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You searched for subject:(DNA Pol IV). Showing records 1 – 2 of 2 total matches.

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Northeastern University

1. Benson, Ryan W. Structure function analysis of Escherichia coli pol IV.

Degree: PhD, Department of Biology, 2013, Northeastern University

Translesion synthesis (TLS) DNA polymerases are low fidelity DNA polymerases responsible for inserting a deoxynucleotide opposite to and extending from replication-blocking DNA lesions that have evaded high fidelity DNA repair pathways. E. coli DinB (DNA Pol IV) is a TLS polymerase of great interest because of its conservation throughout all domains of life and its relatively high intracellular basal level when compared to other DNA polymerases. Alternative activities of DinB other than its TLS ability include: roles in recombination, transcription, and a DNA replication "checkpoint." Using a structure/function strategy, we sought to better understand these activities by utilizing dinB alleles with different catalytic activities, in combination with other mutated genes involved in DNA replication or repair. This approach has allowed us to identify residues of DinB important for its various cellular tasks. In this work we have identified the roles of three highly conserved catalytic residues in the fidelity of lesion bypass of diverse lesions.; We also addressed the underlying mechanisms governing interactions between different bacterial DNA polymerases upon DNA damage treatment, which is likely to activate either DNA polymerase exchange and/or DNA replication checkpoints. By using the dnaE915 allele, encoding a variant of the replicative DNA Pol III catalytic α-subunit (Pol IIIα), we detected a DNA damage treatment-dependent growth arrest at in vivo DinB intracellular concentrations much lower than those in previous studies. A variety of intragenic dinB mutations localized to a specific area of DinB that suppressed any observed growth defects were also identified. We infer that this DinB face is interacting directly or indirectly with DNA Pol IIIα.; Lastly, we discovered a novel TLS independent role of DinB in the tolerance of DNA damage treatment. However, this role does not simply involve protein-protein interactions but requires the catalytic activity of DinB. Therefore, survival is likely the result of the largely error free synthesis of undamaged DNA that is independent of recA mediated recombination, induction of the SOS DNA damage response, or base excision repair. The structure/function analysis undertaken in this work has allowed us to discern and explore several activities of DinB other than its part in canonical DNA damage tolerance through strict TLS. This information will allow greater understanding of the mechanisms regulating both the TLS activity and other alternative roles that these specialized DNA polymerases might be playing in cells experiencing DNA damage or environmental stress.

Subjects/Keywords: DinB; DNA Pol III; DNA Pol IV; E. coli; TLS; Biology

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APA (6th Edition):

Benson, R. W. (2013). Structure function analysis of Escherichia coli pol IV. (Doctoral Dissertation). Northeastern University. Retrieved from http://hdl.handle.net/2047/d20003117

Chicago Manual of Style (16th Edition):

Benson, Ryan W. “Structure function analysis of Escherichia coli pol IV.” 2013. Doctoral Dissertation, Northeastern University. Accessed June 25, 2019. http://hdl.handle.net/2047/d20003117.

MLA Handbook (7th Edition):

Benson, Ryan W. “Structure function analysis of Escherichia coli pol IV.” 2013. Web. 25 Jun 2019.

Vancouver:

Benson RW. Structure function analysis of Escherichia coli pol IV. [Internet] [Doctoral dissertation]. Northeastern University; 2013. [cited 2019 Jun 25]. Available from: http://hdl.handle.net/2047/d20003117.

Council of Science Editors:

Benson RW. Structure function analysis of Escherichia coli pol IV. [Doctoral Dissertation]. Northeastern University; 2013. Available from: http://hdl.handle.net/2047/d20003117


Washington University in St. Louis

2. Haag, Jeremy. Genetic and Biochemical Properties of Arabidopsis RNA Polymerases IV and V.

Degree: PhD, Biology and Biomedical Sciences: Plant and Microbial Biosciences, 2009, Washington University in St. Louis

RNA Polymerases IV and V: Pol IV and Pol V) are plant-specific enzyme complexes with subunit homology to RNA Polymerase II: Pol II). The largest subunits in Pol IV and Pol V, NRPD1 and NRPE1 respectively, share a second largest subunit, NRPD2/NRPE2. The evolutionarily conserved Metal A and Metal B binding sites are required for Pol IV and V in vivo function fitting the prediction that these are functional polymerases. The Defective Chloroplast and Leaves-like: DeCL) domain at the C-terminus of both NRPD1 and NRPE1 is also required for complementation but other domains in the NRPE1 CTD are largely dispensable. Biochemical analysis reveals Pol IV to be a DNA-dependent RNA Polymerase capable of producing RNA from a tripartite template that mimics an open transcription bubble. The Metal A binding site is required for Pol IV in vitro transcription while the enzyme is resistant to alpha-amanitin, a potent Pol II inhibitor. Pol IV has also been found to physically associate with RNA DEPENDENT RNA POLYMERASE 2: RDR2) in vivo providing an explanation for how Pol IV RNA products are channeled specifically to RDR2 for the production of double-stranded RNA and eventual dicing. Biochemical analysis has also revealed that RDR2 is capable of transcribing both single-stranded RNA and DNA in vitro, consistent with previously analyzed RNA-dependent RNA polymerases from plants and other organisms. Advisors/Committee Members: Craig Pikaard.

Subjects/Keywords: Biology; Molecular; Pol IV; Pol V; RDR2; RNA polymerase; RNA-directed DNA methylation; Transcription

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

APA (6th Edition):

Haag, J. (2009). Genetic and Biochemical Properties of Arabidopsis RNA Polymerases IV and V. (Doctoral Dissertation). Washington University in St. Louis. Retrieved from https://openscholarship.wustl.edu/etd/886

Chicago Manual of Style (16th Edition):

Haag, Jeremy. “Genetic and Biochemical Properties of Arabidopsis RNA Polymerases IV and V.” 2009. Doctoral Dissertation, Washington University in St. Louis. Accessed June 25, 2019. https://openscholarship.wustl.edu/etd/886.

MLA Handbook (7th Edition):

Haag, Jeremy. “Genetic and Biochemical Properties of Arabidopsis RNA Polymerases IV and V.” 2009. Web. 25 Jun 2019.

Vancouver:

Haag J. Genetic and Biochemical Properties of Arabidopsis RNA Polymerases IV and V. [Internet] [Doctoral dissertation]. Washington University in St. Louis; 2009. [cited 2019 Jun 25]. Available from: https://openscholarship.wustl.edu/etd/886.

Council of Science Editors:

Haag J. Genetic and Biochemical Properties of Arabidopsis RNA Polymerases IV and V. [Doctoral Dissertation]. Washington University in St. Louis; 2009. Available from: https://openscholarship.wustl.edu/etd/886

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