Michael M. Cox
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View article: Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the <i>E. coli</i> RRS elements
Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the <i>E. coli</i> RRS elements Open
We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Se…
View article: The intrinsically disordered linker in the single-stranded DNA-binding protein influences DNA replication restart and recombination pathways in <i>Escherichia coli</i> K-12
The intrinsically disordered linker in the single-stranded DNA-binding protein influences DNA replication restart and recombination pathways in <i>Escherichia coli</i> K-12 Open
Tetrameric single-stranded (ss) DNA-binding proteins (SSBs) stabilize ssDNA intermediates formed during genome maintenance reactions in Bacteria . SSBs also recruit proteins important for these processes through direct SSB-protein interact…
View article: Molecular insights into the prototypical single-stranded DNA-binding protein from <i>E. coli</i>
Molecular insights into the prototypical single-stranded DNA-binding protein from <i>E. coli</i> Open
The SSB protein of Escherichia coli functions to bind single-stranded DNA wherever it occurs during DNA metabolism. Depending upon conditions, SSB occurs in several different binding modes. In the course of its function, SSB diffuses on ss…
View article: Identification of <i>recG</i> genetic interactions in <i>Escherichia coli</i> by transposon sequencing
Identification of <i>recG</i> genetic interactions in <i>Escherichia coli</i> by transposon sequencing Open
Maintaining the integrity of the genome is of utmost importance for cell division and propagation. In Escherichia coli , the RecG protein has been implicated in processing branched recombination intermediates during DNA repair processes, b…
View article: Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: The<i>E. coli</i>RRS Elements
Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: The<i>E. coli</i>RRS Elements Open
We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Se…
View article: Generation and Repair of Postreplication Gaps in Escherichia coli
Generation and Repair of Postreplication Gaps in Escherichia coli Open
When replication forks encounter template lesions, one result is lesion skipping, where the stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to leave the lesion behind in a postreplication gap. Despite…
View article: Spatiotemporal Dynamics of Single-stranded DNA Intermediates in<i>Escherichia coli</i>
Spatiotemporal Dynamics of Single-stranded DNA Intermediates in<i>Escherichia coli</i> Open
Single-stranded DNA gaps form within the E. coli chromosome during replication, repair and recombination. However, information about the extent of ssDNA creation in the genome is limited. To complement a recent whole-genome sequencing stud…
View article: RecF protein targeting to postreplication (daughter strand) gaps I: DNA binding by RecF and RecFR
RecF protein targeting to postreplication (daughter strand) gaps I: DNA binding by RecF and RecFR Open
In bacteria, the repair of post-replication gaps by homologous recombination requires the action of the recombination mediator proteins RecF, RecO and RecR. Whereas the role of the RecOR proteins to displace the single strand binding prote…
View article: RecF protein targeting to post-replication (daughter strand) gaps II: RecF interaction with replisomes
RecF protein targeting to post-replication (daughter strand) gaps II: RecF interaction with replisomes Open
The bacterial RecF, RecO, and RecR proteins are an epistasis group involved in loading RecA protein into post-replication gaps. However, the targeting mechanism that brings these proteins to appropriate gaps is unclear. Here, we propose th…
View article: RecA and SSB genome-wide distribution in ssDNA gaps and ends in <i>Escherichia coli</i>
RecA and SSB genome-wide distribution in ssDNA gaps and ends in <i>Escherichia coli</i> Open
Single-stranded DNA (ssDNA) gapped regions are common intermediates in DNA transactions. Using a new non-denaturing bisulfite treatment combined with ChIP-seq, abbreviated ‘ssGap-seq’, we explore RecA and SSB binding to ssDNA on a genomic …
View article: Interaction with the carboxy-terminal tip of SSB is critical for RecG function in <i>E. coli</i>
Interaction with the carboxy-terminal tip of SSB is critical for RecG function in <i>E. coli</i> Open
In Escherichia coli, the single-stranded DNA-binding protein (SSB) acts as a genome maintenance organizational hub by interacting with multiple DNA metabolism proteins. Many SSB-interacting proteins (SIPs) form complexes with SSB by dockin…
View article: Interaction with single-stranded DNA-binding protein modulates<i>Escherichia coli</i>RadD DNA repair activities
Interaction with single-stranded DNA-binding protein modulates<i>Escherichia coli</i>RadD DNA repair activities Open
The bacterial RadD enzyme is important for multiple genome maintenance pathways, including RecA DNA strand exchange and RecA-independent suppression of DNA crossover template switching. However, much remains unknown about the precise roles…
View article: Host cell RecA activates a mobile element-encoded mutagenic DNA polymerase
Host cell RecA activates a mobile element-encoded mutagenic DNA polymerase Open
Homologs of the mutagenic Escherichia coli DNA polymerase V (pol V) are encoded by numerous pathogens and mobile elements. We have used Rum pol (RumA′2B), from the integrative conjugative element (ICE), R391, as a model mobile element-enco…
View article: X-ray crystal structure of the Escherichia coli RadD DNA repair protein bound to ADP reveals a novel zinc ribbon domain
X-ray crystal structure of the Escherichia coli RadD DNA repair protein bound to ADP reveals a novel zinc ribbon domain Open
Genome maintenance is an essential process in all cells. In prokaryotes, the RadD protein is important for survival under conditions that include DNA-damaging radiation. Precisely how RadD participates in genome maintenance remains unclear…
View article: The Escherichia coli serS gene promoter region overlaps with the rarA gene
The Escherichia coli serS gene promoter region overlaps with the rarA gene Open
Deletion of the entire gene encoding the RarA protein of Escherichia coli results in a growth defect and additional deficiencies that were initially ascribed to a lack of RarA function. Further work revealed that most of the effects reflec…
View article: RadD is a RecA-dependent accessory protein that accelerates DNA strand exchange
RadD is a RecA-dependent accessory protein that accelerates DNA strand exchange Open
In rapidly growing cells, with recombinational DNA repair required often and a new replication fork passing every 20 min, the pace of RecA-mediated DNA strand exchange is potentially much too slow for bacterial DNA metabolism. The enigmati…
View article: The rarA gene as part of an expanded RecFOR recombination pathway: Negative epistasis and synthetic lethality with ruvB, recG, and recQ
The rarA gene as part of an expanded RecFOR recombination pathway: Negative epistasis and synthetic lethality with ruvB, recG, and recQ Open
The RarA protein, homologous to human WRNIP1 and yeast MgsA, is a AAA + ATPase and one of the most highly conserved DNA repair proteins. With an apparent role in the repair of stalled or collapsed replication forks, the molecular function …
View article: Genomic landscape of single-stranded DNA gapped intermediates in <i>Escherichia coli</i>
Genomic landscape of single-stranded DNA gapped intermediates in <i>Escherichia coli</i> Open
Single-stranded (ss) gapped regions in bacterial genomes (gDNA) are formed on W- and C-strands during replication, repair, and recombination. Using non-denaturing bisulfite treatment to convert C to U on ssDNA, combined with deep sequencin…
View article: The<i>Escherichia coli serS</i>gene promoter region overlaps with the<i>rarA</i>gene
The<i>Escherichia coli serS</i>gene promoter region overlaps with the<i>rarA</i>gene Open
Deletion of the entire gene encoding the RarA protein of Escherichia coli results in a growth defect and additional deficiencies that were initially ascribed to a lack of RarA function. Further work revealed that most of the effects reflec…
View article: Experimental evolution of extremophile levels of radiation resistance in <i>Escherichia coli</i>
Experimental evolution of extremophile levels of radiation resistance in <i>Escherichia coli</i> Open
Recent human development of high-level sources of ionizing radiation (IR) prompts a corresponding need to understand the effects of IR on living systems. One approach has focused on the capacity of some organisms to survive astonishing lev…
View article: The SOS Error-Prone DNA Polymerase V Mutasome and β-Sliding Clamp Acting in Concert on Undamaged DNA and during Translesion Synthesis
The SOS Error-Prone DNA Polymerase V Mutasome and β-Sliding Clamp Acting in Concert on Undamaged DNA and during Translesion Synthesis Open
In the mid 1970s, Miroslav Radman and Evelyn Witkin proposed that Escherichia coli must encode a specialized error-prone DNA polymerase (pol) to account for the 100-fold increase in mutations accompanying induction of the SOS regulon. By t…
View article: Proteome Damage Inflicted by Ionizing Radiation: Advancing a Theme in the Research of Miroslav Radman
Proteome Damage Inflicted by Ionizing Radiation: Advancing a Theme in the Research of Miroslav Radman Open
Oxidative proteome damage has been implicated as a major contributor to cell death and aging. Protein damage and aging has been a particular theme of the recent research of Miroslav Radman. However, the study of how cellular proteins are d…
View article: Redox controls RecA protein activity via reversible oxidation of its methionine residues
Redox controls RecA protein activity via reversible oxidation of its methionine residues Open
Reactive oxygen species (ROS) cause damage to DNA and proteins. Here, we report that the RecA recombinase is itself oxidized by ROS. Genetic and biochemical analyses revealed that oxidation of RecA altered its DNA repair and DNA recombinat…
View article: Corrigendum: Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection
Corrigendum: Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection Open
Corrigendum on: Bruckbauer ST, Martin J, Minkoff BB, Veling MT, Lancaster I, Liu J, Trimarco JD, Bushnell B, Lipzen A, Wood EA, Sussman MR, Pennacchio C and Cox MM (2020) Physiology of Highly Radioresistant Escherichia coli After Experimen…
View article: RecA‐independent recombination: Dependence on the <i>Escherichia coli</i> RarA protein
RecA‐independent recombination: Dependence on the <i>Escherichia coli</i> RarA protein Open
Most, but not all, homologous genetic recombination in bacteria is mediated by the RecA recombinase. The mechanistic origin of RecA‐independent recombination has remained enigmatic. Here, we demonstrate that the RarA protein makes a major …
View article: Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection
Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection Open
Ionizing radiation (IR) is lethal to most organisms at high doses, damaging every cellular macromolecule via induction of reactive oxygen species (ROS). Utilizing experimental evolution and continuing previous work, we have generated the m…
View article: Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair
Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair Open
Several functions have been proposed for the Escherichia coli DNA polymerase IV (pol IV). Although much research has focused on a potential role for pol IV in assisting pol III replisomes in the bypass of lesions, pol IV is rarely found at…