subject:(TrmD)

Brigham Young University

1. Hwang, Jae Yeon. Analyses of mRNA Cleavage by RelE and the Role of tRNA Methyltransferase TrmD Using Bacterial Ribosome Profiling.

Degree: PhD, 2016, Brigham Young University

URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=7443&context=etd

► Protein synthesis is a fundamental and ultimate process in living cells. Cells possess sophisticated machineries and continuously carry out complex processes. Monitoring protein synthesis in… (more)

▼ Protein synthesis is a fundamental and ultimate process in living cells. Cells possess sophisticated machineries and continuously carry out complex processes. Monitoring protein synthesis in living cells not only inform us about the mechanism of translation but also deepen our insights about all aspects of life. Understanding the structure and mechanism of the ribosome and its associated factors helped us enlarge our knowledge on protein synthesis. Recently, with the dramatic advances of high-throughput sequencing and bioinformatics, a new technique called ribosome profiling emerged. By retrieving mRNA fragments protected by translating ribosomes, ribosome profiling reveals global ribosome occupancy along mRNAs in living cells, which can inform us with the identity and quantity of proteins being made. Easily adapted to other organisms, ribosome profiling technique is expanding its application in revealing various cellular activities as well as the knowledge on protein synthesis. Here, we report the mechanism of translating mRNA cleavage by endoribonuclease RelE in vivo. RelE is an endoribonuclease that is induced during nutrient deficiency stress and specifically cleaves translating mRNAs upon binding to the ribosomal A site. Overexpression of RelE in living cells causes growth arrest by inhibiting global translation. We monitored RelE activity in vivo upon overexpression using ribosome profiling. The data show that RelE actively cuts translating mRNAs whenever the ribosomal A site is accessible, resulting in truncated mRNAs. RelE causes the ribosome complexes to accumulate near the 5' end of genes as the process of ribosome rescue, translation, and cleavage by RelE repeats. RelE cleavage specific sub-codon level ribosome profiling data also represent reading frame in Escherichia coli and sequence specificity of RelE cleavage in vivo. We report another ribosome profiling study on a methyltransferase TrmD in E. coli. TrmD is known to methylate G37 (the residue at 3' side of anticodon) of some tRNAs and be responsible for codon-anticodon interaction. We constructed a TrmD depletion E. coli strain, whose deletion results in lethality of cells. Resulting depletion of m¹G37 in the strain leads to growth arrest. Lack of m¹G37 of some tRNAs whose codons start with C showed frequent frameshift when translating the gene message in vitro. By using ribosome profiling, we successfully observed significant difference on translation process when codons interact with anticodons of tRNAs lacking m¹G37. The data reveal slow translation rate or pauses on the tRNAs when missing the appropriate methylation, which corresponds to the previous biochemical data in vitro.

Subjects/Keywords: RelE; endoribonuclease; TrmD; methyltransferase; ribosome profiling; m1G37; Chemistry

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APA (6^th Edition):

Hwang, J. Y. (2016). Analyses of mRNA Cleavage by RelE and the Role of tRNA Methyltransferase TrmD Using Bacterial Ribosome Profiling. (Doctoral Dissertation). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=7443&context=etd

Chicago Manual of Style (16^th Edition):

Hwang, Jae Yeon. “Analyses of mRNA Cleavage by RelE and the Role of tRNA Methyltransferase TrmD Using Bacterial Ribosome Profiling.” 2016. Doctoral Dissertation, Brigham Young University. Accessed January 18, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=7443&context=etd.

MLA Handbook (7^th Edition):

Hwang, Jae Yeon. “Analyses of mRNA Cleavage by RelE and the Role of tRNA Methyltransferase TrmD Using Bacterial Ribosome Profiling.” 2016. Web. 18 Jan 2021.

Vancouver:

Hwang JY. Analyses of mRNA Cleavage by RelE and the Role of tRNA Methyltransferase TrmD Using Bacterial Ribosome Profiling. [Internet] [Doctoral dissertation]. Brigham Young University; 2016. [cited 2021 Jan 18]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=7443&context=etd.

Council of Science Editors:

Hwang JY. Analyses of mRNA Cleavage by RelE and the Role of tRNA Methyltransferase TrmD Using Bacterial Ribosome Profiling. [Doctoral Dissertation]. Brigham Young University; 2016. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=7443&context=etd

Virginia Commonwealth University

2. Hamidi, Zohal. Characterization and Crystallization of the Mycobacterium Tuberculosis trmD.

Degree: MS, Physiology, 2010, Virginia Commonwealth University

URL: https://doi.org/10.25772/XYY2-3Y68 ; https://scholarscompass.vcu.edu/etd/2219

► One third of the world’s population is affected by Tuberculosis (TB), a disease caused by infection with Mycobacterium tuberculosis (MtB). The emergence of multidrug-resistant MtB… (more)

Subjects/Keywords: trmD; Mycobacterium tuberculosis; Life Sciences; Physiology

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APA (6^th Edition):

Hamidi, Z. (2010). Characterization and Crystallization of the Mycobacterium Tuberculosis trmD. (Thesis). Virginia Commonwealth University. Retrieved from https://doi.org/10.25772/XYY2-3Y68 ; https://scholarscompass.vcu.edu/etd/2219

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):

Hamidi, Zohal. “Characterization and Crystallization of the Mycobacterium Tuberculosis trmD.” 2010. Thesis, Virginia Commonwealth University. Accessed January 18, 2021. https://doi.org/10.25772/XYY2-3Y68 ; https://scholarscompass.vcu.edu/etd/2219.

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

MLA Handbook (7^th Edition):

Hamidi, Zohal. “Characterization and Crystallization of the Mycobacterium Tuberculosis trmD.” 2010. Web. 18 Jan 2021.

Vancouver:

Hamidi Z. Characterization and Crystallization of the Mycobacterium Tuberculosis trmD. [Internet] [Thesis]. Virginia Commonwealth University; 2010. [cited 2021 Jan 18]. Available from: https://doi.org/10.25772/XYY2-3Y68 ; https://scholarscompass.vcu.edu/etd/2219.

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

Council of Science Editors:

Hamidi Z. Characterization and Crystallization of the Mycobacterium Tuberculosis trmD. [Thesis]. Virginia Commonwealth University; 2010. Available from: https://doi.org/10.25772/XYY2-3Y68 ; https://scholarscompass.vcu.edu/etd/2219

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

Virginia Commonwealth University

3. Uzzell, Jamar. STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS.

Degree: MS, Biochemistry, 2011, Virginia Commonwealth University

URL: https://doi.org/10.25772/6DKP-1H28 ; https://scholarscompass.vcu.edu/etd/2539

► Thermal stability of theG37 tRNA methyltransferase proteins from Thermotoga maritima and Aquifex aeolicus have been compared using Differential Scanning Calorimetry. It was shown that the… (more)

Subjects/Keywords: TrmD; Thermophilies; Thermophilic; Aquifex aeolicus; Thermotoga maritima; DSC; Differential Scanning Calorimetry; Biochemistry, Biophysics, and Structural Biology; Life Sciences

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APA (6^th Edition):

Uzzell, J. (2011). STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS. (Thesis). Virginia Commonwealth University. Retrieved from https://doi.org/10.25772/6DKP-1H28 ; https://scholarscompass.vcu.edu/etd/2539

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):

Uzzell, Jamar. “STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS.” 2011. Thesis, Virginia Commonwealth University. Accessed January 18, 2021. https://doi.org/10.25772/6DKP-1H28 ; https://scholarscompass.vcu.edu/etd/2539.

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

MLA Handbook (7^th Edition):

Uzzell, Jamar. “STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS.” 2011. Web. 18 Jan 2021.

Vancouver:

Uzzell J. STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS. [Internet] [Thesis]. Virginia Commonwealth University; 2011. [cited 2021 Jan 18]. Available from: https://doi.org/10.25772/6DKP-1H28 ; https://scholarscompass.vcu.edu/etd/2539.

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

Council of Science Editors:

Uzzell J. STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS. [Thesis]. Virginia Commonwealth University; 2011. Available from: https://doi.org/10.25772/6DKP-1H28 ; https://scholarscompass.vcu.edu/etd/2539

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

Virginia Commonwealth University

4. Palesis, Maria Kiouppis. DYNAMICS OF SUBSTRATE INTERACTIONS IN tRNA (m1G37) METHYLTRANSFERASE: IMPLICATIONS FOR DRUG DISCOVERY.

Degree: PhD, Pharmacology & Toxicology, 2012, Virginia Commonwealth University

URL: https://doi.org/10.25772/MPXG-2S81 ; https://scholarscompass.vcu.edu/etd/2725

► The bacterial enzyme t-RNA (m1G37) methyltransferase (TrmD) is an ideal anti-microbial drug target since it is found in all eubacteria, serves an essential role during… (more)

▼ The bacterial enzyme t-RNA (m1G37) methyltransferase (TrmD) is an ideal anti-microbial drug target since it is found in all eubacteria, serves an essential role during protein synthesis, and shares very little sequence or structural homology with its eukaryotic counterpart, Trm5. TrmD, a homodimeric protein, methylates the G37 nucleotide of tRNA using S-adenosyl-L-methionine (SAM) as the methyl donor and thus enables proper codon-anticodon alignment during translation. The two deeply buried binding sites for SAM seen in X-ray crystallography suggest that significant conformational changes must occur for substrate binding and catalytic turnover. Results from molecular dynamics simulations implicate a flexible loop region and a halo-like loop which may be gating the entrance to the active site. Analysis of simulation trajectories indicates an alternating pattern of active site accessibility between the two SAM binding sites, suggesting a single site mechanism for enzyme activity. Isothermal titration calorimetry (ITC), demonstrates that binding of SAM to TrmD is an exothermic reaction resulting from sequential binding at two sites. A similar mode of binding at higher affinities was observed for the product, S-adenosyl-L-homocysteine (SAH) suggesting that product inhibition may be important in vivo. ITC reveals that tRNA binding is an endothermic reaction in which one tRNA molecule binds to one TrmD dimer. This further supports the hypothesis of a single site mechanism for enzyme function. However, mutational analysis using hybrid mutant proteins suggests that catalytic integrity must be maintained in both active sites for maximum enzymatic efficiency. Mutations impeding flexibility of the halo loop were particularly detrimental to enzyme activity. Noncompetitive inhibition of TrmD was observed in the presence of bis-ANS, an extrinsic fluorescent dye. In silico ligand docking of bis-ANS to TrmD suggests that dye interferes with mobility of the flexible linker above the active site. Because SAM is a ubiquitous cofactor in methyltransferase reactions, analogs of this ligand may not be suitable for drug development. It is therefore important to investigate allosteric modes of inhibition. These experiments have identified key, mobile structural elements in the TrmD enzyme important for activity, and provide a basis for further research in the development of allosteric inhibitors for this enzyme. Advisors/Committee Members: W. Michael Holmes.

Subjects/Keywords: tRNA; TrmD; S-adenosyl-L-methionine; S-adenosyl-L-homocysteine; single site activity; tRNA m1G37 methyltransferase; Medical Pharmacology; Medical Sciences; Medicine and Health Sciences

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

APA (6^th Edition):

Palesis, M. K. (2012). DYNAMICS OF SUBSTRATE INTERACTIONS IN tRNA (m1G37) METHYLTRANSFERASE: IMPLICATIONS FOR DRUG DISCOVERY. (Doctoral Dissertation). Virginia Commonwealth University. Retrieved from https://doi.org/10.25772/MPXG-2S81 ; https://scholarscompass.vcu.edu/etd/2725

Chicago Manual of Style (16^th Edition):

Palesis, Maria Kiouppis. “DYNAMICS OF SUBSTRATE INTERACTIONS IN tRNA (m1G37) METHYLTRANSFERASE: IMPLICATIONS FOR DRUG DISCOVERY.” 2012. Doctoral Dissertation, Virginia Commonwealth University. Accessed January 18, 2021. https://doi.org/10.25772/MPXG-2S81 ; https://scholarscompass.vcu.edu/etd/2725.

MLA Handbook (7^th Edition):

Palesis, Maria Kiouppis. “DYNAMICS OF SUBSTRATE INTERACTIONS IN tRNA (m1G37) METHYLTRANSFERASE: IMPLICATIONS FOR DRUG DISCOVERY.” 2012. Web. 18 Jan 2021.

Vancouver:

Palesis MK. DYNAMICS OF SUBSTRATE INTERACTIONS IN tRNA (m1G37) METHYLTRANSFERASE: IMPLICATIONS FOR DRUG DISCOVERY. [Internet] [Doctoral dissertation]. Virginia Commonwealth University; 2012. [cited 2021 Jan 18]. Available from: https://doi.org/10.25772/MPXG-2S81 ; https://scholarscompass.vcu.edu/etd/2725.

Council of Science Editors:

Palesis MK. DYNAMICS OF SUBSTRATE INTERACTIONS IN tRNA (m1G37) METHYLTRANSFERASE: IMPLICATIONS FOR DRUG DISCOVERY. [Doctoral Dissertation]. Virginia Commonwealth University; 2012. Available from: https://doi.org/10.25772/MPXG-2S81 ; https://scholarscompass.vcu.edu/etd/2725

University of Cambridge

5. Whitehouse, Andrew John. Inhibition of enzymes from mycobacteria using fragment-based approaches.

Degree: PhD, 2019, University of Cambridge

URL: https://doi.org/10.17863/CAM.44905 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.787885

► The work described in this thesis is focused on the application of fragment-based approaches for two essential mycobacterial target proteins, fumarate hydratase (fumarase) from Mycobacterium… (more)

Subjects/Keywords: Mycobacterium abscessus; Mycobacterium tuberculosis; TrmD; fragment-based; fumarate hydratase; fumarase; tRNA (m1G37) methyltransferase; differential scanning fluorimetry; isothermal titration calorimetry; nontuberculous mycobacteria; allosteric; deconstruction-reconstruction; X-ray crystallography; fragment-merging; tuberculosis; cystic fibrosis

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

APA (6^th Edition):

Whitehouse, A. J. (2019). Inhibition of enzymes from mycobacteria using fragment-based approaches. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.44905 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.787885

Chicago Manual of Style (16^th Edition):

Whitehouse, Andrew John. “Inhibition of enzymes from mycobacteria using fragment-based approaches.” 2019. Doctoral Dissertation, University of Cambridge. Accessed January 18, 2021. https://doi.org/10.17863/CAM.44905 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.787885.

MLA Handbook (7^th Edition):

Whitehouse, Andrew John. “Inhibition of enzymes from mycobacteria using fragment-based approaches.” 2019. Web. 18 Jan 2021.

Vancouver:

Whitehouse AJ. Inhibition of enzymes from mycobacteria using fragment-based approaches. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Jan 18]. Available from: https://doi.org/10.17863/CAM.44905 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.787885.

Council of Science Editors:

Whitehouse AJ. Inhibition of enzymes from mycobacteria using fragment-based approaches. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://doi.org/10.17863/CAM.44905 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.787885

University of Cambridge

6. Whitehouse, Andrew John. Inhibition of enzymes from mycobacteria using fragment-based approaches.

Degree: PhD, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/297851

► The work described in this thesis is focused on the application of fragment-based approaches for two essential mycobacterial target proteins, fumarate hydratase (fumarase) from Mycobacterium… (more)

Subjects/Keywords: Mycobacterium abscessus; Mycobacterium tuberculosis; TrmD; fragment-based; fumarate hydratase; fumarase; tRNA (m1G37) methyltransferase; differential scanning fluorimetry; isothermal titration calorimetry; nontuberculous mycobacteria; allosteric; deconstruction-reconstruction; X-ray crystallography; fragment-merging; tuberculosis; cystic fibrosis

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

APA (6^th Edition):

Whitehouse, A. J. (n.d.). Inhibition of enzymes from mycobacteria using fragment-based approaches. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/297851

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

Chicago Manual of Style (16^th Edition):

Whitehouse, Andrew John. “Inhibition of enzymes from mycobacteria using fragment-based approaches.” Doctoral Dissertation, University of Cambridge. Accessed January 18, 2021. https://www.repository.cam.ac.uk/handle/1810/297851.

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

MLA Handbook (7^th Edition):

Whitehouse, Andrew John. “Inhibition of enzymes from mycobacteria using fragment-based approaches.” Web. 18 Jan 2021.

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

Vancouver:

Whitehouse AJ. Inhibition of enzymes from mycobacteria using fragment-based approaches. [Internet] [Doctoral dissertation]. University of Cambridge; [cited 2021 Jan 18]. Available from: https://www.repository.cam.ac.uk/handle/1810/297851.

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

Council of Science Editors:

Whitehouse AJ. Inhibition of enzymes from mycobacteria using fragment-based approaches. [Doctoral Dissertation]. University of Cambridge; Available from: https://www.repository.cam.ac.uk/handle/1810/297851

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

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