Literature DB >> 25387798

Ribonucleotides in bacterial DNA.

Jeremy W Schroeder1, Justin R Randall, Lindsay A Matthews, Lyle A Simmons.   

Abstract

In all living cells, DNA is the storage medium for genetic information. Being quite stable, DNA is well-suited for its role in storage and propagation of information, but RNA is also covalently included in DNA through various mechanisms. Recent studies also demonstrate useful aspects of including ribonucleotides in the genome during repair. Therefore, our understanding of the consequences of RNA inclusion into bacterial genomic DNA is just beginning, but with its high frequency of occurrence the consequences and potential benefits are likely to be numerous and diverse. In this review, we discuss the processes that cause ribonucleotide inclusion in genomic DNA, the pathways important for ribonucleotide removal and the consequences that arise should ribonucleotides remain nested in genomic DNA.

Entities:  

Keywords:  DNA polymerase; DNA repair; genome stability; mismatch repair; ribonucleotides

Mesh:

Substances:

Year:  2014        PMID: 25387798      PMCID: PMC4428996          DOI: 10.3109/10409238.2014.981647

Source DB:  PubMed          Journal:  Crit Rev Biochem Mol Biol        ISSN: 1040-9238            Impact factor:   8.250


  139 in total

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Review 2.  Proficient and accurate bypass of persistent DNA lesions by DinB DNA polymerases.

Authors:  Daniel F Jarosz; Veronica G Godoy; Graham C Walker
Journal:  Cell Cycle       Date:  2007-04-23       Impact factor: 4.534

3.  Investigating the mechanisms of ribonucleotide excision repair in Escherichia coli.

Authors:  Alexandra Vaisman; John P McDonald; Stephan Noll; Donald Huston; Gregory Loeb; Myron F Goodman; Roger Woodgate
Journal:  Mutat Res       Date:  2014-02-01       Impact factor: 2.433

4.  Structural mechanism of ribonucleotide discrimination by a Y-family DNA polymerase.

Authors:  Kevin N Kirouac; Zucai Suo; Hong Ling
Journal:  J Mol Biol       Date:  2011-02-03       Impact factor: 5.469

5.  Escherichia coli UmuC active site mutants: effects on translesion DNA synthesis, mutagenesis and cell survival.

Authors:  Wojciech Kuban; Alexandra Vaisman; John P McDonald; Kiyonobu Karata; Wei Yang; Myron F Goodman; Roger Woodgate
Journal:  DNA Repair (Amst)       Date:  2012-07-10

6.  Novel 3'-ribonuclease and 3'-phosphatase activities of the bacterial non-homologous end-joining protein, DNA ligase D.

Authors:  Hui Zhu; Stewart Shuman
Journal:  J Biol Chem       Date:  2005-05-15       Impact factor: 5.157

7.  DNA mismatch correction in a defined system.

Authors:  R S Lahue; K G Au; P Modrich
Journal:  Science       Date:  1989-07-14       Impact factor: 47.728

8.  An error-prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a 'steric gate' residue for discrimination against ribonucleotides.

Authors:  Angela M DeLucia; Nigel D F Grindley; Catherine M Joyce
Journal:  Nucleic Acids Res       Date:  2003-07-15       Impact factor: 16.971

9.  RNase H2-initiated ribonucleotide excision repair.

Authors:  Justin L Sparks; Hyongi Chon; Susana M Cerritelli; Thomas A Kunkel; Erik Johansson; Robert J Crouch; Peter M Burgers
Journal:  Mol Cell       Date:  2012-08-02       Impact factor: 17.970

Review 10.  Mechanism and evolution of DNA primases.

Authors:  Robert D Kuchta; Gudrun Stengel
Journal:  Biochim Biophys Acta       Date:  2009-06-21
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  12 in total

1.  RNase HIII Is Important for Okazaki Fragment Processing in Bacillus subtilis.

Authors:  Taylor M Nye; Katherine J Wozniak; Justin R Randall; Lyle A Simmons
Journal:  J Bacteriol       Date:  2019-03-13       Impact factor: 3.490

2.  RNase HII Saves rnhA Mutant Escherichia coli from R-Loop-Associated Chromosomal Fragmentation.

Authors:  Elena A Kouzminova; Farid F Kadyrov; Andrei Kuzminov
Journal:  J Mol Biol       Date:  2017-08-15       Impact factor: 5.469

Review 3.  Ribonucleotide discrimination by translesion synthesis DNA polymerases.

Authors:  Alexandra Vaisman; Roger Woodgate
Journal:  Crit Rev Biochem Mol Biol       Date:  2018-07-04       Impact factor: 8.250

Review 4.  The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria.

Authors:  Emma K McLean; Taylor M Nye; Frances C Lowder; Lyle A Simmons
Journal:  Annu Rev Microbiol       Date:  2022-06-02       Impact factor: 16.232

5.  Sources of thymidine and analogs fueling futile damage-repair cycles and ss-gap accumulation during thymine starvation in Escherichia coli.

Authors:  T V Pritha Rao; Andrei Kuzminov
Journal:  DNA Repair (Amst)       Date:  2019-01-16

6.  The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response.

Authors:  Ivan Erill; Susana Campoy; Sefa Kılıç; Jordi Barbé
Journal:  Front Mol Biosci       Date:  2016-07-20

7.  Division of labor among Mycobacterium smegmatis RNase H enzymes: RNase H1 activity of RnhA or RnhC is essential for growth whereas RnhB and RnhA guard against killing by hydrogen peroxide in stationary phase.

Authors:  Richa Gupta; Debashree Chatterjee; Michael S Glickman; Stewart Shuman
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

8.  Bacillus subtilis PcrA Helicase Removes Trafficking Barriers.

Authors:  María Moreno-Del Álamo; Begoña Carrasco; Rubén Torres; Juan Carlos Alonso
Journal:  Cells       Date:  2021-04-17       Impact factor: 6.600

9.  RnhP is a plasmid-borne RNase HI that contributes to genome maintenance in the ancestral strain Bacillus subtilis NCIB 3610.

Authors:  Taylor M Nye; Emma K McLean; Andrew M Burrage; Devon D Dennison; Daniel B Kearns; Lyle A Simmons
Journal:  Mol Microbiol       Date:  2020-09-25       Impact factor: 3.501

10.  Ultraviolet-induced RNA:DNA hybrids interfere with chromosomal DNA synthesis.

Authors:  Elena A Kouzminova; Andrei Kuzminov
Journal:  Nucleic Acids Res       Date:  2021-04-19       Impact factor: 16.971

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