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Book: Replicating and repairing the genome

Kreuzer, Kenneth N.

from basic mechanisms to modern genetic technologies

2020

Author's details	Kenneth N. Kreuzer
Language	English
Size	xiv, 423 Seiten, Illustrationen
Publisher	World Scientific
Publishing place	New Jersey
Publishing country	United States
Document type	Book
HBZ-ID	HT020472519
ISBN	978-981-12-1569-8 ; 9789811215704 ; 981-12-1569-3 ; 9811215707
Database	Catalogue ZB MED Medicine, Health

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2020 A 843	available for loan (reading room)	Lesesaal EG

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Article ; Online: DNA damage responses in prokaryotes: regulating gene expression, modulating growth patterns, and manipulating replication forks.

Kreuzer, Kenneth N

Cold Spring Harbor perspectives in biology

2013 Volume 5, Issue 11, Page(s) a012674

Abstract: Recent advances in the area of bacterial DNA damage responses are reviewed here. The SOS pathway is still the major paradigm of bacterial DNA damage response, and recent studies have clarified the mechanisms of SOS induction and key physiological roles ... ...

Abstract	Recent advances in the area of bacterial DNA damage responses are reviewed here. The SOS pathway is still the major paradigm of bacterial DNA damage response, and recent studies have clarified the mechanisms of SOS induction and key physiological roles of SOS including a very major role in genetic exchange and variation. When considering diverse bacteria, it is clear that SOS is not a uniform pathway with one purpose, but rather a platform that has evolved for differing functions in different bacteria. Relating in part to the SOS response, the field has uncovered multiple apparent cell-cycle checkpoints that assist cell survival after DNA damage and remarkable pathways that induce programmed cell death in bacteria. Bacterial DNA damage responses are also much broader than SOS, and several important examples of LexA-independent regulation will be reviewed. Finally, some recent advances that relate to the replication and repair of damaged DNA will be summarized.
MeSH term(s)	Apoptosis ; Bacteria/genetics ; Bacterial Proteins/metabolism ; Cell Survival ; DNA Damage ; DNA Repair ; DNA Replication ; Deinococcus/genetics ; Deinococcus/physiology ; Drug Resistance, Bacterial ; Escherichia coli/genetics ; Escherichia coli/physiology ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Mycobacterium/genetics ; Mycobacterium/physiology ; Rec A Recombinases/metabolism ; SOS Response, Genetics ; Serine Endopeptidases/metabolism
Chemical Substances	Bacterial Proteins ; LexA protein, Bacteria ; Rec A Recombinases (EC 2.7.7.-) ; Serine Endopeptidases (EC 3.4.21.-)
Language	English
Publishing date	2013-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ISSN	1943-0264
ISSN (online)	1943-0264
DOI	10.1101/cshperspect.a012674
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Article ; Online: Mutations that Separate the Functions of the Proofreading Subunit of the Escherichia coli Replicase.

Whatley, Zakiya / Kreuzer, Kenneth N

G3 (Bethesda, Md.)

2015 Volume 5, Issue 6, Page(s) 1301–1311

Abstract: The dnaQ gene of Escherichia coli encodes the ε subunit of DNA polymerase III, which provides the 3' → 5' exonuclease proofreading activity of the replicative polymerase. Prior studies have shown that loss of ε leads to high mutation frequency, partially ...

Abstract	The dnaQ gene of Escherichia coli encodes the ε subunit of DNA polymerase III, which provides the 3' → 5' exonuclease proofreading activity of the replicative polymerase. Prior studies have shown that loss of ε leads to high mutation frequency, partially constitutive SOS, and poor growth. In addition, a previous study from our laboratory identified dnaQ knockout mutants in a screen for mutants specifically defective in the SOS response after quinolone (nalidixic acid) treatment. To explain these results, we propose a model whereby, in addition to proofreading, ε plays a distinct role in replisome disassembly and/or processing of stalled replication forks. To explore this model, we generated a pentapeptide insertion mutant library of the dnaQ gene, along with site-directed mutants, and screened for separation of function mutants. We report the identification of separation of function mutants from this screen, showing that proofreading function can be uncoupled from SOS phenotypes (partially constitutive SOS and the nalidixic acid SOS defect). Surprisingly, the two SOS phenotypes also appear to be separable from each other. These findings support the hypothesis that ε has additional roles aside from proofreading. Identification of these mutants, especially those with normal proofreading but SOS phenotype(s), also facilitates the study of the role of ε in SOS processes without the confounding results of high mutator activity associated with dnaQ knockout mutants.
MeSH term(s)	Amino Acid Motifs ; Amino Acid Sequence ; DNA Polymerase III/chemistry ; DNA Polymerase III/genetics ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Molecular Sequence Data ; Mutagenesis, Insertional/genetics ; Mutagenesis, Site-Directed ; Mutation/genetics ; Mutation Rate ; Nalidixic Acid/metabolism ; Phenotype ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Protein Subunits/genetics ; SOS Response (Genetics)
Chemical Substances	Escherichia coli Proteins ; Protein Subunits ; Nalidixic Acid (3B91HWA56M) ; DNA Polymerase III (EC 2.7.7.-) ; dnaQ protein, E coli (EC 2.7.7.7)
Language	English
Publishing date	2015-04-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1534/g3.115.017285
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Article ; Online: Functions that Protect Escherichia coli from Tightly Bound DNA-Protein Complexes Created by Mutant EcoRII Methyltransferase.

Henderson, Morgan L / Kreuzer, Kenneth N

PloS one

2015 Volume 10, Issue 5, Page(s) e0128092

Abstract: Expression of mutant EcoRII methyltransferase protein (M.EcoRII-C186A) in Escherichia coli leads to tightly bound DNA-protein complexes (TBCs), located sporadically on the chromosome rather than in tandem arrays. The mechanisms behind the lethality ... ...

Abstract	Expression of mutant EcoRII methyltransferase protein (M.EcoRII-C186A) in Escherichia coli leads to tightly bound DNA-protein complexes (TBCs), located sporadically on the chromosome rather than in tandem arrays. The mechanisms behind the lethality induced by such sporadic TBCs are not well studied, nor is it clear whether very tight binding but non-covalent complexes are processed in the same way as covalent DNA-protein crosslinks (DPCs). Using 2D gel electrophoresis, we found that TBCs induced by M.EcoRII-C186A block replication forks in vivo. Specific bubble molecules were detected as spots on the 2D gel, only when M.EcoRII-C186A was induced, and a mutation that eliminates a specific EcoRII methylation site led to disappearance of the corresponding spot. We also performed a candidate gene screen for mutants that are hypersensitive to TBCs induced by M.EcoRII-C186A. We found several gene products necessary for protection against these TBCs that are known to also protect against DPCs induced with wild-type M.EcoRII (after 5-azacytidine incorporation): RecA, RecBC, RecG, RuvABC, UvrD, FtsK, XerCD and SsrA (tmRNA). In contrast, the RecFOR pathway and Rep helicase are needed for protection against TBCs but not DPCs induced by M.EcoRII. We propose that stalled fork processing by RecFOR and RecA promotes release of tightly bound (but non-covalent) blocking proteins, perhaps by licensing Rep helicase-driven dissociation of the blocking M.EcoRII-C186A. Our studies also argued against the involvement of several proteins that might be expected to protect against TBCs. We took the opportunity to directly compare the sensitivity of all tested mutants to two quinolone antibiotics, which target bacterial type II topoisomerases and induce a unique form of DPC. We uncovered rep, ftsK and xerCD as novel quinolone hypersensitive mutants, and also obtained evidence against the involvement of a number of functions that might be expected to protect against quinolones.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Chromosomes, Bacterial ; DNA Replication ; DNA, Bacterial/metabolism ; DNA-Cytosine Methylases/genetics ; DNA-Cytosine Methylases/metabolism ; Escherichia coli/drug effects ; Escherichia coli/enzymology ; Escherichia coli Proteins/metabolism ; Mutation ; Quinolones/pharmacology ; Recombination, Genetic
Chemical Substances	Anti-Bacterial Agents ; DNA, Bacterial ; Escherichia coli Proteins ; Quinolones ; DNA modification methylase EcoRII (EC 2.1.1.-) ; DNA-Cytosine Methylases (EC 2.1.1.-)
Language	English
Publishing date	2015-05-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0128092
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Article: Interplay between DNA replication and recombination in prokaryotes.

Kreuzer, Kenneth N

Annual review of microbiology

2005 Volume 59, Page(s) 43–67

Abstract: The processes of DNA replication and recombination are intertwined at many different levels. In diverse systems, extensive DNA replication can be triggered by genetic recombination, with assembly of a replication complex onto a D-loop recombination ... ...

Abstract	The processes of DNA replication and recombination are intertwined at many different levels. In diverse systems, extensive DNA replication can be triggered by genetic recombination, with assembly of a replication complex onto a D-loop recombination intermediate. This and related pathways of replisome assembly allow the completion of DNA replication when forks initiated at a conventional replication origin fail before completing replication of the genome. In addition, the repair of double-strand breaks or gaps by homologous recombination requires at least limited DNA replication to replace the missing information. An intricate interplay between replication and recombination is also evident during the termination of bacterial DNA replication and during the induction of the bacterial SOS response to DNA damage.
MeSH term(s)	Bacteriophage T4/genetics ; DNA Repair ; DNA Replication ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Escherichia coli/virology ; Recombination, Genetic ; SOS Response (Genetics)
Chemical Substances	DNA, Bacterial
Language	English
Publishing date	2005
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	207931-8
ISSN	0066-4227
ISSN	0066-4227
DOI	10.1146/annurev.micro.59.030804.121255
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Article ; Online: Functions that Protect Escherichia coli from Tightly Bound DNA-Protein Complexes Created by Mutant EcoRII Methyltransferase.

Morgan L Henderson / Kenneth N Kreuzer

PLoS ONE, Vol 10, Iss 5, p e

2015 Volume 0128092

Abstract	Expression of mutant EcoRII methyltransferase protein (M.EcoRII-C186A) in Escherichia coli leads to tightly bound DNA-protein complexes (TBCs), located sporadically on the chromosome rather than in tandem arrays. The mechanisms behind the lethality induced by such sporadic TBCs are not well studied, nor is it clear whether very tight binding but non-covalent complexes are processed in the same way as covalent DNA-protein crosslinks (DPCs). Using 2D gel electrophoresis, we found that TBCs induced by M.EcoRII-C186A block replication forks in vivo. Specific bubble molecules were detected as spots on the 2D gel, only when M.EcoRII-C186A was induced, and a mutation that eliminates a specific EcoRII methylation site led to disappearance of the corresponding spot. We also performed a candidate gene screen for mutants that are hypersensitive to TBCs induced by M.EcoRII-C186A. We found several gene products necessary for protection against these TBCs that are known to also protect against DPCs induced with wild-type M.EcoRII (after 5-azacytidine incorporation): RecA, RecBC, RecG, RuvABC, UvrD, FtsK, XerCD and SsrA (tmRNA). In contrast, the RecFOR pathway and Rep helicase are needed for protection against TBCs but not DPCs induced by M.EcoRII. We propose that stalled fork processing by RecFOR and RecA promotes release of tightly bound (but non-covalent) blocking proteins, perhaps by licensing Rep helicase-driven dissociation of the blocking M.EcoRII-C186A. Our studies also argued against the involvement of several proteins that might be expected to protect against TBCs. We took the opportunity to directly compare the sensitivity of all tested mutants to two quinolone antibiotics, which target bacterial type II topoisomerases and induce a unique form of DPC. We uncovered rep, ftsK and xerCD as novel quinolone hypersensitive mutants, and also obtained evidence against the involvement of a number of functions that might be expected to protect against quinolones.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article ; Online: Initiation of bacteriophage T4 DNA replication and replication fork dynamics: a review in the Virology Journal series on bacteriophage T4 and its relatives.

Kreuzer, Kenneth N / Brister, J Rodney

Virology journal

2010 Volume 7, Page(s) 358

Abstract: Bacteriophage T4 initiates DNA replication from specialized structures that form in its genome. Immediately after infection, RNA-DNA hybrids (R-loops) occur on (at least some) replication origins, with the annealed RNA serving as a primer for leading- ... ...

Abstract	Bacteriophage T4 initiates DNA replication from specialized structures that form in its genome. Immediately after infection, RNA-DNA hybrids (R-loops) occur on (at least some) replication origins, with the annealed RNA serving as a primer for leading-strand synthesis in one direction. As the infection progresses, replication initiation becomes dependent on recombination proteins in a process called recombination-dependent replication (RDR). RDR occurs when the replication machinery is assembled onto D-loop recombination intermediates, and in this case, the invading 3' DNA end is used as a primer for leading strand synthesis. Over the last 15 years, these two modes of T4 DNA replication initiation have been studied in vivo using a variety of approaches, including replication of plasmids with segments of the T4 genome, analysis of replication intermediates by two-dimensional gel electrophoresis, and genomic approaches that measure DNA copy number as the infection progresses. In addition, biochemical approaches have reconstituted replication from origin R-loop structures and have clarified some detailed roles of both replication and recombination proteins in the process of RDR and related pathways. We will also discuss the parallels between T4 DNA replication modes and similar events in cellular and eukaryotic organelle DNA replication, and close with some current questions of interest concerning the mechanisms of replication, recombination and repair in phage T4.
MeSH term(s)	Bacteriophage T4/enzymology ; Bacteriophage T4/physiology ; DNA Replication ; DNA, Viral/metabolism ; Models, Biological ; Recombination, Genetic ; Replication Origin ; Viral Proteins/metabolism ; Virus Replication
Chemical Substances	DNA, Viral ; Viral Proteins
Language	English
Publishing date	2010-12-03
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/1743-422X-7-358
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Article ; Online: Functions that protect Escherichia coli from DNA-protein crosslinks.

Krasich, Rachel / Wu, Sunny Yang / Kuo, H Kenny / Kreuzer, Kenneth N

DNA repair

2015 Volume 28, Page(s) 48–59

Abstract: Pathways for tolerating and repairing DNA-protein crosslinks (DPCs) are poorly defined. We used transposon mutagenesis and candidate gene approaches to identify DPC-hypersensitive Escherichia coli mutants. DPCs were induced by azacytidine (aza-C) ... ...

Abstract	Pathways for tolerating and repairing DNA-protein crosslinks (DPCs) are poorly defined. We used transposon mutagenesis and candidate gene approaches to identify DPC-hypersensitive Escherichia coli mutants. DPCs were induced by azacytidine (aza-C) treatment in cells overexpressing cytosine methyltransferase; hypersensitivity was verified to depend on methyltransferase expression. We isolated hypersensitive mutants that were uncovered in previous studies (recA, recBC, recG, and uvrD), hypersensitive mutants that apparently activate phage Mu Gam expression, and novel hypersensitive mutants in genes involved in DNA metabolism, cell division, and tRNA modification (dinG, ftsK, xerD, dnaJ, hflC, miaA, mnmE, mnmG, and ssrA). Inactivation of SbcCD, which can cleave DNA at protein-DNA complexes, did not cause hypersensitivity. We previously showed that tmRNA pathway defects cause aza-C hypersensitivity, implying that DPCs block coupled transcription/translation complexes. Here, we show that mutants in tRNA modification functions miaA, mnmE and mnmG cause defects in aza-C-induced tmRNA tagging, explaining their hypersensitivity. In order for tmRNA to access a stalled ribosome, the mRNA must be cleaved or released from RNA polymerase. Mutational inactivation of functions involved in mRNA processing and RNA polymerase elongation/release (RNase II, RNaseD, RNase PH, RNase LS, Rep, HepA, GreA, GreB) did not cause aza-C hypersensitivity; the mechanism of tmRNA access remains unclear.
MeSH term(s)	Azacitidine/toxicity ; DNA Damage ; DNA Repair ; Escherichia coli/drug effects ; Escherichia coli/genetics ; Escherichia coli/physiology ; Escherichia coli Proteins/genetics ; RNA, Bacterial/metabolism ; Transcription, Genetic/drug effects
Chemical Substances	Escherichia coli Proteins ; RNA, Bacterial ; tmRNA ; Azacitidine (M801H13NRU)
Language	English
Publishing date	2015-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2015.01.016
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Article ; Online: Fork regression is an active helicase-driven pathway in bacteriophage T4.

Long, David T / Kreuzer, Kenneth N

EMBO reports

2009 Volume 10, Issue 4, Page(s) 394–399

Abstract: Reactivation of stalled replication forks requires specialized mechanisms that can recognize the fork structure and promote downstream processing events. Fork regression has been implicated in several models of fork reactivation as a crucial processing ... ...

Abstract	Reactivation of stalled replication forks requires specialized mechanisms that can recognize the fork structure and promote downstream processing events. Fork regression has been implicated in several models of fork reactivation as a crucial processing step that supports repair. However, it has also been suggested that regressed forks represent pathological structures rather than physiological intermediates of repair. To investigate the biological role of fork regression in bacteriophage T4, we tested several mechanistic models of regression: strand exchange-mediated extrusion, topology-driven fork reversal and helicase-mediated extrusion. Here, we report that UvsW, a T4 branch-specific helicase, is necessary for the accumulation of regressed forks in vivo, and that UvsW-catalysed regression is the dominant mechanism of origin-fork processing that contributes to double-strand end formation. We also show that UvsW resolves purified fork intermediates in vitro by fork regression. Regression is therefore part of an active, UvsW-driven pathway of fork processing in bacteriophage T4.
MeSH term(s)	Bacteriophage T4/genetics ; Bacteriophage T4/metabolism ; DNA Helicases/genetics ; DNA Helicases/metabolism ; DNA Replication/genetics ; DNA Replication/physiology ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemical Substances	Viral Proteins ; DNA Helicases (EC 3.6.4.-) ; UvsW protein, Bacteriophage T4 (EC 5.99.-)
Language	English
Publishing date	2009-03-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.1038/embor.2009.13
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Article ; Online: Regression supports two mechanisms of fork processing in phage T4.

Long, David T / Kreuzer, Kenneth N

Proceedings of the National Academy of Sciences of the United States of America

2008 Volume 105, Issue 19, Page(s) 6852–6857

Abstract: Replication forks routinely encounter damaged DNA and tightly bound proteins, leading to fork stalling and inactivation. To complete DNA synthesis, it is necessary to remove fork-blocking lesions and reactivate stalled fork structures, which can occur by ...

Abstract	Replication forks routinely encounter damaged DNA and tightly bound proteins, leading to fork stalling and inactivation. To complete DNA synthesis, it is necessary to remove fork-blocking lesions and reactivate stalled fork structures, which can occur by multiple mechanisms. To study the mechanisms of stalled fork reactivation, we used a model fork intermediate, the origin fork, which is formed during replication from the bacteriophage T4 origin, ori(34). The origin fork accumulates within the T4 chromosome in a site-specific manner without the need for replication inhibitors or DNA damage. We report here that the origin fork is processed in vivo to generate a regressed fork structure. Furthermore, origin fork regression supports two mechanisms of fork resolution that can potentially lead to fork reactivation. Fork regression generates both a site-specific double-stranded end (DSE) and a Holliday junction. Each of these DNA elements serves as a target for processing by the T4 ATPase/exonuclease complex [gene product (gp) 46/47] and Holliday junction-cleaving enzyme (EndoVII), respectively. In the absence of both gp46 and EndoVII, regressed origin forks are stabilized and persist throughout infection. In the presence of EndoVII, but not gp46, there is significantly less regressed origin fork accumulation apparently due to cleavage of the regressed fork Holliday junction. In the presence of gp46, but not EndoVII, regressed origin fork DSEs are processed by degradation of the DSE and a pathway that includes recombination proteins. Although both mechanisms can occur independently, they may normally function together as a single fork reactivation pathway.
MeSH term(s)	Amsacrine/pharmacology ; Bacteriophage T4/drug effects ; Bacteriophage T4/enzymology ; Bacteriophage T4/genetics ; DNA Replication/drug effects ; Endodeoxyribonucleases/metabolism ; Escherichia coli/drug effects ; Escherichia coli/virology ; Hydroxyurea/pharmacology ; Models, Biological ; Mutation/genetics ; Replication Origin/drug effects ; Viral Proteins/metabolism
Chemical Substances	Viral Proteins ; Amsacrine (00DPD30SOY) ; Endodeoxyribonucleases (EC 3.1.-) ; endodeoxyribonuclease VII (EC 3.1.22.-) ; Hydroxyurea (X6Q56QN5QC)
Language	English
Publishing date	2008-05-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.0711999105
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