+publisher:"Cornell University" +contributor:("Hanson, Maureen R.")

1. Liao, Juiyun. SUBSTRATES, STRUCTURES, AND FUNCTIONS OF THE CHLOROPLAST CLP PROTEASE SYSTEM IN ARABIDOPSIS THALIANA.

Degree: PhD, Plant Biology, 2019, Cornell University

► The caseinolytic proteolytic machinery (CLP) is an essential and abundant protease of the chloroplast protease network. It is composed of multiple components (a proteolytic core… (more)

▼ The caseinolytic proteolytic machinery (CLP) is an essential and abundant protease of the chloroplast protease network. It is composed of multiple components (a proteolytic core CLPP/R/T, chaperones CLPC1/C2/D, and adaptors CLPS1/F). Mostly based on functional and structural information from bacterial Clp systems, it is postulated that these chloroplast CLP chaperones are aided by the CLP adaptors to select and deliver substrates to the proteolytic chamber (protease core) for degradation. The chloroplast CLPPRT proteolytic core is different and far more complex than the bacterial or mitochondria Clp core. The chloroplast CLP core is a hetero-oligomeric tetradecamer that is associated with additional accessory proteins unique to higher plants. Furthermore, the chloroplast CLPP and CLPR subunits have C-terminal extensions with unknown functions. It is unclear why chloroplast CLP core shows such high complexity and how these different CLP subunits contribute to the proteolytic system. Finally, relatively few chloroplast CLP substrates have been identified. To better understand the chloroplast CLP protease system, I applied an in vivo trapping approach for substrate identification and crosslinking (XL) mass spectrometry (MS) for investigation of the proximity and possible protein-protein interactions between these CLP components. Functional complementation showed that CLPP5 is crucial for CLP catalysis, whereas CLPP3 plays an essential role in CLP structure but its catalytic activity is dispensable. However, in vivo trapping using CLPPRT complexes with a reduced number of catalytic triads through the presence of one or more catalytically inactivated CLPP3/5 subunits did not identify proteins trapped in these CLPPRT complexes. This suggests that reduced proteolytic capacity within CLP cores does not result in a bottleneck for protein degradation in vivo. XL-MS of affinity-purified CLP core complexes or affinity purified CLPC-TRAP complexes identified several putative domains and motifs involved in the CLP protein-protein interactions. The newly established workflow of in vitro DSSO crosslinking using plant proteins paves the way for a more detailed exploration of the 3D structure and possible regulation of the chloroplast CLP machinery. Advisors/Committee Members: Van Wijk, Klaas (chair), Hanson, Maureen R. (committee member), Qian, Shu-Bing (committee member).

Subjects/Keywords: CLP; subtrate; trapping; Proteolysis; Biochemistry; Botany; protease; Plant sciences

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APA (6^th Edition):

Liao, J. (2019). SUBSTRATES, STRUCTURES, AND FUNCTIONS OF THE CHLOROPLAST CLP PROTEASE SYSTEM IN ARABIDOPSIS THALIANA. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/67299

Chicago Manual of Style (16^th Edition):

Liao, Juiyun. “SUBSTRATES, STRUCTURES, AND FUNCTIONS OF THE CHLOROPLAST CLP PROTEASE SYSTEM IN ARABIDOPSIS THALIANA.” 2019. Doctoral Dissertation, Cornell University. Accessed January 20, 2021. http://hdl.handle.net/1813/67299.

MLA Handbook (7^th Edition):

Liao, Juiyun. “SUBSTRATES, STRUCTURES, AND FUNCTIONS OF THE CHLOROPLAST CLP PROTEASE SYSTEM IN ARABIDOPSIS THALIANA.” 2019. Web. 20 Jan 2021.

Vancouver:

Liao J. SUBSTRATES, STRUCTURES, AND FUNCTIONS OF THE CHLOROPLAST CLP PROTEASE SYSTEM IN ARABIDOPSIS THALIANA. [Internet] [Doctoral dissertation]. Cornell University; 2019. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/1813/67299.

Council of Science Editors:

Liao J. SUBSTRATES, STRUCTURES, AND FUNCTIONS OF THE CHLOROPLAST CLP PROTEASE SYSTEM IN ARABIDOPSIS THALIANA. [Doctoral Dissertation]. Cornell University; 2019. Available from: http://hdl.handle.net/1813/67299

Cornell University

2. Sun, Tao. Trans-Acting Factors Essential For Plant Organelle Rna Editing.

Degree: PhD, Plant Biology, 2014, Cornell University

URL: http://hdl.handle.net/1813/38935

► In higher plants, RNA editing is a C-to-U conversion that corrects chloroplast and mitochondrial transcripts that are otherwise defective. Although plant RNA editing has been… (more)

▼ In higher plants, RNA editing is a C-to-U conversion that corrects chloroplast and mitochondrial transcripts that are otherwise defective. Although plant RNA editing has been known for over two decades, the molecular mechanism is poorly understood. Until recently, all the known trans-acting factors were members of the Pentatricopeptide Repeat (PPR) protein family, which serve as recognition factors via specific interaction with cis-elements upstream of the C targets. An additional editing factor, RIP1, was identified by a proteomics study. RIP1 is a dual-targeted protein that selectively interacts with PPR editing factors and affects 14 editing events in chloroplasts and over 400 editing events in mitochondria. RIP1 belongs to a small protein family, 5 members of which were later shown to be major editing factors. Homology searching with the RIP protein led to the discovery of ORRM1, a hybrid protein which possesses a RIP-like domain at its N terminus and an RNA Recognition Motif (RRM) domain at its C terminus. Loss of ORRM1 results in editing defects in multiple plastid sites. A transient complementation assay indicates that the editing activity of ORRM1 is carried by the RRM, which places it in a different family than RIP proteins. Additional members of the ORRM1 family might be involved in plant RNA editing. A plastid-targeted protein immunoprecipitated with a functional epitopetagged ORRM1. Loss of this protein leads to editing defects at many plastid sites, most of which are also controlled by ORRM1. Homology searches with this plastid protein identified several related proteins which are all organelle-targeted. The function of this new family still needs further investigation. So far, four types of trans-acting factors have been identified for plant organelle RNA editing, which reveals an unexpected complexity of the editing machinery. Advisors/Committee Members: Hanson, Maureen R (chair), Van Wijk, Klaas (committee member), Lazarowitz, Sondra Gale (committee member).

Subjects/Keywords: plant RNA editing; chloroplast and mitochondria

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APA (6^th Edition):

Sun, T. (2014). Trans-Acting Factors Essential For Plant Organelle Rna Editing. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/38935

Chicago Manual of Style (16^th Edition):

Sun, Tao. “Trans-Acting Factors Essential For Plant Organelle Rna Editing.” 2014. Doctoral Dissertation, Cornell University. Accessed January 20, 2021. http://hdl.handle.net/1813/38935.

MLA Handbook (7^th Edition):

Sun, Tao. “Trans-Acting Factors Essential For Plant Organelle Rna Editing.” 2014. Web. 20 Jan 2021.

Vancouver:

Sun T. Trans-Acting Factors Essential For Plant Organelle Rna Editing. [Internet] [Doctoral dissertation]. Cornell University; 2014. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/1813/38935.

Council of Science Editors:

Sun T. Trans-Acting Factors Essential For Plant Organelle Rna Editing. [Doctoral Dissertation]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/38935

Cornell University

3. Worley, Jay. Investigation Of The Interconnected Roles Of Cmal And Hopaa1-1 In The Virulence Of Pseudomonas Syringae Pv.Tomato Dc3000 In Nicotiana Benthamiana.

Degree: PhD, Microbiology, 2013, Cornell University

URL: http://hdl.handle.net/1813/33876

► Pseudomonas syringae pv. tomato DC3000 (DC3000) is a model plant pathogenic bacterium that infects tomato and Arabidopsis thaliana. It requires the phytotoxin coronatine and the… (more)

▼ Pseudomonas syringae pv. tomato DC3000 (DC3000) is a model plant pathogenic bacterium that infects tomato and Arabidopsis thaliana. It requires the phytotoxin coronatine and the delivery of type III effector proteins (T3Es) into the host cell cytoplasm for defense suppression and virulence. CmaL is a small protein found to be necessary for coronatine production. Coronatine is a potent molecular mimic of jasmonoyl-isoleucine, a plant hormone conjugate involved in regulating plant defenses. Coronatine is constructed of two amide bond-linked moieties, coronafacic acid and coronamic acid. CmaL was shown to be required for the production of L-allo-isoleucine, a precursor for coronamic acid biosynthesis. DC3000 mutants lacking both cmaL and the T3E gene hopAA1-1 are reduced in speck formation in tomato. hopAA1-1 is member of the conserved effector locus, a group of effector genes located adjacent to the genes encoding the type three secretion apparatus that are widespread among P. syringae strains. HopAA1-1 is toxic to both plants and yeast upon expression within them. To gain insight into the basis for its toxicity in eukaryotic cells, the subcellular localization of HopAA1-1 was investigated. HopAA1-1 was found to colocalize with plant peroxisomes. Truncated derivatives of HopAA1-1 that are not cytotoxic and cannot promote symptom formation do not localize with peroxisomes. Additionally, other truncated derivatives of HopAA1-1 colocalize with the endoplasmic reticulum in addition to peroxisomes, suggesting that HopAA1 -1 interacts with the endomembrane system. A DC3000 mutant with 28 T3E genes deleted (DC3000D28E) is a recently developed tool for investigating effector functions. DC3000D28E derivatives with small sets of effector genes progressively restored show increasing virulence wh en inoculated by infiltration with a blunt syringe into the model plant Nicotiana benthamiana. Because of its location in a cluster of effector genes, cmaL was inadvertently deleted in the construction of DC3000D28E. The importance of coronatine and its partial redundancy with HopAA1-1 in promoting an early stage of pathogenesis was revealed by restoring cmaL and hopAA1-1 to selected DC3000D28E derivatives and assaying the strains by dip inoculation of N. benthamiana leaves, which requires bacteria to follow a natural infection route through stomata. Advisors/Committee Members: Collmer, Alan Raymond (chair), Martin, Gregory B (committee member), Hanson, Maureen R (committee member).

Subjects/Keywords: Bacteriology; Pseudomonas syringae; Plant Pathology

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APA (6^th Edition):

Worley, J. (2013). Investigation Of The Interconnected Roles Of Cmal And Hopaa1-1 In The Virulence Of Pseudomonas Syringae Pv.Tomato Dc3000 In Nicotiana Benthamiana. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/33876

Chicago Manual of Style (16^th Edition):

Worley, Jay. “Investigation Of The Interconnected Roles Of Cmal And Hopaa1-1 In The Virulence Of Pseudomonas Syringae Pv.Tomato Dc3000 In Nicotiana Benthamiana.” 2013. Doctoral Dissertation, Cornell University. Accessed January 20, 2021. http://hdl.handle.net/1813/33876.

MLA Handbook (7^th Edition):

Worley, Jay. “Investigation Of The Interconnected Roles Of Cmal And Hopaa1-1 In The Virulence Of Pseudomonas Syringae Pv.Tomato Dc3000 In Nicotiana Benthamiana.” 2013. Web. 20 Jan 2021.

Vancouver:

Worley J. Investigation Of The Interconnected Roles Of Cmal And Hopaa1-1 In The Virulence Of Pseudomonas Syringae Pv.Tomato Dc3000 In Nicotiana Benthamiana. [Internet] [Doctoral dissertation]. Cornell University; 2013. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/1813/33876.

Council of Science Editors:

Worley J. Investigation Of The Interconnected Roles Of Cmal And Hopaa1-1 In The Virulence Of Pseudomonas Syringae Pv.Tomato Dc3000 In Nicotiana Benthamiana. [Doctoral Dissertation]. Cornell University; 2013. Available from: http://hdl.handle.net/1813/33876

Cornell University

4. Elliott, Leah. Analysis Of The Assembly Of Saccharomyces Cerevisiae Cytochrome C Oxidase Subunit Cox2 By The Oxa1 And Cox18 Translocases.

Degree: PhD, Genetics, 2013, Cornell University

URL: http://hdl.handle.net/1813/34300

► Oxa1 and Cox18 are members of a conserved protein family of integral inner membrane translocases responsible for insertion of other proteins into the membranes of… (more)

▼ Oxa1 and Cox18 are members of a conserved protein family of integral inner membrane translocases responsible for insertion of other proteins into the membranes of chloroplasts, bacteria and mitochondria. In Saccharomyces cerevisiae both Oxa1 and Cox18 are required for the translocation of the hydrophilic domains of cytochrome c oxidase subunit Cox2 into the inner membrane space. Deletions in either oxa1 or cox18 result in yeast strains unable to respire. Over-expression of OXA1 does not allow for respiration in strains with deletions in cox18, but does allow for export of the C-terminus of Cox2. This suggests that Cox18 also has a role in the assembly of Cox2 into functional cytochrome c oxidase following the translocation of the C-terminus. I identified a physical interaction between Cox18 and the noncanonical chaperone Cox20, which is dependent on the presence of the Cox2 peptide. I isolated spontaneous respiring pseudorevertants from cox18 deletion strains carrying OXA1 on a high copy plasmid. Several of these pseudorevertants have mutations in residue 291 of the plasmid borne Oxa1. Substitution of charged residues, both positive and negative, at position 291 results in OXA1 alleles that can compensate for a deletion in cox18 when present in high copy number or when expressed from the chromosomal locus. Neutral substitutions at residue 291 of Oxa1 result in alleles that fail to compliment cox18 when present in high copy. These results show that the presence of a charged residue at position 291 allows Oxa1 to assemble Cox2 independent of Cox18 and its partner Mss2. The mutant alleles all retain Oxa1 function to various degrees. In addition, the alleles with charged residues compensate for a mss2 deletion. Cox20 is not required for assembly by these mutant proteins, although Cox20's chaperoning of Cox2 processing is required. Therefore, these mutant alleles are not simply replacing Cox18 in its normal complexes. Rather, they may interact with the Cox2 peptide in a novel way that makes it competent for assembly. Advisors/Committee Members: Fox, Thomas D. (chair), Hanson, Maureen R (committee member), Pleiss, Jeffrey A. (committee member).

Subjects/Keywords: cytochrome c oxidase; mitochondria; Cox20

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

APA (6^th Edition):

Elliott, L. (2013). Analysis Of The Assembly Of Saccharomyces Cerevisiae Cytochrome C Oxidase Subunit Cox2 By The Oxa1 And Cox18 Translocases. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/34300

Chicago Manual of Style (16^th Edition):

Elliott, Leah. “Analysis Of The Assembly Of Saccharomyces Cerevisiae Cytochrome C Oxidase Subunit Cox2 By The Oxa1 And Cox18 Translocases.” 2013. Doctoral Dissertation, Cornell University. Accessed January 20, 2021. http://hdl.handle.net/1813/34300.

MLA Handbook (7^th Edition):

Elliott, Leah. “Analysis Of The Assembly Of Saccharomyces Cerevisiae Cytochrome C Oxidase Subunit Cox2 By The Oxa1 And Cox18 Translocases.” 2013. Web. 20 Jan 2021.

Vancouver:

Elliott L. Analysis Of The Assembly Of Saccharomyces Cerevisiae Cytochrome C Oxidase Subunit Cox2 By The Oxa1 And Cox18 Translocases. [Internet] [Doctoral dissertation]. Cornell University; 2013. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/1813/34300.

Council of Science Editors:

Elliott L. Analysis Of The Assembly Of Saccharomyces Cerevisiae Cytochrome C Oxidase Subunit Cox2 By The Oxa1 And Cox18 Translocases. [Doctoral Dissertation]. Cornell University; 2013. Available from: http://hdl.handle.net/1813/34300

Cornell University

5. Rowland, Elden Ernest. PROTEOLYTIC MATURATION AND PROTEIN DEGRADATION IN ARABIDOPSIS THALIANA CHLOROPLASTS.

Degree: PhD, Plant Biology, 2017, Cornell University

URL: http://hdl.handle.net/1813/58987

► Proteolysis is crucial for the maturation, regulation and recycling of the chloroplast proteome. Although several dozen chloroplast proteases are known, information concerning their substrates and… (more)

▼ Proteolysis is crucial for the maturation, regulation and recycling of the chloroplast proteome. Although several dozen chloroplast proteases are known, information concerning their substrates and functions is limited. In particular, little is known about the structural features of substrates that trigger their proteolysis. Most chloroplast proteins are nuclear encoded and are targeted through an N-terminal chloroplast transit peptide (cTP) that is removed by stromal processing peptidase (SPP). To better understand proteolytic maturation, the soluble N-terminal proteome of the Arabidopsis thaliana chloroplast was characterized. A cTP cleavage motif was observed that suggests other peptidases, in addition to SPP, are involved in chloroplast protein maturation. There was a clear preference for small uncharged amino acids at the processed protein N-terminus suggesting the existence of a chloroplast specific ‘N-end rule’. The soluble chloroplast peptidases PREP and OOP have been shown to degrade small polypeptides in vitro and are thought to be responsible for removal of cTP fragments and other degradation products. The CLP protease system can degrade intact protein substrates with the aid of ATP dependent (AAA+) CLPC chaperones that unfold and feed substrates into the CLP proteolytic core. An array of proteomic tools were used to compare Arabidopsis mutants deficient in the above peptidases with wild type. Degradation products, including cTPs, were found to accumulate in peptidase mutants indicative, of rate-limited or blocked degradation pathways. Incomplete or altered N-terminal maturation for chloroplast proteins was dependent on the type and severity of the peptidase deficiency. These results provide molecular details to help explain dwarf, chlorotic mutant phenotypes and demonstrate the interplay between protein import, proteolytic processing and the downstream degradation of damaged or unwanted proteins in the chloroplast. Substrate and sequence cleavage specificity was determined for soluble chloroplast glutamyl-endopeptidase (CGEP) and the plastoglobule localized metallopeptidase PGM48. Structural models were used to predict peptidase substrate binding mechanisms. Advisors/Committee Members: Van Wijk, Klaas (chair), Hanson, Maureen R. (committee member), Owens, Thomas G. (committee member), Cilia, Michelle (committee member).

Subjects/Keywords: Plant sciences; Biochemistry; Arabidopsis; chloroplast; N-terminal proteome; protease; proteolytic degradation; proteolytic maturation

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APA (6^th Edition):

Rowland, E. E. (2017). PROTEOLYTIC MATURATION AND PROTEIN DEGRADATION IN ARABIDOPSIS THALIANA CHLOROPLASTS. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/58987

Chicago Manual of Style (16^th Edition):

Rowland, Elden Ernest. “PROTEOLYTIC MATURATION AND PROTEIN DEGRADATION IN ARABIDOPSIS THALIANA CHLOROPLASTS.” 2017. Doctoral Dissertation, Cornell University. Accessed January 20, 2021. http://hdl.handle.net/1813/58987.

MLA Handbook (7^th Edition):

Rowland, Elden Ernest. “PROTEOLYTIC MATURATION AND PROTEIN DEGRADATION IN ARABIDOPSIS THALIANA CHLOROPLASTS.” 2017. Web. 20 Jan 2021.

Vancouver:

Rowland EE. PROTEOLYTIC MATURATION AND PROTEIN DEGRADATION IN ARABIDOPSIS THALIANA CHLOROPLASTS. [Internet] [Doctoral dissertation]. Cornell University; 2017. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/1813/58987.

Council of Science Editors:

Rowland EE. PROTEOLYTIC MATURATION AND PROTEIN DEGRADATION IN ARABIDOPSIS THALIANA CHLOROPLASTS. [Doctoral Dissertation]. Cornell University; 2017. Available from: http://hdl.handle.net/1813/58987

Cornell University

6. Villarino Pizarro, Gonzalo. Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress.

Degree: PhD, Horticultural Biology, 2014, Cornell University

URL: http://hdl.handle.net/1813/38983

► Abiotic stresses, such as salinity and drought, are among the most limiting factors to crop yield. In sodic saline soils, sodium chloride (NaCl) disrupts normal… (more)

▼ Abiotic stresses, such as salinity and drought, are among the most limiting factors to crop yield. In sodic saline soils, sodium chloride (NaCl) disrupts normal plant growth and development. Many studies have used both forward and reverse genetic techniques to understand the complex interactions of plant systems with abiotic stress. These approaches have been invaluable in deciphering some mechanisms of plant salt stress tolerance. Salt tolerance research has also been an important part of basic plant biology, increasing the understanding in areas encompassing gene regulation, mineral nutrition, signaling components, ion transport and osmoregulation. To better understand the detrimental effects of NaCl, as well the fundamental questions associated with salt tolerance, transcript regulation in response to NaCl stress was undertaken using ultra-high-throughput RNA sequencing technology (RNA-seq). RNA-seq has quickly become the method of choice to perform transcriptomic analysis owing to many advantages over existing platforms. The transcriptomic research presented here was carried out in Petunia hybrida, a salt resistant Solanaceous plant that has also been an excellent model species in molecular genetic research regarding flower development and senescence, synthesis and regulation of volatiles, and so on. In chapter one, to bypass the absence of an available Petunia genome, a de-novo assembled Petunia transcriptome was reconstructed by assembling over one- hundred million Illumina cDNA reads with Trinity software. The de-novo assembled contigs represents the most in-depth transcriptome ever reported for a Petunia species, which can be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome. The transcriptome has been made publically available on the SOL Genomics Network (SGN) http://solgenomics.net. Using this newly assembled reference transcriptome, more than 7,000 differentially expressed genes were identified within 24 h of acute NaCl stress. Genes related to regulation of reactive oxygen species, transport, and signal transduction as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. Gene ontology analyses revealed that plants by 24 h after acute NaCl undertook many changes occurring at the molecular level including genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. RNA-seq, despite the many advantages it offers, it is a relatively new methodology with developments and improvements to be made. At the end of chapter one a modification to the library preparation protocol is presented whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. This methodological improvement could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments. In chapter two, root and leaf transcriptomic response to salt stress was investigated, utilizing the Petunia… Advisors/Committee Members: Mattson, Neil S. (chair), Mattson, Neil S. (chair), Hanson, Maureen R (committee member), Scanlon, Michael J. (committee member), Nero, Debra (committee member), Hanson, Maureen R (committee member), Scanlon, Michael J. (committee member), Nero, Debra (committee member).

Subjects/Keywords: transcriptomics; RNA-seq; Salt stress

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

APA (6^th Edition):

Villarino Pizarro, G. (2014). Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/38983

Chicago Manual of Style (16^th Edition):

Villarino Pizarro, Gonzalo. “Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress.” 2014. Doctoral Dissertation, Cornell University. Accessed January 20, 2021. http://hdl.handle.net/1813/38983.

MLA Handbook (7^th Edition):

Villarino Pizarro, Gonzalo. “Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress.” 2014. Web. 20 Jan 2021.

Vancouver:

Villarino Pizarro G. Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress. [Internet] [Doctoral dissertation]. Cornell University; 2014. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/1813/38983.

Council of Science Editors:

Villarino Pizarro G. Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress. [Doctoral Dissertation]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/38983

Cornell University

7. Ismail, Aziana. Molecular Analysis Of An Rna Editing Cis-Element And Its Trans-Acting Factor.

Degree: M.S., Genetics, Genetics, 2011, Cornell University

URL: http://hdl.handle.net/1813/29203

► In angiosperm organelles, RNA editing alters specific cytidines to uridines. The mechanism involves recognition of cis-sequences surrounding specific Cs by nuclear-encoded proteins, but the particular… (more)

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

APA (6^th Edition):

Ismail, A. (2011). Molecular Analysis Of An Rna Editing Cis-Element And Its Trans-Acting Factor. (Masters Thesis). Cornell University. Retrieved from http://hdl.handle.net/1813/29203

Chicago Manual of Style (16^th Edition):

Ismail, Aziana. “Molecular Analysis Of An Rna Editing Cis-Element And Its Trans-Acting Factor.” 2011. Masters Thesis, Cornell University. Accessed January 20, 2021. http://hdl.handle.net/1813/29203.

MLA Handbook (7^th Edition):

Ismail, Aziana. “Molecular Analysis Of An Rna Editing Cis-Element And Its Trans-Acting Factor.” 2011. Web. 20 Jan 2021.

Vancouver:

Ismail A. Molecular Analysis Of An Rna Editing Cis-Element And Its Trans-Acting Factor. [Internet] [Masters thesis]. Cornell University; 2011. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/1813/29203.

Council of Science Editors:

Ismail A. Molecular Analysis Of An Rna Editing Cis-Element And Its Trans-Acting Factor. [Masters Thesis]. Cornell University; 2011. Available from: http://hdl.handle.net/1813/29203

Cornell University

8. Germain, Arnaud. 3' To 5' Exoribonucleases In Arabidopsis Thaliana Plastids.

Degree: PhD, Plant Biology, 2012, Cornell University

URL: http://hdl.handle.net/1813/30968

► Chloroplast genes and metabolic activities are regulated by the products of nuclear genes, acting mostly at the post-transcriptional level. Polynucleotide phosphorylase (PNP) and Ribonuclease R… (more)

▼ Chloroplast genes and metabolic activities are regulated by the products of nuclear genes, acting mostly at the post-transcriptional level. Polynucleotide phosphorylase (PNP) and Ribonuclease R (RNR1) are the two known nucleus-encoded exoribonucleases and are necessary for the correct maturation and degradation of RNAs. PNP catalyzes both the processive 3' to 5' phosphorolysis of chloroplast RNA and its processive polymerization depending on the ratio between inorganic phosphate (Pi) and nucleotide diphosphates (NDPs). RNR1 is a hydrolytically processive 3' to 5' exoribonuclease that releases 5' monophosphate nucleotides. This study used both null mutants and single amino acid substitutions in the two core catalytic domains of PNP to investigate its role in many aspects of chloroplast RNA metabolism. The phenotypic characterization of null mutants (pnp1-1 to 1-3) showed a chlorotic phenotype in young leaves that became less severe as leaves matured, and molecular analysis demonstrated the involvement of PNP in the 3' maturation, stabilization and/or degradation of many chloroplast RNAs, as well as its importance in the excised intron lariat degradation pathway. Two mutations in the first core domain demonstrated a role for this region in PNP activity, however the residual activity of the PNP mutants permitted the construction of otherwise lethal pnp/rnr double mutants. The resulting rnr1 mutant plants with reduced PNP activity are chlorotic and display a global reduction in RNA abundance. Such a counterintuitive outcome following the loss of RNA degradation activity suggests a major importance of RNA maturation as a determinant of RNA stability. The detailed analysis of the double mutant transcriptome revealed that RNR1 completes the maturation of mRNAs 3' termini created by PNPase in a two-step maturation process. In contrast to the double mutant, the rnr1 single mutant, known to have a substantial decline in rRNA levels, over-accumulated most of the mRNA species examined when compared to the wild-type. Combined with the reduced number of ribosomes, it was not unexpected to find most of the excess mRNAs species present in non-polysomal fractions. Half-life measurements demonstrated a substantial increase in the stability of most mRNA species tested, supporting the hypothesis that RNR1 plays important roles in the maintenance of both chloroplast rRNA and mRNA homeostasis. Because of the dependence of PNPase activity on the Pi:NDP ratio in vitro, we investigated a potential link between PNP and phosphate (P) metabolism of the plant. We found that P-deprived pnp mutants develop aborted clusters of lateral roots while a global analysis of metabolites and transcripts supported the hypothesis that the activity of PNP is involved in plant acclimation to P availability. The most recent results, involving a double mutant lacking both PNP and the endonuclease RNase E, indicate that not only exonucleolytic processing but also endonucleolytic processing is involved in stabilizing chloroplast RNAs. Taken together, these studies… Advisors/Committee Members: Stern, David (chair), Pleiss, Jeffrey A. (committee member), Hanson, Maureen R (committee member).

Subjects/Keywords: Chloroplast; rna; Exonuclease

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

APA (6^th Edition):

Germain, A. (2012). 3' To 5' Exoribonucleases In Arabidopsis Thaliana Plastids. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/30968

Chicago Manual of Style (16^th Edition):

Germain, Arnaud. “3' To 5' Exoribonucleases In Arabidopsis Thaliana Plastids.” 2012. Doctoral Dissertation, Cornell University. Accessed January 20, 2021. http://hdl.handle.net/1813/30968.

MLA Handbook (7^th Edition):

Germain, Arnaud. “3' To 5' Exoribonucleases In Arabidopsis Thaliana Plastids.” 2012. Web. 20 Jan 2021.

Vancouver:

Germain A. 3' To 5' Exoribonucleases In Arabidopsis Thaliana Plastids. [Internet] [Doctoral dissertation]. Cornell University; 2012. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/1813/30968.

Council of Science Editors:

Germain A. 3' To 5' Exoribonucleases In Arabidopsis Thaliana Plastids. [Doctoral Dissertation]. Cornell University; 2012. Available from: http://hdl.handle.net/1813/30968

Cornell University

9. Hines, Kevin Matthew. THE ROLE OF CHLOROPLAST CARBONIC ANHYDRASES IN THE DEVELOPMENT OF C3 PHOTOSYNTHESIZING PLANTS.

Degree: PhD, Biochemistry, Molecular and Cell Biology, 2019, Cornell University

URL: http://hdl.handle.net/1813/70137

► Carbonic anhydrase (CA, EC: 4.2.1.1) is a zinc-bond metalloenzyme that rapidly catalyzes the reversable hydration between carbon dioxide and water with bicarbonate. C3 photosynthesizing plants… (more)

▼ Carbonic anhydrase (CA, EC: 4.2.1.1) is a zinc-bond metalloenzyme that rapidly catalyzes the reversable hydration between carbon dioxide and water with bicarbonate. C3 photosynthesizing plants contain very highly expressed CAs in their chloroplasts, which can represent over 2% of all soluble protein. However, no single role has been assigned to CA and its activity in the stroma, although they are proposed to have a myriad of duties, from oxidative stress tolerance and plant defense to macromolecule biosynthesis and pH buffering. Previous research exploring the function of chloroplast CA have focused largely on deactivating or deleting βCA1, the most highly expressed CA and the first to be identified in the chloroplast. However, no study has completely removed all CA enzymes from the chloroplast stroma and observed the effects. Using the model Nicotiana tabacum (tobacco), I identified two stromal CAs, βCA1 and βCA5, and produced CRISPR/Cas9 mutants targeting both genes. While the single knockout lines Δβca1 and Δβca5 had no striking phenotypic differences compared to WT plants, Δβca1ca5 leaves developed large necrotic lesions. Leaf development of Δβca1ca5 plants normalized at the high CO2 concentration of 9000ppm. High CO2-grown Δβca1ca5 mutants had no measurable defect in photosynthetic capacity when measured at ambient CO2 Δβca1ca5 seedling germination and development is negatively affected when seedling development occurs at ambient CO2. A series of complementation experiments using altered forms of βCA1 were carried out in Δβca1ca5 plants. Constructs expressing full length βCA1 and βCA5 proteins complemented the Δβca1ca5 mutation, but inactivated (ΔZn-βCA1) and cytoplasm-localized (Δ62-βCA1) forms of βCA1 failed to reverse the mutant phenotype. When infected with tobacco mosaic virus (TMV) Δβca1 and Δβca1ca5 tobacco failed to show the hypersensitive response (HR), while expression of ΔZn-βCA1 restored the response. Thus, stromal CAs play major roles in plant development and defense. Advisors/Committee Members: Hanson, Maureen R. (chair), Owens, Thomas (committee member), van Wijk, Klaas (committee member).

Subjects/Keywords: Carbonic anhydrase; Chloroplast; CRISPR; Nicotiana; Photosynthesis; Plant Development

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APA (6^th Edition):

Hines, K. M. (2019). THE ROLE OF CHLOROPLAST CARBONIC ANHYDRASES IN THE DEVELOPMENT OF C3 PHOTOSYNTHESIZING PLANTS. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/70137

Chicago Manual of Style (16^th Edition):

Hines, Kevin Matthew. “THE ROLE OF CHLOROPLAST CARBONIC ANHYDRASES IN THE DEVELOPMENT OF C3 PHOTOSYNTHESIZING PLANTS.” 2019. Doctoral Dissertation, Cornell University. Accessed January 20, 2021. http://hdl.handle.net/1813/70137.

MLA Handbook (7^th Edition):

Hines, Kevin Matthew. “THE ROLE OF CHLOROPLAST CARBONIC ANHYDRASES IN THE DEVELOPMENT OF C3 PHOTOSYNTHESIZING PLANTS.” 2019. Web. 20 Jan 2021.

Vancouver:

Hines KM. THE ROLE OF CHLOROPLAST CARBONIC ANHYDRASES IN THE DEVELOPMENT OF C3 PHOTOSYNTHESIZING PLANTS. [Internet] [Doctoral dissertation]. Cornell University; 2019. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/1813/70137.

Council of Science Editors:

Hines KM. THE ROLE OF CHLOROPLAST CARBONIC ANHYDRASES IN THE DEVELOPMENT OF C3 PHOTOSYNTHESIZING PLANTS. [Doctoral Dissertation]. Cornell University; 2019. Available from: http://hdl.handle.net/1813/70137

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