancy and persistence, leading to chronic infections and failure of antibiotic treatment. Despite the importance of the TA interaction, very little is known about the specificity of the VapC toxin for its substrate or for VapB-VapC complex formation. I characterized the interaction between VapC toxins and VapB antitoxins from NTHi, as well as the target specificity of the VapC toxins. In order to address this question, I made single amino acid mutations in the VapB2 antitoxin from NTHi to characterize its interaction with the VapC2 toxin and determine which residues are important for the TA interaction. The results identified two single amino acid residues in the C-terminal region of the VapB2 antitoxin that are important for its ability to neutralize its cognate VapC2 toxin: W48 and F52. Additionally, I attempted to alter the VapB1 antitoxin’s specificity by making a mutation that would allow it to neutralize its non-cognate VapC2 toxin. I mutated the VapB1 antitoxin to contain the important tryptophan residue identified by my previous work to be important in the VapB2-VapC2 interaction (W48). This VapB1 mutant (T47W) neutralizes both its cognate VapC1 toxin and VapC2, its non-cognate toxin. Additionally, identification of the RNA targets of VapC toxins is crucial to understanding how toxins control the establishment and maintenance of bacterial dormancy. I used RNA sequencing and Northern blot analysis to reveal that both VapC1 and VapC2 cleave tRNAfMet, which inhibits protein synthesis. Overexpression of tRNAfMet suppresses VapC1 toxicity, suggesting that translation inhibition results from the depletion of tRNAfMet Additionally, I identified a GC pair at the tRNAfMet anticodon stem-loop junction that appears to play a key role in VapC-specific cleavage of the tRNA. Together, these findings support a mechanism of VapC1- and VapC2-induced dormancy by sequence-specific cleavage of tRNAfMet, neutralized by a highly specific interaction with their cognate VapB antitoxins.

Subjects/Keywords: Toxin-antitoxin systems; VapBC; tRNA cleavage.

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Walling, L. R. (2020). Specificity Determinants of Homologous VapBC Toxin-Antitoxin Systems. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/35510

Chicago Manual of Style (16^th Edition):

Walling, Lauren R. “Specificity Determinants of Homologous VapBC Toxin-Antitoxin Systems.” 2020. Doctoral Dissertation, University of Rochester. Accessed January 15, 2021. http://hdl.handle.net/1802/35510.

MLA Handbook (7^th Edition):

Walling, Lauren R. “Specificity Determinants of Homologous VapBC Toxin-Antitoxin Systems.” 2020. Web. 15 Jan 2021.

Vancouver:

Walling LR. Specificity Determinants of Homologous VapBC Toxin-Antitoxin Systems. [Internet] [Doctoral dissertation]. University of Rochester; 2020. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/1802/35510.

Council of Science Editors:

Walling LR. Specificity Determinants of Homologous VapBC Toxin-Antitoxin Systems. [Doctoral Dissertation]. University of Rochester; 2020. Available from: http://hdl.handle.net/1802/35510

University of Toronto

27. Andrusiak, Tara. Biomimetic Aminoacylation: Investigating Detection of Acylation and the Effect of α-Amino Protection.

Degree: 2009, University of Toronto

URL: http://hdl.handle.net/1807/18143

►

Direct synthesis of aminoacyl-tRNA occurs using α-N-tBoc-protected aminoacyl phosphates and lanthanum salts. Deprotection of aminoacyl tRNA is essential prior to translation; however, the conditions of… (more)

Subjects/Keywords: aminoacylation; tRNA; 0487

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Andrusiak, T. (2009). Biomimetic Aminoacylation: Investigating Detection of Acylation and the Effect of α-Amino Protection. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/18143

Chicago Manual of Style (16^th Edition):

Andrusiak, Tara. “Biomimetic Aminoacylation: Investigating Detection of Acylation and the Effect of α-Amino Protection.” 2009. Masters Thesis, University of Toronto. Accessed January 15, 2021. http://hdl.handle.net/1807/18143.

MLA Handbook (7^th Edition):

Andrusiak, Tara. “Biomimetic Aminoacylation: Investigating Detection of Acylation and the Effect of α-Amino Protection.” 2009. Web. 15 Jan 2021.

Vancouver:

Andrusiak T. Biomimetic Aminoacylation: Investigating Detection of Acylation and the Effect of α-Amino Protection. [Internet] [Masters thesis]. University of Toronto; 2009. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/1807/18143.

Council of Science Editors:

Andrusiak T. Biomimetic Aminoacylation: Investigating Detection of Acylation and the Effect of α-Amino Protection. [Masters Thesis]. University of Toronto; 2009. Available from: http://hdl.handle.net/1807/18143

University of Vermont

28. Patterson, Pryce. Nonsense Mutation in AIMP2 Reduces Protein Expression and Causes a Severe Neurodevelopmental Disorder.

Degree: Biochemistry, 2019, University of Vermont

URL: https://scholarworks.uvm.edu/hcoltheses/314

► In mammalian cells, a multi-tRNA synthetase complex containing eight aminoacyl-tRNA synthetases, which catalyze nine different reactions, is thought to make protein synthesis more efficient… (more)

▼ In mammalian cells, a multi-tRNA synthetase complex containing eight aminoacyl-tRNA synthetases, which catalyze nine different reactions, is thought to make protein synthesis more efficient by keeping components of the translational machinery in close proximity. Aminoacyl tRNA synthetase-interacting multifunctional protein 2 (AIMP2) is one of three non-catalytic components of this complex and is essential for its formation and stability. A homozygous nonsense variant (Y35Ter) of AIMP2 appears in the genotypes of patients with severe neurodevelopmental phenotypes. To determine the effect this variant has on expression at the mRNA and protein level, as well as progression of cells through the cell cycle, patient fibroblasts were studied. Fluorescent microscopy and western blotting, along with puromycin-labeling, cell synchronization, and mRNA analysis, were used to determine the cellular impact of this mutation. Through this study, it was determined that this mutation in AIMP2 causes decreased AIMP2 protein levels and altered mRNA expression. Along with that, the puromycin assay showed a lower rate of protein synthesis in patient fibroblasts when compared to ATCC control cells. There was also a slight decrease in the amount of leucyl-tRNA synthetase (LARS) in patient cells. This protein is a member of the multi-tRNA synthetase complex and the observed decrease could indicate that the protein level of other members of the complex are lower in patient cells. While the cell cycle study did not provide any significant results, this could be due to the fact that fibroblasts were used and not neuronal cells. This study showed that a homozygous nonsense variant (Y35Ter) of AIMP2 impacts expression at the mRNA and protein level while also decreasing protein synthesis. Further research into the specific mechanism behind this mutation is needed in order to possibly develop a treatment option for patients presenting with the resulting symptoms. Advisors/Committee Members: Christopher Francklyn, Ph.D., Matthias Brewer, Ph.D..

Subjects/Keywords: AIMP2; Multi-tRNA synthetase complex; neurodevelopmental disorder

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APA (6^th Edition):

Patterson, P. (2019). Nonsense Mutation in AIMP2 Reduces Protein Expression and Causes a Severe Neurodevelopmental Disorder. (Thesis). University of Vermont. Retrieved from https://scholarworks.uvm.edu/hcoltheses/314

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Patterson, Pryce. “Nonsense Mutation in AIMP2 Reduces Protein Expression and Causes a Severe Neurodevelopmental Disorder.” 2019. Thesis, University of Vermont. Accessed January 15, 2021. https://scholarworks.uvm.edu/hcoltheses/314.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Patterson, Pryce. “Nonsense Mutation in AIMP2 Reduces Protein Expression and Causes a Severe Neurodevelopmental Disorder.” 2019. Web. 15 Jan 2021.

Vancouver:

Patterson P. Nonsense Mutation in AIMP2 Reduces Protein Expression and Causes a Severe Neurodevelopmental Disorder. [Internet] [Thesis]. University of Vermont; 2019. [cited 2021 Jan 15]. Available from: https://scholarworks.uvm.edu/hcoltheses/314.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Patterson P. Nonsense Mutation in AIMP2 Reduces Protein Expression and Causes a Severe Neurodevelopmental Disorder. [Thesis]. University of Vermont; 2019. Available from: https://scholarworks.uvm.edu/hcoltheses/314

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Adelaide

29. Yang, Xiujuan. Roles of a glutamyl-tRNA synthetase in controlling early anther development in rice.

Degree: 2018, University of Adelaide

URL: http://hdl.handle.net/2440/118188

► In seed-propagated plants, the formation and development of the male reproductive organ, the anther, is indispensable for plant propagation. In grain crops, crop productivity is… (more)

▼ In seed-propagated plants, the formation and development of the male reproductive organ, the anther, is indispensable for plant propagation. In grain crops, crop productivity is highly dependent on male fertility and thereafter successful fertilisation between male and female gametophytes. Understanding the molecular mechanisms determining anther development and formation of pollen grains in important crops such as rice (Oryza sativa) and barley (Hordeum vulgare) is important for fundamental biology and agricultural practice. In flowering plants, the male development starts from the formation of anther primordia, and subsequent cell division and differentiation establish the appropriate anther cell organisation. After morphogenesis, the anther in higher plants mostly contains centrally localised germinal cells surrounded by four layers of anther wall composed by the epidermis, endothecium, middle layer and tapetum, from the outer to the inner. The mature pollen grain is formed via meiosis and mitosis supported by the degeneration of anther wall layers such as the innermost tissue tapetum as well as the middle layer. Although previous investigations uncovered that various regulators such as leucine-rich repeat receptor-like kinases (LRR-RLKs), glutaredoxins, transcription factors, hormones and small RNAs are involved in anther cell fate specification, the role of genes responsible for physiological homeostasis in early male development remains unknown. Plant aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyse the attachment of amino acids onto their cognate transfer RNAs (tRNAs), playing a central role during the translation of genetic information from messenger RNA to protein. However, little is known about their molecular characteristics and roles in plant development. In the research for this thesis bioinformatics analysis was conducted and 141 aaRSs sequences were obtained from Arabidopsis (Arabidopsis thaliana), rice and Physcomitrella patens. In these sequences, beside the conserved motifs such as HIGH, KMSKS, Motif 2, Motif 3 required for the enzymatic functions, additional new domains such as GST_C (glutathione S-transferase C terminus), WHEP and OB (oligonucleotide binding motif) fold were observed. These may function in tRNA binding or protein-protein interaction. Sequence prediction showed that these plant aaRSs have subcellular localisation in cytosol, mitochondria and chloroplasts, which may be related with evolutionary origin, signal peptide, and intra/extracellular stimulations. Notably, the aaRS genes encoding cytosolic ones are more active in reproductive tissues while genes encoding organellar ones are more expressed in vegetative tissues. Together, we provide an informative source for future research and highlight the essential roles of aaRSs in plant. To understand the function of aaRS in plant male development, one male sterile mutant called osers1 (oryza sativa glutamyl-trna synthetase 1) was isolated from a mutant library and subjected to functional analysis. Although osers1 shows… Advisors/Committee Members: Zhang, Dabing (advisor), Mather, Diane (advisor), School of Agriculture, Food and Wine (school).

Subjects/Keywords: Aminoacyl-tRNA synthetase; anther; ROS; rice

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Yang, X. (2018). Roles of a glutamyl-tRNA synthetase in controlling early anther development in rice. (Thesis). University of Adelaide. Retrieved from http://hdl.handle.net/2440/118188

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Yang, Xiujuan. “Roles of a glutamyl-tRNA synthetase in controlling early anther development in rice.” 2018. Thesis, University of Adelaide. Accessed January 15, 2021. http://hdl.handle.net/2440/118188.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Yang, Xiujuan. “Roles of a glutamyl-tRNA synthetase in controlling early anther development in rice.” 2018. Web. 15 Jan 2021.

Vancouver:

Yang X. Roles of a glutamyl-tRNA synthetase in controlling early anther development in rice. [Internet] [Thesis]. University of Adelaide; 2018. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/2440/118188.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Yang X. Roles of a glutamyl-tRNA synthetase in controlling early anther development in rice. [Thesis]. University of Adelaide; 2018. Available from: http://hdl.handle.net/2440/118188

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

30. Carlsten, Jonas. Mediator and its role in non-coding RNA and chromatin regualtion.

Degree: 2014, University of Gothenburg / Göteborgs Universitet

URL: http://hdl.handle.net/2077/35458

► Mediator is a multiprotein complex required for the regulation of RNA Polymerase II (Pol II) transcription. Mediator transmits regulatory signals from activators and repressors to… (more)

▼ Mediator is a multiprotein complex required for the regulation of RNA Polymerase II (Pol II) transcription. Mediator transmits regulatory signals from activators and repressors to the Pol II machinery at the promoter, but the complex has also many other functions related to control of gene transcription. This thesis aims to expand our knowledge of Mediator’s involvement in regulation of the specialized chromatin structures found at telomeres and centromeres as well as its role in regulation of non-coding RNA transcription. A fine-tuned balance between the histone deacetylase Sir2 and the histone acetyltransferase Sas2 determines the location of the boundary between active and inactive chromatin at budding yeast telomeres. In our work, we demonstrate that Mediator interacts with heterochromatin at telomeres and directs the position of this boundary. Mutations in Mediator subunits cause a depletion of the complex from heterochromatin, which changes the balance between Sir2 and Sas2, and ultimately results in desilencing of subtelomeric regions. Telomeres are important regulators of replicative life span, which is reduced as a consequence of mutations in the Mediator complex. The Schizosaccharomcyes pombe centromeres are also characterized by silent heterochromatin, which is assembled and maintained through a complex multifactorial system. In our work, we find that Mediator is involved in formation of these heterochromatin structures. Loss of the Mediator subunit Med20 causes disruption of heterochromatin and leads to increased transcriptional activity at the centromere. The med20∆ mutant also causes reduced levels of CENP-ACnp1, a centromere specific form of histone H3 found at centromeres, and chromosome instability during cell division. In our work, we find that inactivation of the RNA degrading complex the exosome can reverse the increased levels of pericentromeric transcription observed in med20∆ cells, but that it fails to alleviate the chromosome segregation defects. Furthermore, loss of Med20 leads to a changed pattern of siRNA products, which is not further affected in the med20∆/rrp6∆ strain. Our results therefore suggest that Mediator and the exosome act in partially independent pathways to influence centromere function. We also demonstrate that Mediator influences RNA polymerase III (Pol III) transcription. Deletion of med20+ results in increased transcription of ribosomal protein genes, but also affects Pol III transcription causing an accumulation of aberrant tRNA transcripts with evidence of incorrect transcription termination. The aberrant transcripts are polyadenylated and targeted for degradation by the exosome. The effects of Mediator on Pol III transcription are distinct from those involving Maf1, the classical repressor of Pol III activity. Based on our findings we suggest that fission yeast Mediator takes part in a pathway that coordinates expression of ribosomal protein genes with Pol III transcription. Work in this thesis demonstrates that Mediator regulates the chromatin structure of several…

Subjects/Keywords: Mediator; transcription; centromere; telomere; tRNA; exosome

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Carlsten, J. (2014). Mediator and its role in non-coding RNA and chromatin regualtion. (Thesis). University of Gothenburg / Göteborgs Universitet. Retrieved from http://hdl.handle.net/2077/35458

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Carlsten, Jonas. “Mediator and its role in non-coding RNA and chromatin regualtion.” 2014. Thesis, University of Gothenburg / Göteborgs Universitet. Accessed January 15, 2021. http://hdl.handle.net/2077/35458.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Carlsten, Jonas. “Mediator and its role in non-coding RNA and chromatin regualtion.” 2014. Web. 15 Jan 2021.

Vancouver:

Carlsten J. Mediator and its role in non-coding RNA and chromatin regualtion. [Internet] [Thesis]. University of Gothenburg / Göteborgs Universitet; 2014. [cited 2021 Jan 15]. Available from: http://hdl.handle.net/2077/35458.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Carlsten J. Mediator and its role in non-coding RNA and chromatin regualtion. [Thesis]. University of Gothenburg / Göteborgs Universitet; 2014. Available from: http://hdl.handle.net/2077/35458

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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Open Access Theses and Dissertations