@article {805,
	title = {Structure of the SSB-DNA polymerase III interface and its role in DNA replication.},
	journal = {EMBO J},
	volume = {30},
	year = {2011},
	month = {2011 Oct 19},
	pages = {4236-47},
	abstract = {Interactions between single-stranded DNA-binding proteins (SSBs) and the DNA replication machinery are found in all organisms, but the roles of these contacts remain poorly defined. In Escherichia coli, SSB{\textquoteright}s association with the χ subunit of the DNA polymerase III holoenzyme has been proposed to confer stability to the replisome and to aid delivery of primers to the lagging-strand DNA polymerase. Here, the SSB-binding site on χ is identified crystallographically and biochemical and cellular studies delineate the consequences of destabilizing the χ/SSB interface. An essential role for the χ/SSB interaction in lagging-strand primer utilization is not supported. However, sequence changes in χ that block complex formation with SSB lead to salt-dependent uncoupling of leading- and lagging-strand DNA synthesis and to a surprising obstruction of the leading-strand DNA polymerase in vitro, pointing to roles for the χ/SSB complex in replisome establishment and maintenance. Destabilization of the χ/SSB complex in vivo produces cells with temperature-dependent cell cycle defects that appear to arise from replisome instability.},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Base Sequence, DNA Polymerase III, DNA Replication, DNA, Single-Stranded, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Holoenzymes, Molecular Sequence Data},
	issn = {1460-2075},
	doi = {10.1038/emboj.2011.305},
	author = {Marceau, Aimee H and Bahng, Soon and Massoni, Shawn C and George, Nicholas P and Sandler, Steven J and Marians, Kenneth J and Keck, James L}
}
@article {806,
	title = {RecA4142 causes SOS constitutive expression by loading onto reversed replication forks in Escherichia coli K-12.},
	journal = {J Bacteriol},
	volume = {192},
	year = {2010},
	month = {2010 May},
	pages = {2575-82},
	abstract = {Escherichia coli initiates the SOS response when single-stranded DNA (ssDNA) produced by DNA damage is bound by RecA and forms a RecA-DNA filament. recA SOS constitutive [recA(Con)] mutants induce the SOS response in the absence of DNA damage. It has been proposed that recA(Con) mutants bind to ssDNA at replication forks, although the specific mechanism is unknown. Previously, it had been shown that recA4142(F217Y), a novel recA(Con) mutant, was dependent on RecBCD for its high SOS constitutive [SOS(Con)] expression. This was presumably because RecA4142 was loaded at a double-strand end (DSE) of DNA. Herein, it is shown that recA4142 SOS(Con) expression is additionally dependent on ruvAB (replication fork reversal [RFR] activity only) and recJ (5{\textquoteright}-->3{\textquoteright} exonuclease), xonA (3{\textquoteright}-->5{\textquoteright} exonuclease) and partially dependent on recQ (helicase). Lastly, sbcCD mutations (Mre11/Rad50 homolog) in recA4142 strains caused full SOS(Con) expression in an ruvAB-, recBCD-, recJ-, and xonA-independent manner. It is hypothesized that RuvAB catalyzes RFR, RecJ and XonA blunt the DSE (created by the RFR), and then RecBCD loads RecA4142 onto this end to produce SOS(Con) expression. In sbcCD mutants, RecA4142 can bind other DNA substrates by itself that are normally degraded by the SbcCD nuclease.},
	keywords = {Bacterial Proteins, Deoxyribonucleases, DNA Helicases, DNA Replication, Endodeoxyribonucleases, Escherichia coli K12, Escherichia coli Proteins, Exodeoxyribonuclease V, Exodeoxyribonucleases, Exonucleases, Microscopy, Fluorescence, Mutation, Rec A Recombinases, SOS Response (Genetics)},
	issn = {1098-5530},
	doi = {10.1128/JB.01623-09},
	author = {Long, Jarukit Edward and Massoni, Shawn C and Sandler, Steven J}
}
@article {808,
	title = {Suppression of constitutive SOS expression by recA4162 (I298V) and recA4164 (L126V) requires UvrD and RecX in Escherichia coli K-12.},
	journal = {Mol Microbiol},
	volume = {73},
	year = {2009},
	month = {2009 Jul},
	pages = {226-39},
	abstract = {Sensing DNA damage and initiation of genetic responses to repair DNA damage are critical to cell survival. In Escherichia coli, RecA polymerizes on ssDNA produced by DNA damage creating a RecA-DNA filament that interacts with the LexA repressor inducing the SOS response. RecA filament stability is negatively modulated by RecX and UvrD. recA730 (E38K) and recA4142 (F217Y) constitutively express the SOS response. recA4162 (I298V) and recA4164 (L126V) are intragenic suppressors of the constitutive SOS phenotype of recA730. Herein, it is shown that these suppressors are not allele specific and can suppress SOS(C) expression of recA730 and recA4142 in cis and in trans. recA4162 and recA4164 single mutants (and the recA730 and recA4142 derivatives) are Rec(+), UV(R) and are able to induce the SOS response after UV treatment like wild-type. UvrD and RecX are required for the suppression in two (recA730,4164 and recA4142,4162) of the four double mutants tested. To explain the data, one model suggests that recA(C) alleles promote SOS(C) expression by mimicking RecA filament structures that induce SOS and the suppressor alleles mimic RecA filament at end of SOS. UvrD and RecX are attracted to these latter structures to help dismantle or destabilize the RecA filament.},
	keywords = {Alleles, DNA Helicases, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Mutation, Missense, Rec A Recombinases, SOS Response (Genetics), Substrate Specificity},
	issn = {1365-2958},
	doi = {10.1111/j.1365-2958.2009.06765.x},
	author = {Long, Jarukit E and Renzette, Nicholas and Sandler, Steven J}
}
@article {393,
	title = {Two functions of the C-terminal domain of Escherichia coli Rob: mediating "sequestration-dispersal" as a novel off-on switch for regulating Rob{\textquoteright}s activity as a transcription activator and preventing degradation of Rob by Lon protease.},
	journal = {J Mol Biol},
	volume = {388},
	year = {2009},
	month = {2009 May 8},
	pages = {415-30},
	abstract = {In Escherichia coli, Rob activates transcription of the SoxRS/MarA/Rob regulon. Previous work revealed that Rob resides in three to four immunostainable foci, that dipyridyl and bile salts are inducers of its activity, and that inducers bind to Rob{\textquoteright}s C-terminal domain (CTD). We propose that sequestration inactivates Rob by blocking its access to the transcriptional machinery and that inducers activate Rob by mediating its dispersal, allowing interaction with RNA polymerase. To test "sequestration-dispersal" as a new mechanism for regulating the activity of transcriptional activators, we fused Rob{\textquoteright}s CTD to SoxS and used indirect immunofluorescence microscopy to determine the effect of inducers on SoxS-Rob{\textquoteright}s cellular localization. Unlike native SoxS, which is uniformly distributed throughout the cell, SoxS-Rob is sequestered without an inducer, but is rapidly dispersed when cells are treated with an inducer. In this manner, Rob{\textquoteright}s CTD serves as an anti-sigma factor in regulating the co-sigma-factor-like activity of SoxS when fused to it. Rob{\textquoteright}s CTD also protects its N-terminus from Lon protease, since Lon{\textquoteright}s normally rapid degradation of SoxS is blocked in the chimera. Accordingly, Rob{\textquoteright}s CTD has novel regulatory properties that can be bestowed on another E. coli protein.},
	keywords = {Decanoic Acids, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Reporter, Microscopy, Fluorescence, Models, Biological, Protease La, Protein Structure, Tertiary, Pyridines, Recombinant Fusion Proteins, Trans-Activators, Transcription, Genetic},
	issn = {1089-8638},
	doi = {10.1016/j.jmb.2009.03.023},
	author = {Griffith, Kevin L and Fitzpatrick, M Megan and Keen, Edward F and Wolf, Richard E}
}
@article {811,
	title = {UvrD303, a hyperhelicase mutant that antagonizes RecA-dependent SOS expression by a mechanism that depends on its C terminus.},
	journal = {J Bacteriol},
	volume = {191},
	year = {2009},
	month = {2009 Mar},
	pages = {1429-38},
	abstract = {Genomic integrity is critical for an organism{\textquoteright}s survival and ability to reproduce. In Escherichia coli, the UvrD helicase has roles in nucleotide excision repair and methyl-directed mismatch repair and can limit reactions by RecA under certain circumstances. UvrD303 (D403A D404A) is a hyperhelicase mutant, and when expressed from a multicopy plasmid, it results in UV sensitivity (UV(s)), recombination deficiency, and antimutability. In order to understand the molecular mechanism underlying the UV(s) phenotype of uvrD303 cells, this mutation was transferred to the E. coli chromosome and studied in single copy. It is shown here that uvrD303 mutants are UV sensitive, recombination deficient, and antimutable and additionally have a moderate defect in inducing the SOS response after UV treatment. The UV-sensitive phenotype is epistatic with recA and additive with uvrA and is partially suppressed by removing the LexA repressor. Furthermore, uvrD303 is able to inhibit constitutive SOS expression caused by the recA730 mutation. The ability of UvrD303 to antagonize SOS expression was dependent on its 40 C-terminal amino acids. It is proposed that UvrD303, via its C terminus, can decrease the levels of RecA activity in the cell.},
	keywords = {DNA Helicases, DNA, Bacterial, Escherichia coli K12, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Mutation, Rec A Recombinases, Recombination, Genetic, SOS Response (Genetics), Ultraviolet Rays},
	issn = {1098-5530},
	doi = {10.1128/JB.01415-08},
	author = {Centore, Richard C and Leeson, Michael C and Sandler, Steven J}
}
@article {810,
	title = {Differential requirements of two recA mutants for constitutive SOS expression in Escherichia coli K-12.},
	journal = {PLoS One},
	volume = {3},
	year = {2008},
	month = {2008},
	pages = {e4100},
	abstract = {BACKGROUND: Repairing DNA damage begins with its detection and is often followed by elicitation of a cellular response. In E. coli, RecA polymerizes on ssDNA produced after DNA damage and induces the SOS Response. The RecA-DNA filament is an allosteric effector of LexA auto-proteolysis. LexA is the repressor of the SOS Response. Not all RecA-DNA filaments, however, lead to an SOS Response. Certain recA mutants express the SOS Response (recA(C)) in the absence of external DNA damage in log phase cells.

METHODOLOGY/PRINCIPAL FINDINGS: Genetic analysis of two recA(C) mutants was used to determine the mechanism of constitutive SOS (SOS(C)) expression in a population of log phase cells using fluorescence of single cells carrying an SOS reporter system (sulAp-gfp). SOS(C) expression in recA4142 mutants was dependent on its initial level of transcription, recBCD, recFOR, recX, dinI, xthA and the type of medium in which the cells were grown. SOS(C) expression in recA730 mutants was affected by none of the mutations or conditions tested above.

CONCLUSIONS/SIGNIFICANCE: It is concluded that not all recA(C) alleles cause SOS(C) expression by the same mechanism. It is hypothesized that RecA4142 is loaded on to a double-strand end of DNA and that the RecA filament is stabilized by the presence of DinI and destabilized by RecX. RecFOR regulate the activity of RecX to destabilize the RecA filament. RecA730 causes SOS(C) expression by binding to ssDNA in a mechanism yet to be determined.},
	keywords = {Escherichia coli K12, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Bacterial, Models, Biological, Mutation, Rec A Recombinases, SOS Response (Genetics)},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0004100},
	author = {Long, Jarukit Edward and Renzette, Nicholas and Centore, Richard C and Sandler, Steven J}
}
@article {472,
	title = {Highly conserved genes in Geobacter species with expression patterns indicative of acetate limitation.},
	journal = {Microbiology},
	volume = {154},
	year = {2008},
	month = {2008 Sep},
	pages = {2589-99},
	abstract = {Analysis of the genome of Geobacter sulfurreducens revealed four genes encoding putative symporters with homology to ActP, an acetate transporter in Escherichia coli. Three of these genes, aplA, aplB and aplC, are highly similar (over 90 \% identical) and fell within a tight phylogenetic cluster (Group I) consisting entirely of Geobacter homologues. Transcript levels for all three genes increased in response to acetate limitation. The fourth gene, aplD, is phylogenetically distinct (Group II) and its expression was not influenced by acetate availability. Deletion of any one of the three genes in Group I did not significantly affect acetate-dependent growth, suggesting functional redundancy. Attempts to recover mutants in which various combinations of two of these genes were deleted were unsuccessful, suggesting that at least two of these three transporter genes are required to support growth. Closely related Group I apl genes were found in the genomes of other Geobacter species whose genome sequences are available. Furthermore, related genes could be detected in genomic DNA extracted from a subsurface environment undergoing in situ uranium bioremediation. The transporter genes recovered from the subsurface were most closely related to Group I apl genes found in the genomes of cultured Geobacter species that were isolated from contaminated subsurface environments. The increased expression of these genes in response to acetate limitation, their high degree of conservation among Geobacter species and the ease with which they can be detected in environmental samples suggest that Group I apl genes of the Geobacteraceae may be suitable biomarkers for acetate limitation. Monitoring the expression of these genes could aid in the design of strategies for acetate-mediated in situ bioremediation of uranium-contaminated groundwater.},
	keywords = {Acetates, Biodegradation, Environmental, DNA, Bacterial, Escherichia coli, Escherichia coli Proteins, Gene Deletion, Gene Expression, Genes, Bacterial, Genome, Bacterial, Geobacter, Membrane Transport Proteins, Phylogeny, Uranium},
	issn = {1350-0872},
	doi = {10.1099/mic.0.2008/017244-0},
	author = {Risso, Carla and Meth{\'e}, Barbara A and Elifantz, Hila and Holmes, Dawn E and Lovley, Derek R}
}
@article {394,
	title = {Inducible protein degradation in Bacillus subtilis using heterologous peptide tags and adaptor proteins to target substrates to the protease ClpXP.},
	journal = {Mol Microbiol},
	volume = {70},
	year = {2008},
	month = {2008 Nov},
	pages = {1012-25},
	abstract = {The ability to manipulate protein levels is useful for dissecting regulatory pathways, elucidating gene function and constructing synthetic biological circuits. We engineered an inducible protein degradation system for use in Bacillus subtilis based on Escherichia coli and Caulobacter crescentusssrA tags and SspB adaptors that deliver proteins to ClpXP for proteolysis. In this system, modified ssrA degradation tags are fused onto the 3{\textquoteright} end of the genes of interest. Unlike wild-type ssrA, these modified tags require the adaptor protein SspB to target tagged proteins for proteolysis. In the absence of SspB, the tagged proteins accumulate to near physiological levels. By inducing SspB expression from a regulated promoter, the tagged substrates are rapidly delivered to the B. subtilis ClpXP protease for degradation. We used this system to degrade the reporter GFP and several native B. subtilis proteins, including, the transcription factor ComA, two sporulation kinases (KinA, KinB) and the sporulation and chromosome partitioning protein Spo0J. We also used modified E. coli and C. crescentus ssrA tags to independently control the degradation of two different proteins in the same cell. These tools will be useful for studying biological processes in B. subtilis and can potentially be modified for use in other bacteria.},
	keywords = {Alleles, Bacillus subtilis, Bacterial Proteins, Carrier Proteins, Caulobacter crescentus, DNA-Binding Proteins, Endopeptidase Clp, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genetic Vectors, Green Fluorescent Proteins, Plasmids, Promoter Regions, Genetic, Protein Engineering, RNA, Bacterial, Substrate Specificity},
	issn = {1365-2958},
	doi = {10.1111/j.1365-2958.2008.06467.x},
	author = {Griffith, Kevin L and Grossman, Alan D}
}
@article {812,
	title = {RecA-mediated SOS induction requires an extended filament conformation but no ATP hydrolysis.},
	journal = {Mol Microbiol},
	volume = {69},
	year = {2008},
	month = {2008 Sep},
	pages = {1165-79},
	abstract = {The Escherichia coli SOS response to DNA damage is modulated by the RecA protein, a recombinase that forms an extended filament on single-stranded DNA and hydrolyzes ATP. The RecA K72R (recA2201) mutation eliminates the ATPase activity of RecA protein. The mutation also limits the capacity of RecA to form long filaments in the presence of ATP. Strains with this mutation do not undergo SOS induction in vivo. We have combined the K72R variant of RecA with another mutation, RecA E38K (recA730). In vitro, the double mutant RecA E38K/K72R (recA730,2201) mimics the K72R mutant protein in that it has no ATPase activity. The double mutant protein will form long extended filaments on ssDNA and facilitate LexA cleavage almost as well as wild-type, and do so in the presence of ATP. Unlike recA K72R, the recA E38K/K72R double mutant promotes SOS induction in vivo after UV treatment. Thus, SOS induction does not require ATP hydrolysis by the RecA protein, but does require formation of extended RecA filaments. The RecA E38K/K72R protein represents an improved reagent for studies of the function of ATP hydrolysis by RecA in vivo and in vitro.},
	keywords = {Adenosine Triphosphate, Amino Acid Substitution, Bacterial Proteins, DNA, Bacterial, DNA, Single-Stranded, Escherichia coli, Escherichia coli Proteins, Hydrolysis, Rec A Recombinases, Serine Endopeptidases, SOS Response (Genetics), Ultraviolet Rays},
	issn = {1365-2958},
	doi = {10.1111/j.1365-2958.2008.06341.x},
	author = {Gruenig, Marielle C and Renzette, Nicholas and Long, Edward and Chitteni-Pattu, Sindhu and Inman, Ross B and Cox, Michael M and Sandler, Steven J}
}
@article {813,
	title = {Requirements for ATP binding and hydrolysis in RecA function in Escherichia coli.},
	journal = {Mol Microbiol},
	volume = {67},
	year = {2008},
	month = {2008 Mar},
	pages = {1347-59},
	abstract = {RecA is essential for recombination, DNA repair and SOS induction in Escherichia coli. ATP hydrolysis is known to be important for RecA{\textquoteright}s roles in recombination and DNA repair. In vitro reactions modelling SOS induction minimally require ssDNA and non-hydrolyzable ATP analogues. This predicts that ATP hydrolysis will not be required for SOS induction in vivo. The requirement of ATP binding and hydrolysis for SOS induction in vivo is tested here through the study of recA4159 (K72A) and recA2201 (K72R). RecA4159 is thought to have reduced affinity for ATP. RecA2201 binds, but does not hydrolyse ATP. Neither mutant was able to induce SOS expression after UV irradiation. RecA2201, unlike RecA4159, could form filaments on DNA and storage structures as measured with RecA-GFP. RecA2201 was able to form hybrid filaments and storage structures and was either recessive or dominant to RecA(+), depending on the ratio of the two proteins. RecA4159 was unable to enter RecA(+) filaments on DNA or storage structures and was recessive to RecA(+). It is concluded that ATP hydrolysis is essential for SOS induction. It is proposed that ATP binding is essential for storage structure formation and ability to interact with other RecA proteins in a filament.},
	keywords = {Adenosine Triphosphate, Chromosomes, Bacterial, Escherichia coli, Escherichia coli Proteins, Hydrolysis, Mutation, Protein Binding, Rec A Recombinases, Ultraviolet Rays},
	issn = {1365-2958},
	doi = {10.1111/j.1365-2958.2008.06130.x},
	author = {Renzette, Nicholas and Sandler, Steven J}
}
@article {814,
	title = {XthA (Exonuclease III) regulates loading of RecA onto DNA substrates in log phase Escherichia coli cells.},
	journal = {Mol Microbiol},
	volume = {67},
	year = {2008},
	month = {2008 Jan},
	pages = {88-101},
	abstract = {Exonucleases can modify DNA substrates created during DNA replication, recombination and repair. In Escherichia coli, the effects of several 3{\textquoteright}-5{\textquoteright} exonucleases on RecA loading were studied by assaying RecA-GFP foci formation. Mutations in xthA (ExoIII), xseAB (ExoVII), xni (ExoIX), exoX (ExoX) and tatD (ExoXI) increased the number of RecA-GFP foci twofold to threefold in a population of log phase cells grown in minimal medium. These increases depend on xonA. Epistasis analysis shows that ExoVII, ExoX, ExoIX and ExoXI function in a common pathway, distinct from ExoIII (and ExoI is upstream of both pathways). It is shown (paradoxically) that in xthA mutants, RecA-GFP loading is predominantly RecBCD-dependent and that xthA recB double mutants are viable. Experiments show that while log phase xthA cells have twofold more double-stranded breaks (DSBs) than wild type, they do not induce the SOS response. The increase in RecA loading is independent of the base excision repair (BER) proteins Nth, MutM and Nei. It is proposed that log phase cells produce DSBs that do not induce the SOS response. Furthermore, ExoI, ExoIII and the other 3{\textquoteright}-5{\textquoteright} exonucleases process these DSBs, antagonizing the RecBCD pathway of RecA loading, thus regulating the availability of these substrates for recombination.},
	keywords = {DNA Breaks, Double-Stranded, DNA Repair, DNA, Bacterial, Epistasis, Genetic, Escherichia coli K12, Escherichia coli Proteins, Exodeoxyribonucleases, Green Fluorescent Proteins, Microbial Viability, Rec A Recombinases, Recombinant Fusion Proteins, SOS Response (Genetics)},
	issn = {0950-382X},
	doi = {10.1111/j.1365-2958.2007.06026.x},
	author = {Centore, Richard C and Lestini, Roxane and Sandler, Steven J}
}
@article {818,
	title = {DinI and RecX modulate RecA-DNA structures in Escherichia coli K-12.},
	journal = {Mol Microbiol},
	volume = {63},
	year = {2007},
	month = {2007 Jan},
	pages = {103-15},
	abstract = {RecA plays a central role in recombination, DNA repair and SOS induction through forming a RecA-DNA helical filament. Biochemical observations show that at low ratios to RecA, DinI and RecX stabilize and destabilize RecA-DNA filaments, respectively, and that the C-terminal 17 residues of RecA are important for RecX function. RecA-DNA filament formation was assayed in vivo using RecA-GFP foci formation in log-phase and UV-irradiated cells. In log-phase cells, dinI mutants have fewer foci than wild type and that recX mutants have more foci than wild type. A recADelta17::gfp mutant had more foci like a recX mutant. dinI recX double mutants have the same number of foci as dinI mutants alone, suggesting that dinI is epistatic to recX. After UV treatment, the dinI, recX and dinI recX mutants differed in their ability to form foci. All three mutants had fewer foci than wild type. The dinI mutant{\textquoteright}s foci persisted longer than wild-type foci. Roles of DinI and RecX after UV treatment differed from those during log-phase growth and may reflect the different DNA substrates, population of proteins or amounts during the SOS response. These experiments give new insight into the roles of these proteins.},
	keywords = {Bacterial Proteins, DNA, Bacterial, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Bacterial, Rec A Recombinases},
	issn = {0950-382X},
	doi = {10.1111/j.1365-2958.2006.05496.x},
	author = {Renzette, Nicholas and Gumlaw, Nathan and Sandler, Steven J}
}
@article {816,
	title = {A hand-off mechanism for primosome assembly in replication restart.},
	journal = {Mol Cell},
	volume = {26},
	year = {2007},
	month = {2007 Jun 22},
	pages = {781-93},
	abstract = {Collapsed DNA replication forks must be reactivated through origin-independent reloading of the replication machinery (replisome) to ensure complete duplication of cellular genomes. In E. coli, the PriA-dependent pathway is the major replication restart mechanism and requires primosome proteins PriA, PriB, and DnaT for replisome reloading. However, the molecular mechanisms that regulate origin-independent replisome loading are not fully understood. Here, we demonstrate that assembly of primosome protein complexes represents a key regulatory mechanism, as inherently weak PriA-PriB and PriB-DnaT interactions are strongly stimulated by single-stranded DNA. Furthermore, the binding site on PriB for single-stranded DNA partially overlaps the binding sites for PriA and DnaT, suggesting a dynamic primosome assembly process in which single-stranded DNA is handed off from one primosome protein to another as a repaired replication fork is reactivated. This model helps explain how origin-independent initiation of DNA replication is restricted to repaired replication forks, preventing overreplication of the genome.},
	keywords = {Binding Sites, DNA Helicases, DNA Replication, DNA, Bacterial, DNA, Single-Stranded, DNA-Binding Proteins, DNA-Directed DNA Polymerase, Escherichia coli, Escherichia coli Proteins, Genome, Bacterial, Models, Biological, Multienzyme Complexes, Protein Binding, Replication Origin},
	issn = {1097-2765},
	doi = {10.1016/j.molcel.2007.05.012},
	author = {Lopper, Matthew and Boonsombat, Ruethairat and Sandler, Steven J and Keck, James L}
}
@article {817,
	title = {UvrD limits the number and intensities of RecA-green fluorescent protein structures in Escherichia coli K-12.},
	journal = {J Bacteriol},
	volume = {189},
	year = {2007},
	month = {2007 Apr},
	pages = {2915-20},
	abstract = {RecA is important for recombination, DNA repair, and SOS induction. In Escherichia coli, RecBCD, RecFOR, and RecJQ prepare DNA substrates onto which RecA binds. UvrD is a 3{\textquoteright}-to-5{\textquoteright} helicase that participates in methyl-directed mismatch repair and nucleotide excision repair. uvrD deletion mutants are sensitive to UV irradiation, hypermutable, and hyper-rec. In vitro, UvrD can dissociate RecA from single-stranded DNA. Other experiments suggest that UvrD removes RecA from DNA where it promotes unproductive reactions. To test if UvrD limits the number and/or the size of RecA-DNA structures in vivo, an uvrD mutation was combined with recA-gfp. This recA allele allows the number of RecA structures and the amount of RecA at these structures to be assayed in living cells. uvrD mutants show a threefold increase in the number of RecA-GFP foci, and these foci are, on average, nearly twofold higher in relative intensity. The increased number of RecA-green fluorescent protein foci in the uvrD mutant is dependent on recF, recO, recR, recJ, and recQ. The increase in average relative intensity is dependent on recO and recQ. These data support an in vivo role for UvrD in removing RecA from the DNA.},
	keywords = {DNA Helicases, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli K12, Escherichia coli Proteins, Green Fluorescent Proteins, Molecular Sequence Data, Mutagenesis, Rec A Recombinases, Recombinant Fusion Proteins},
	issn = {0021-9193},
	doi = {10.1128/JB.01777-06},
	author = {Centore, Richard C and Sandler, Steven J}
}
@article {512,
	title = {Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information.},
	journal = {Gene},
	volume = {384},
	year = {2006},
	month = {2006 Dec 15},
	pages = {73-95},
	abstract = {RpoS, the sigma S subunit of RNA polymerase, is vital during the growth and survival of Geobacter sulfurreducens under conditions typically encountered in its native subsurface environments. We investigated the conservation of sites that may be important for RpoS function in G. sulfurreducens. We also employed sequence information and expression microarray data to predict G. sulfurreducens genome sites that may be related to RpoS regulation. Hierarchical clustering identified three clusters of significantly downregulated genes in the rpoS deletion mutant. The search for conserved overrepresented motifs in co-regulated operons identified likely -35 and -10 promoter elements upstream of a number of functionally important G. sulfurreducens operons that were downregulated in the rpoS deletion mutant. Putative -35/-10 promoter elements were also identified in the G. sulfurreducens genome using sequence similarity searches to matrices of -35/-10 promoter elements found in G. sulfurreducens and in Escherichia coli. Due to a sufficient degree of sequence similarity between -35/-10 promoter elements for RpoS, RpoD, and other sigma factors, both the sequence similarity searches and the search for conserved overrepresented motifs using microarray data may identify promoter elements for both RpoS and other sigma factors.},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Base Sequence, Citrates, Computational Biology, Conserved Sequence, DNA-Directed RNA Polymerases, Escherichia coli, Escherichia coli Proteins, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genes, Bacterial, Genome, Bacterial, Geobacter, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Operon, Promoter Regions, Genetic, Sigma Factor, Transcription, Genetic},
	issn = {0378-1119},
	doi = {10.1016/j.gene.2006.06.025},
	author = {Yan, Bin and N{\'u}{\~n}ez, Cinthia and Ueki, Toshiyuki and Esteve-N{\'u}{\~n}ez, Abraham and Puljic, Marko and Adkins, Ronald M and Meth{\'e}, Barbara A and Lovley, Derek R and Krushkal, Julia}
}
@article {819,
	title = {A novel dnaC mutation that suppresses priB rep mutant phenotypes in Escherichia coli K-12.},
	journal = {Mol Microbiol},
	volume = {60},
	year = {2006},
	month = {2006 May},
	pages = {973-83},
	abstract = {The loading of a replisome in prokaryotic and eukaryotic cells at an origin of DNA replication and during replication restart is a highly ordered and regulated process. During replication restart in Escherichia coli, the PriA, PriB, PriC, DnaT and Rep proteins form multiple pathways that bind to repaired replication forks. These complexes are then recognized by DnaC as sites to load DnaB, the replicative helicase. Several dnaC mutations have been isolated that suppress phenotypes of some replication restart mutants. A new dnaC mutation (dnaC824) is reported here that efficiently suppresses priB rep mutant phenotypes. Furthermore, it is shown that dnaC824 will suppress phenotypes of priB priA300, rep priA300 and priB priC strains. Unlike other dnaC suppressors, it can only weakly suppress the absence of priA. Others have reported a different type of dnaC mutation, dnaC1331, is able to mimic priB mutant phenotypes. This is supported herein by showing that like dnaC1331, a priB mutation is synthetically lethal with a dam mutation and this can be rescued by a mutH mutation. Furthermore, priB dam lethality can also be suppressed by dnaC824. Like a priB mutation, a dnaC1331 mutation causes a priA2::kan-like phenotype when combined with priA300. Lastly, we show that dnaC824 is dominant to wild type and that dnaC1331 is recessive to wild type. Several models are discussed for the action of these mutant dnaC proteins in replication restart.},
	keywords = {DNA Replication, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Genes, Dominant, Genes, Lethal, Genes, Recessive, Mutant Proteins, Mutation, Phenotype, Suppression, Genetic},
	issn = {0950-382X},
	doi = {10.1111/j.1365-2958.2006.05147.x},
	author = {Boonsombat, Ruethairat and Yeh, Su-Ping and Milne, Amy and Sandler, Steven J}
}
@article {396,
	title = {Characterization of TetD as a transcriptional activator of a subset of genes of the Escherichia coli SoxS/MarA/Rob regulon.},
	journal = {Mol Microbiol},
	volume = {56},
	year = {2005},
	month = {2005 May},
	pages = {1103-17},
	abstract = {In Escherichia coli, SoxS, MarA and Rob form a closely related subset of the AraC/XylS family of positive regulators, sharing approximately 42\% amino acid sequence identity over the length of SoxS and the ability to activate transcription of a common set of target genes that provide resistance to redox-cycling compounds and antibiotics. On the basis of its approximately 43\% amino acid sequence identity with SoxS, MarA and Rob, TetD, encoded by transposon Tn10, appears to be a fourth member of the subset. However, although its expression has been shown to be negatively regulated by TetC and not inducible by tetracycline, the physiological function of TetD is unknown. Accordingly, in the work presented here, we initiate a molecular characterization of TetD. We show that expression of TetD activates transcription of a subset of the SoxS/MarA/Rob regulon genes and confers resistance to redox-cycling compounds and antibiotics. We show that mutations in the putative TetD binding site of a TetD-activatable promoter and a mutation in the protein{\textquoteright}s N-terminal DNA recognition helix interfere with transcription activation, thereby indicating that TetD directly activates target gene transcription. Finally, we show that TetD, like SoxS and MarA, is intrinsically unstable; however, unlike SoxS and MarA, TetD is not degraded by Lon or any of the cell{\textquoteright}s known cytoplasmic ATP-dependent proteases. Thus, we conclude that TetD is a bona fide member of the SoxS/MarA/Rob subfamily of positive regulators.},
	keywords = {Amino Acid Sequence, Binding Sites, DNA, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Multigene Family, Promoter Regions, Genetic, Regulon, Tetracycline Resistance, Trans-Activators, Transcription Factors, Transcription, Genetic},
	issn = {0950-382X},
	doi = {10.1111/j.1365-2958.2005.04599.x},
	author = {Griffith, Kevin L and Becker, Stephen M and Wolf, Richard E}
}
@article {820,
	title = {Localization of RecA in Escherichia coli K-12 using RecA-GFP.},
	journal = {Mol Microbiol},
	volume = {57},
	year = {2005},
	month = {2005 Aug},
	pages = {1074-85},
	abstract = {RecA is important in recombination, DNA repair and repair of replication forks. It functions through the production of a protein-DNA filament. To study the localization of RecA in live Escherichia coli cells, the RecA protein was fused to the green fluorescence protein (GFP). Strains with this gene have recombination/DNA repair activities three- to tenfold below wild type (or about 1000-fold above that of a recA null mutant). RecA-GFP cells have a background of green fluorescence punctuated with up to five foci per cell. Two types of foci have been defined: 4,6-diamidino-2-phenylindole (DAPI)-sensitive foci that are bound to DNA and DAPI-insensitive foci that are DNA-less aggregates/storage structures. In log phase cells, foci were not localized to any particular region. After UV irradiation, the number of foci increased and they localized to the cell centre. This suggested colocalization with the DNA replication factory. recA, recB and recF strains showed phenotypes and distributions of foci consistent with the predicted effects of these mutations.},
	keywords = {Chromosomes, Bacterial, DNA Replication, DNA, Bacterial, Escherichia coli, Escherichia coli Proteins, Green Fluorescent Proteins, Mutation, Rec A Recombinases, Recombinant Fusion Proteins, Recombination, Genetic, Ultraviolet Rays},
	issn = {0950-382X},
	doi = {10.1111/j.1365-2958.2005.04755.x},
	author = {Renzette, Nicholas and Gumlaw, Nathan and Nordman, Jared T and Krieger, Marlee and Yeh, Su-Ping and Long, Edward and Centore, Richard and Boonsombat, Ruethairat and Sandler, Steven J}
}
@article {821,
	title = {Requirements for replication restart proteins during constitutive stable DNA replication in Escherichia coli K-12.},
	journal = {Genetics},
	volume = {169},
	year = {2005},
	month = {2005 Apr},
	pages = {1799-806},
	abstract = {Constitutive stable DNA replication (cSDR) is a mechanism for replisome loading in Escherichia coli K-12. This occurs in a dnaA-independent fashion in an rnhA mutant. cSDR is dependent on recA, priA, and transcription. In this report, it is shown that dnaA rnhA mutants using cSDR for initiation of their DNA replication additionally require priB, but not priC, for viability. Two subtle priA missense mutations either eliminated the ability to grow using cSDR (priA301 C479Y) or resulted in very small colonies (priA300 K230R). DnaC809, a priA suppressor, failed to allow priA or priB mutants to grow using cSDR to initiate DNA replication. Furthermore, unlike dnaC(+) strains, dnaC809 strains require priC for cSDR. DnaC809,820, a priC-independent suppressor of priA2::kan phenotypes, allowed priA and priC (but not priB) mutants to grow using cSDR to initiate DNA replication. It is also shown that rep and rnhA mutations are synthetically lethal. DnaC809 and dnaC809,820 mutations suppress this lethality. Rep is further shown to be required for cSDR in a dnaC809 strain. A model whereby these different sets of replication restart proteins interact preferentially with substrates associated with either RecA or SSB during replication restart and cSDR, respectively, is proposed.},
	keywords = {Bacterial Proteins, DNA, DNA Replication, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genome, Bacterial, Macromolecular Substances, Models, Genetic, Mutation, Mutation, Missense, Phenotype, Rec A Recombinases, RNA, SOS Response (Genetics)},
	issn = {0016-6731},
	doi = {10.1534/genetics.104.036962},
	author = {Sandler, Steven J}
}
@article {822,
	title = {Allele specific synthetic lethality between priC and dnaAts alleles at the permissive temperature of 30 degrees C in E. coli K-12.},
	journal = {BMC Microbiol},
	volume = {4},
	year = {2004},
	month = {2004},
	pages = {47},
	abstract = {BACKGROUND: DnaA is an essential protein in the regulation and initiation of DNA replication in many bacteria. It forms a protein-DNA complex at oriC to which DnaC loads DnaB. DNA replication forks initiated at oriC by DnaA can collapse on route to the terminus for a variety of reasons. PriA, PriB, PriC, DnaT, Rep and DnaC form multiple pathways to restart repaired replication forks. DnaC809 and dnaC809,820 are suppressors of priA2::kan mutant phenotypes. The former requires PriC and Rep while the latter is independent of them. RnhA339::cat mutations allow DnaA-independent initiation of DNA replication.

RESULTS: It is shown herein that a priC303::kan mutation is synthetically lethal with either a dnaA46 or dnaA508 temperature sensitive mutation at the permissive temperature of 30 degrees C. The priC-dnaA lethality is specific for the dnaA allele. The priC303::kan mutant was viable when placed in combination with either dnaA5, dnaA167, dnaA204 or dnaA602. The priC-dnaA508 and priC-dnaA46 lethality could be suppressed by rnhA339::cat. The priC-dnaA508 lethality could be suppressed by a dnaC809,820 mutation, but not dnaC809. Neither of the dnaC mutations could suppress the priC-dnaA46 lethality.

CONCLUSIONS: A hitherto unknown function for either DnaA in replication restart or PriC in initiation of DNA replication that occurs in certain dnaA temperature sensitive mutant strains at the permissive temperature of 30 degrees C has been documented. Models considering roles for PriC during initiation of DNA replication and roles for DnaA in replication restart were tested and found not to decisively explain the data. Other roles of dnaA in transcription and nucleoid structure are additionally considered.},
	keywords = {Alleles, Bacterial Proteins, DNA Replication, DNA-Binding Proteins, Escherichia coli K12, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Lethal, Mutation, Temperature},
	issn = {1471-2180},
	doi = {10.1186/1471-2180-4-47},
	author = {Hinds, Tania and Sandler, Steven J}
}
@article {824,
	title = {A dnaT mutant with phenotypes similar to those of a priA2::kan mutant in Escherichia coli K-12.},
	journal = {Genetics},
	volume = {167},
	year = {2004},
	month = {2004 Jun},
	pages = {569-78},
	abstract = {The ability to repair damaged replication forks and restart them is important for cell survival. DnaT is essential for replication restart in vitro and yet no definite genetic analysis has been done in Escherichia coli K-12. To begin, dnaT822, an in-frame six-codon (87-92) deletion was constructed. DnaT822 mutants show colony size, cell morphology, inability to properly partition nucleoids, UV sensitivity, and basal SOS expression similar to priA2::kan mutants. DnaT822 priA2::kan double mutants had phenotypes similar to those of the single mutants. DnaT822 and dnaT822 priA2::kan mutant phenotypes were fully suppressed by dnaC809. Previously, a dominant temperature-sensitive lethal mutation, dnaT1, had been isolated in E. coli 15T(-). DnaT1 was found to have a base-pair change relative to the E. coli 15T(-) and E. coli K-12 dnaT genes that led to a single amino acid change: R152C. A plasmid-encoded E. coli K-12 mutant dnaT gene with the R152C amino acid substitution did not display a dominant temperature-sensitive lethal phenotype in a dnaT(+) strain of E. coli K-12. Instead, this mutant dnaT gene was found to complement the E. coli K-12 dnaT822 mutant phenotypes. The significance of these results is discussed in terms of models for replication restart.},
	keywords = {Base Sequence, Codon, DNA Primers, DNA Repair, DNA Replication, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli K12, Escherichia coli Proteins, Molecular Sequence Data, Mutation, Plasmids, Polymerase Chain Reaction, Sequence Deletion},
	issn = {0016-6731},
	doi = {10.1534/genetics.103.025296},
	author = {McCool, Jesse D and Ford, Christopher C and Sandler, Steven J}
}
@article {397,
	title = {Genetic evidence for pre-recruitment as the mechanism of transcription activation by SoxS of Escherichia coli: the dominance of DNA binding mutations of SoxS.},
	journal = {J Mol Biol},
	volume = {344},
	year = {2004},
	month = {2004 Nov 12},
	pages = {1-10},
	abstract = {SoxS, the direct transcriptional activator of the Escherichia coli superoxide (SoxRS) regulon, displays several unusual characteristics which suggest that it is unlikely to activate transcription by the ususal recruitment mechanism. Thus, agents that generate superoxide endogenously and thereby provoke the defense response elicit the de novo synthesis of SoxS, and with the SoxS binding site being highly degenerate, the number of SoxS binding sites per cell far exceeds the number of SoxS molecules per cell. To account for these distinctive features of the SoxRS system, we proposed "pre-recruitment" as the mechanism by which SoxS activates transcription of the regulon{\textquoteright}s genes. In pre-recruitment, newly synthesized SoxS molecules form binary complexes with RNA polymerase in solution. These complexes provide the information content to allow the 2500 molecules of SoxS per cell to scan the 65,000 SoxS binding sites per cell for the 200 binding sites per cell that reside within SoxS-dependent promoters. As a test of whether SoxS activates transcription by recruitment or pre-recruitment, we determined the dominance relationships of SoxS mutations conferring defective DNA binding. We found that soxS DNA binding mutations are dominant to the wild-type allele, a result consistent with the pre-recruitment hypothesis, but opposite to that expected for an activator that functions by recruitment. Moreover, whereas positive control mutations of activators functioning by recruitment are usually dominant, a soxS positive control mutation was not. Lastly, with the SoxRS system as an example, we discuss the physiological requirement for stringent regulation of transcriptional activators that function by pre-recruitment.},
	keywords = {Base Sequence, Binding Sites, DNA, Bacterial, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Bacterial, Genes, Dominant, Mutation, Regulon, Trans-Activators, Transcriptional Activation},
	issn = {0022-2836},
	doi = {10.1016/j.jmb.2004.09.007},
	author = {Griffith, Kevin L and Wolf, Richard E}
}
@article {823,
	title = {Measurement of SOS expression in individual Escherichia coli K-12 cells using fluorescence microscopy.},
	journal = {Mol Microbiol},
	volume = {53},
	year = {2004},
	month = {2004 Sep},
	pages = {1343-57},
	abstract = {Many recombination, DNA repair and DNA replication mutants have high basal levels of SOS expression as determined by a sulAp-lacZ reporter gene system on a population of cells. Two opposing models to explain how the SOS expression is distributed in these cells are: (i) the {\textquoteright}Uniform Expression Model (UEM){\textquoteright} where expression is evenly distributed in all cells or (ii) the {\textquoteright}Two Population Model (TPM){\textquoteright} where some cells are highly induced while others are not at all. To distinguish between these two models, a method to quantify SOS expression in individual bacterial cells was developed by fusing an SOS promoter (sulAp) to the green fluorescent protein (gfp) reporter gene and inserting it at attlambda on the Escherichia coli chromosome. It is shown that the fluorescence in sulAp-gfp cells is regulated by RecA and LexA. This system was then used to distinguish between the two models for several mutants. The patterns displayed by priA, dnaT, recG, uvrD, dam, ftsK, rnhA, polA and xerC mutants were explained best by the TPM while only lexA (def), lexA3 (ind-) and recA defective mutants were explained best by the UEM. These results are discussed in a context of how the processes of DNA replication and recombination may affect cells in a population differentially.},
	keywords = {Adenosine Triphosphatases, DNA Damage, DNA Helicases, DNA Repair, Escherichia coli K12, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Reporter, Microscopy, Fluorescence, Models, Genetic, Promoter Regions, Genetic, Recombinant Fusion Proteins, SOS Response (Genetics), Ultraviolet Rays},
	issn = {0950-382X},
	doi = {10.1111/j.1365-2958.2004.04225.x},
	author = {McCool, Jesse D and Long, Edward and Petrosino, Joseph F and Sandler, Hilary A and Rosenberg, Susan M and Sandler, Steven J}
}
@article {398,
	title = {Proteolytic degradation of Escherichia coli transcription activators SoxS and MarA as the mechanism for reversing the induction of the superoxide (SoxRS) and multiple antibiotic resistance (Mar) regulons.},
	journal = {Mol Microbiol},
	volume = {51},
	year = {2004},
	month = {2004 Mar},
	pages = {1801-16},
	abstract = {In Escherichia coli, the SoxRS regulon confers resistance to redox-cycling compounds, and the Mar regulon provides a defence against multiple antibiotics. The response regulators, SoxS and MarA, are synthesized de novo in response to their inducing signals and directly activate transcription of a common set of target genes. Although the mechanisms of transcription activation by SoxS and MarA have been well studied, little is known about how the systems are shut-off once the inducing stress has subsided, except that de novo synthesis of the regulators is known to cease almost immediately. Here, we induced the SoxRS regulon and determined that, upon removal of the inducer, expression of the regulon{\textquoteright}s genes quickly returns to the preinduced level. This rapid shut-off indicates that the system is reset by an active process. We found that SoxS is unstable and infer that SoxS degradation is responsible for the rapid return of the system to the ground state upon removal of the inducing signal. We also found that MarA is unstable and that the instability of both proteins is intrinsic and unregulated. We used null mutations of protease genes to identify the proteases involved in the degradation of SoxS and MarA. Among single protease mutations, only lon mutations increased the half-life of SoxS and MarA. In addition, SoxS appeared to be nearly completely stable in a lon ftsH double mutant. Using hexahistidine tags placed at the respective ends of the activators, we found that access to the amino-terminus is essential for the proteolytic degradation.},
	keywords = {Base Sequence, Blotting, Western, DNA Primers, DNA-Binding Proteins, Drug Resistance, Bacterial, Drug Resistance, Multiple, Bacterial, Endopeptidases, Escherichia coli, Escherichia coli Proteins, Genes, Bacterial, Half-Life, Hydrolysis, Kinetics, Mutation, Oxidation-Reduction, Promoter Regions, Genetic, Regulon, Trans-Activators, Transcription, Genetic},
	issn = {0950-382X},
	author = {Griffith, Kevin L and Shah, Ishita M and Wolf, Richard E}
}
@article {399,
	title = {A comprehensive alanine scanning mutagenesis of the Escherichia coli transcriptional activator SoxS: identifying amino acids important for DNA binding and transcription activation.},
	journal = {J Mol Biol},
	volume = {322},
	year = {2002},
	month = {2002 Sep 13},
	pages = {237-57},
	abstract = {SoxS is the direct transcriptional activator of the superoxide regulon. SoxS recognizes a highly degenerate "soxbox" DNA sequence, and activates transcription from class I and class II promoters. SoxS is the smallest member of the AraC/XylS family of transcription regulators whose hallmark is dual helix-turn-helix (HTH) DNA-binding motifs. Evidence suggests that the N-terminal HTH motif of SoxS interacts with a highly conserved region of the soxbox termed recognition element 1 (RE1), while the C-terminal HTH motif interacts with the less conserved recognition element 2 (RE2). In the work described here, we prepared a complete library of 101 SoxS mutants containing single alanine substitutions of SoxS, and we characterized the mutant proteins in vivo and in vitro. With SoxS being closely related to MarA, we analyzed the effects of the SoxS mutations in the context of the MarA-mar crystal structure and with respect to the NMR study of MarA-DNA complexes in solution. From the properties of the alanine substitutions, we conclude the following. (1) Surface-exposed residues of helix 3 and helix 6, the recognition helices of the dual HTH motifs, are important to DNA binding and transcription activation; however, substitutions of residues predicted from the MarA-mar crystal structure to make contact with the sugar-phosphate backbone are more detrimental to DNA binding than mutations predicted to make base-specific contacts. (2) Substitution of several residues within the recognition helix predicted to make base-specific contacts with RE2 have relatively little effect on DNA-binding, suggesting the possibility of alternative protein-DNA interactions than those inferred from the MarA-mar crystal structure. (3) DNA binding and transcription activation were reduced by substitution of conserved amino acid residues comprising the hydrophobic core, presumably because they disrupt the structural integrity of SoxS. (4) Mutant K30A appears to be a positive control mutant defective in a protein-protein interaction with RNA polymerase that is required for transcription activation at all SoxS-dependent promoters because it binds and bends DNA normally but fails to activate transcription from both classes of promoters. Alanine substitutions of surface-exposed residues H3, K5, D9, S31, and V45 confer a similar phenotype. Since these residues are near K30 on the surface of the protein, the surface formed by the six residues may be used to make protein-protein interactions with RNA polymerase that are required for transcription activation at both class I and class II SoxS-dependent promoters. (5) Mutants F74A, D75A, M78A, D79A and Q85A appear to define a surface required for protein-protein interaction with RNA polymerase specifically at class II promoters because these positive control mutants bind and bend DNA normally but are defective in activation of class II promoters but not class I promoters. These SoxS mutants that bind and bend DNA normally but are defective in transcription activation represent the first positive control mutants with putative defects in protein-protein interactions with RNA polymerase among the SoxS/MarA/Rob subset of the AraC/XylS family of transcription regulators.},
	keywords = {Alanine, Amino Acid Substitution, Base Sequence, Binding Sites, DNA, DNA-Binding Proteins, Electrophoretic Mobility Shift Assay, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Lethal, Hydrophobic and Hydrophilic Interactions, Lac Operon, Models, Molecular, Mutagenesis, Nucleic Acid Conformation, Phenotype, Phosphates, Promoter Regions, Genetic, Protein Binding, Protein Structure, Tertiary, Structure-Activity Relationship, Trans-Activators, Transcriptional Activation},
	issn = {0022-2836},
	author = {Griffith, Kevin L and Wolf, Richard E}
}
@article {400,
	title = {Evidence for "pre-recruitment" as a new mechanism of transcription activation in Escherichia coli: the large excess of SoxS binding sites per cell relative to the number of SoxS molecules per cell.},
	journal = {Biochem Biophys Res Commun},
	volume = {291},
	year = {2002},
	month = {2002 Mar 8},
	pages = {979-86},
	abstract = {In response to the oxidative stress imposed by redox-cycling compounds like paraquat, Escherichia coli induces the synthesis of SoxS, which then activates the transcription of approximately 100 genes. The DNA binding site for SoxS-dependent transcription activation, the "soxbox," is highly degenerate, suggesting that the genome contains a large number of SoxS binding sites. To estimate the number of soxboxes in the cell, we searched the E. coli genome for SoxS binding sites using as query sequence the previously determined optimal SoxS binding sequence. We found approximately 12,500 sequences that match the optimal binding sequence under the conditions of our search; this agrees with our previous estimate, based on information theory, that a random sequence the size of the E. coli genome contains approximately 13,000 soxboxes. Thus, fast-growing cells with 4-6 genomes per cell have approximately 65,000 soxboxes. This large number of potential SoxS binding sites per cell raises the interesting question of how SoxS distinguishes between the functional soxboxes located within the promoters of target genes and the plethora of equivalent but nonfunctional binding sites scattered throughout the chromosome. To address this question, we treated cells with paraquat and used Western blot analysis to determine the kinetics of SoxS accumulation per cell; we also determined the kinetics of SoxS-activated gene expression. The abundance of SoxS reached a maximum of 2,500 molecules per cell 20 min after induction and gradually declined to approximately 500 molecules per cell over the next 1.5 h. Given that activation of target gene expression began almost immediately and given the large disparity between the number of SoxS molecules per cell, 2,500, and the number of SoxS binding sites per cell, 65,000, we infer that SoxS is not likely to activate transcription by the usual "recruitment" pathway, as this mechanism would require a number of SoxS molecules similar to the number of soxboxes. Instead, we propose that SoxS first interacts in solution with RNA polymerase and then the binary complex scans the chromosome for promoters that contain a soxbox properly positioned and oriented for transcription activation. We name this new pathway "pre-recruitment."},
	keywords = {Bacterial Proteins, Binding Sites, Blotting, Western, Cell Division, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genome, Bacterial, Kinetics, Numerical Analysis, Computer-Assisted, Oxidative Stress, Paraquat, Protein Transport, Trans-Activators, Transcription Factors, Transcriptional Activation},
	issn = {0006-291X},
	doi = {10.1006/bbrc.2002.6559},
	author = {Griffith, Kevin L and Shah, Ishita M and Myers, Todd E and O{\textquoteright}Neill, Michael C and Wolf, Richard E}
}
@article {826,
	title = {Effects of mutations involving cell division, recombination, and chromosome dimer resolution on a priA2::kan mutant.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {98},
	year = {2001},
	month = {2001 Jul 17},
	pages = {8203-10},
	abstract = {Recombinational repair of replication forks can occur either to a crossover (XO) or noncrossover (non-XO) depending on Holliday junction resolution. Once the fork is repaired by recombination, PriA is important for restarting these forks in Escherichia coli. PriA mutants are Rec(-) and UV sensitive and have poor viability and 10-fold elevated basal levels of SOS expression. PriA sulB mutant cells and their nucleoids were studied by differential interference contrast and fluorescence microscopy of 4{\textquoteright},6-diamidino-2-phenylindole-stained log phase cells. Two populations of cells were seen. Eighty four percent appeared like wild type, and 16\% of the cells were filamented and had poorly partitioned chromosomes (Par(-)). To probe potential mechanisms leading to the two populations of cells, mutations were added to the priA sulB mutant. Mutating sulA or introducing lexA3 decreased, but did not eliminate filamentation or defects in partitioning. Mutating either recA or recB virtually eliminated the Par(-) phenotype. Filamentation in the recB mutant decreased to 3\%, but increased to 28\% in the recA mutant. The ability to resolve and/or branch migrate Holliday junctions also appeared crucial in the priA mutant because removing either recG or ruvC was lethal. Lastly, it was tested whether the ability to resolve chromosome dimers caused by XOs was important in a priA mutant by mutating dif and the C-terminal portion of ftsK. Mutation of dif showed no change in phenotype whereas ftsK1cat was lethal with priA2kan. A model is proposed where the PriA-independent pathway of replication restart functions at forks that have been repaired to non-XOs.},
	keywords = {Adenosine Triphosphatases, Bacterial Proteins, Cell Division, Chromosomes, Bacterial, Dimerization, DNA Helicases, Endodeoxyribonucleases, Escherichia coli, Escherichia coli Proteins, Exodeoxyribonuclease V, Exodeoxyribonucleases, Gene Expression, Membrane Proteins, Mutagenesis, Rec A Recombinases, Recombination, Genetic, SOS Response (Genetics)},
	issn = {0027-8424},
	doi = {10.1073/pnas.121007698},
	author = {McCool, J D and Sandler, S J}
}
@article {825,
	title = {PriA mutations that affect PriA-PriC function during replication restart.},
	journal = {Mol Microbiol},
	volume = {41},
	year = {2001},
	month = {2001 Aug},
	pages = {697-704},
	abstract = {In Escherichia coli, repair and restart of collapsed replication forks is thought to be essential for cell growth. The replication restart proteins, PriA, PriB, PriC, DnaB, DnaC, DnaG, DnaT and Rep, form redundant pathways that recognize repaired replication forks and restart them. Recognition, modulation of specific DNA structures and loading of the replicative helicase by the replication restart proteins, is likely to be important for replication restart. It has been hypothesized that PriB and PriC function with PriA in genetically separate and redundant PriA-PriB and PriA-PriC pathways. In this study, the del(priB)302 or priC303:kan mutations were used to isolate the PriA-PriB and PriA-PriC pathways genetically so that the effects of three priA missense mutations, priA300 (K230R), priA301 (C479Y) and priA306 (L557P), on these pathways could be assessed. In a wild-type background, the three priA mutations had little, if any, effect on the phenotypes of UV resistance, basal levels of SOS expression and cell viability. In the priB mutant, priA300 and priA301 caused dramatic negative changes in the three phenotypes listed above (and others), whereas the third priA mutant allele, priA306, showed very little negative effect. In the priC mutant, all three priA mutations behaved similarly, producing little, if any, changes in phenotypes. We conclude that priA300 and priA301 mostly affect the PriA-PriC pathway and do so more than priA306. We suggest that PriA{\textquoteright}s helicase activity is important for the PriA-PriC pathway of replication restart.},
	keywords = {Bacterial Proteins, Bacteriophage mu, Cell Division, DNA Replication, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Genes, Lethal, Genotype, Models, Biological, Mutation, Missense, Phenotype, Replication Protein A, SOS Response (Genetics), Ultraviolet Rays},
	issn = {0950-382X},
	author = {Sandler, S J and McCool, J D and Do, T T and Johansen, R U}
}
@article {402,
	title = {Systematic mutagenesis of the DNA binding sites for SoxS in the Escherichia coli zwf and fpr promoters: identifying nucleotides required for DNA binding and transcription activation.},
	journal = {Mol Microbiol},
	volume = {40},
	year = {2001},
	month = {2001 Jun},
	pages = {1141-54},
	abstract = {SoxS is the direct transcriptional activator of at least 15 genes of the Escherichia coli superoxide regulon. SoxS is small (107 amino acids), binds DNA as a monomer and recognizes a highly degenerate DNA binding site, termed {\textquoteright}soxbox{\textquoteright}. Like other members of the AraC/XylS family, SoxS has two putative helix-turn-helix (HTH) DNA-binding motifs, and it has been proposed that each HTH motif recognizes a highly conserved recognition element of the soxbox. To determine which nucleotides are important for SoxS binding, we conducted a systematic mutagenesis of the DNA binding sites for SoxS in the zwf and fpr promoters and determined the effect of the soxbox mutations on SoxS DNA binding and transcription activation in vivo by measuring beta-galactosidase activity in strains with fusions to lacZ. We found that the sequences GCAC and CAAA, termed recognition elements 1 and 2 (RE 1 and RE 2), respectively, are critical for SoxS binding, as mutations within these elements severely hinder or eliminate SoxS-dependent transcription activation; substitutions within RE 2 (CAAA), however, are tolerated better than changes within RE 1 (GCAC). Although substitutions at the seven positions separating the two REs had only a modest effect on SoxS binding, AT basepairs were favoured within this {\textquoteright}spacer{\textquoteright} region, presumably because, by facilitating DNA bending, they help bring the two recognition elements into proper juxtaposition. We also found that the {\textquoteright}invariant A{\textquoteright} present at position 1 of 14/15 functional soxboxes identified thus far is important for SoxS binding, as a change to any other nucleotide at this position reduced SoxS-dependent transcription by approximately 50\%. In addition, positions surrounding the REs seem to show a context effect, in that certain substitutions there have little or no effect when the RE has the optimal binding sequence, but produce a pronounced effect when the RE has a suboptimal sequence. We propose that these nucleotides play an important role in effecting differential expression from the various promoters. Lastly, we used gel retardation assays to show that alterations in transcription activation in vivo are caused by effects on DNA binding. Based on this exhaustive mutagenesis, we propose the following optimal sequence for SoxS binding: AnVGCACWWWnKRHCAAAHn (n = A, C, G, T; V = A, C, G; W = A, T; K = G, T; R = A, G; H = A, C, T).},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Base Sequence, Binding Sites, Carrier Proteins, DNA, Bacterial, Electrophoresis, Escherichia coli, Escherichia coli Proteins, Molecular Sequence Data, Mutagenesis, Promoter Regions, Genetic, Trans-Activators, Transcription Factors, Transcriptional Activation},
	issn = {0950-382X},
	author = {Griffith, K L and Wolf, R E}
}
@article {829,
	title = {Role of PriA in replication fork reactivation in Escherichia coli.},
	journal = {J Bacteriol},
	volume = {182},
	year = {2000},
	month = {2000 Jan},
	pages = {9-13},
	keywords = {Bacterial Proteins, DNA Primase, DNA Repair, DNA Replication, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Models, Genetic, Replication Protein A},
	issn = {0021-9193},
	author = {Sandler, S J and Marians, K J}
}
@article {830,
	title = {dnaC mutations suppress defects in DNA replication- and recombination-associated functions in priB and priC double mutants in Escherichia coli K-12.},
	journal = {Mol Microbiol},
	volume = {34},
	year = {1999},
	month = {1999 Oct},
	pages = {91-101},
	abstract = {PriA, PriB and PriC were originally discovered as proteins essential for the PhiX174 in vitro DNA replication system. Recent studies have shown that PriA mutants are poorly viable, have high basal levels of SOS expression (SOSH), are recombination deficient (Rec-), sensitive to UV irradiation (UVS) and sensitive to rich media. These data suggest that priA{\textquoteright}s role may be more complex than previously thought and may involve both DNA replication and homologous recombination. Based on the PhiX174 system, mutations in priB and priC should cause phenotypes like those seen in priA2:kan mutants. To test this, mutations in priB and priC were constructed. We found that, contrary to the PhiX174 model, del(priB)302 and priC303:kan mutants have almost wild-type phenotypes. Most unexpectedly, we then found that the priBC double mutant had very poor viability and/or a slow growth rate (even less than a priA2:kan mutant). This suggests that priB and priC have a redundant and important role in Escherichia coli. The priA2:kan suppressor, dnaC809, partially suppressed the poor viability/slow growth phenotype of the priBC double mutant. The resulting triple mutant (priBC dnaC809 ) had small colony size, recombination deficiency and levels of SOS expression similar to a priA2:kan mutant. The priBC dnaC809 mutant, however, was moderately UVR and had good viability, unlike a priA2:kan mutant. Additional mutations in the triple mutant were selected to suppress the slow growth phenotype. One suppressor restored all phenotypes tested to nearly wild-type levels. This mutation was identified as dnaC820 (K178N) [mapping just downstream of dnaC809 (E176G)]. Experiments suggest that dnaC820 makes dnaC809 suppression of priA and or priBC mutants priB and or priC independent. A model is proposed for the roles of these proteins in terms of restarting collapsed replication forks from recombinational intermediates.},
	keywords = {Bacterial Proteins, Bacteriophage mu, Cell Division, DNA Replication, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Mutation, Phenotype, Recombination, Genetic, Replication Protein A, SOS Response (Genetics), Substrate Specificity, Suppression, Genetic},
	issn = {0950-382X},
	author = {Sandler, S J and Marians, K J and Zavitz, K H and Coutu, J and Parent, M A and Clark, A J}
}
@article {403,
	title = {Interdependence of the position and orientation of SoxS binding sites in the transcriptional activation of the class I subset of Escherichia coli superoxide-inducible promoters.},
	journal = {Mol Microbiol},
	volume = {34},
	year = {1999},
	month = {1999 Nov},
	pages = {414-30},
	abstract = {SoxS is the direct transcriptional activator of the member genes of the Escherichia coli superoxide regulon. At class I SoxS-dependent promoters, e.g. zwf and fpr, whose SoxS binding sites ({\textquoteright}soxbox{\textquoteright}) lie upstream of the -35 region of the promoter, activation requires the C-terminal domain of the RNA polymerase alpha-subunit, while at class II SoxS-dependent promoters, e.g. fumC and micF, whose binding sites overlap the -35 region, activation is independent of the alpha-CTD. To determine whether SoxS activation of its class I promoters shows the same helical phase-dependent spacing requirement as class I promoters activated by catabolite gene activator protein, we increased the 7 bp distance between the 20 bp zwf soxbox and the zwf -35 promoter hexamer by 5 bp and 11 bp, and we decreased the 15 bp distance between the 20 bp fpr soxbox and the fpr -35 promoter hexamer by the same amounts. In both cases, displacement of the binding site by a half or full turn of the DNA helix prevented transcriptional activation. With constructs containing the binding site of one gene fused to the promoter of the other, we demonstrated that the positional requirements are a function of the specific binding site, not the promoter. Supposing that opposite orientation of the SoxS binding site at the two promoters might account for the positional requirements, we placed the zwf and fpr soxboxes in the reverse orientation at the various positions upstream of the promoters and determined the effect of orientation on transcription activation. We found that reversing the orientation of the zwf binding site converts its positional requirement to that of the fpr binding site in its normal orientation, and vice versa. Analysis by molecular information theory of DNA sequences known to bind SoxS in vitro is consistent with the opposite orientation of the zwf and fpr soxboxes.},
	keywords = {Bacterial Proteins, Base Sequence, Binding Sites, Escherichia coli, Escherichia coli Proteins, Molecular Sequence Data, Plasmids, Promoter Regions, Genetic, Sequence Analysis, DNA, Superoxides, Trans-Activators, Transcription Factors, Transcription, Genetic, Transcriptional Activation},
	issn = {0950-382X},
	author = {Wood, T I and Griffith, K L and Fawcett, W P and Jair, K W and Schneider, T D and Wolf, R E}
}
@article {833,
	title = {RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange.},
	journal = {Genes Dev},
	volume = {12},
	year = {1998},
	month = {1998 May 1},
	pages = {1248-53},
	abstract = {With the discovery that the Saccharomyces cerevisiae Rad51 protein is both structurally and functionally similar to the Escherichia coli RecA protein, the RecA paradigm for homologous recombination was extended to the Eucarya. The ubiquitous presence of RecA and Rad51 protein homologs raises the question of whether this archetypal protein exists within the third domain of life, the Archaea. Here we present the isolation of a Rad51/RecA protein homolog from the archaeon Sulfolobus solfataricus, and show that this protein, RadA, possesses the characteristics of a DNA strand exchange protein: The RadA protein is a DNA-dependent ATPase, forms a nucleoprotein filament on DNA, and catalyzes DNA pairing and strand exchange.},
	keywords = {Adenosine Triphosphatases, Archaeal Proteins, Bacterial Proteins, DNA Helicases, DNA, Archaeal, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Genes, Archaeal, Nucleoproteins, Rad51 Recombinase, Rec A Recombinases, Recombinant Proteins, Recombination, Genetic, Sulfolobus},
	issn = {0890-9369},
	author = {Seitz, E M and Brockman, J P and Sandler, S J and Clark, A J and Kowalczykowski, S C}
}
@article {834,
	title = {Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms.},
	journal = {J Mol Evol},
	volume = {44},
	year = {1997},
	month = {1997 May},
	pages = {528-41},
	abstract = {Protein sequences with similarities to Escherichia coli RecA were compared across the major kingdoms of eubacteria, archaebacteria, and eukaryotes. The archaeal sequences branch monophyletically and are most closely related to the eukaryotic paralogous Rad51 and Dmc1 groups. A multiple alignment of the sequences suggests a modular structure of RecA-like proteins consisting of distinct segments, some of which are conserved only within subgroups of sequences. The eukaryotic and archaeal sequences share an N-terminal domain which may play a role in interactions with other factors and nucleic acids. Several positions in the alignment blocks are highly conserved within the eubacteria as one group and within the eukaryotes and archaebacteria as a second group, but compared between the groups these positions display nonconservative amino acid substitutions. Conservation within the RecA-like core domain identifies possible key residues involved in ATP-induced conformational changes. We propose that RecA-like proteins derive evolutionarily from an assortment of independent domains and that the functional homologs of RecA in noneubacteria comprise an array of RecA-like proteins acting in series or cooperatively.},
	keywords = {Amino Acid Sequence, Animals, Archaeal Proteins, Bacteria, Bacterial Proteins, Cell Cycle Proteins, Consensus Sequence, Conserved Sequence, DNA-Binding Proteins, Escherichia coli Proteins, Evolution, Molecular, Humans, Molecular Sequence Data, Phylogeny, Rad51 Recombinase, Rec A Recombinases, Sequence Alignment},
	issn = {0022-2844},
	author = {Brendel, V and Brocchieri, L and Sandler, S J and Clark, A J and Karlin, S}
}
@article {836,
	title = {Differential suppression of priA2::kan phenotypes in Escherichia coli K-12 by mutations in priA, lexA, and dnaC.},
	journal = {Genetics},
	volume = {143},
	year = {1996},
	month = {1996 May},
	pages = {5-13},
	abstract = {First identified as an essential component of the phi X174 in vitro DNA replication system, PriA has ATPase, helicase, translocase, and primosome-assembly activities. priA1::kan strains of Escherichia coli are sensitive to UV irradiation, deficient in homologous recombination following transduction, and filamentous. priA2::kan strains have eightfold higher levels of uninduced SOS expression than wild type. We show that (1) priA1::kan strains have eightfold higher levels of uninduced SOS expression, (2) priA2::kan strains are UVS and Rec-, (3) lexA3 suppresses the high basal levels of SOS expression of a priA2::kan strain, and (4) plasmid-encoded priA300 (K230R), a mutant allele retaining only the primosome-assembly activity of priA+, restores both UVR and Rec+ phenotypes to a priA2::kan strain. Finally, we have isolated 17 independent UVR Rec+ revertants of priA2::kan strains that carry extragenic suppressors. All 17 map in the C-terminal half of the dnaC gene. DnaC loads the DnaB helicase onto DNA as a prelude for primosome assembly and DNA replication. We conclude that priA{\textquoteright}s primosome-assembly activity is essential for DNA repair and recombination and that the dnaC suppressor mutations allow these processes to occur in the absence of priA.},
	keywords = {Bacterial Proteins, Bacteriophage phi X 174, beta-Galactosidase, Chromosomes, Bacterial, DNA Helicases, DNA Replication, DNA-Binding Proteins, Dose-Response Relationship, Radiation, Escherichia coli, Escherichia coli Proteins, Genes, Bacterial, Genetic Markers, Mutagenesis, Phenotype, Recombination, Genetic, Replication Protein A, Repressor Proteins, Serine Endopeptidases, Suppression, Genetic, Transduction, Genetic, Ultraviolet Rays},
	issn = {0016-6731},
	author = {Sandler, S J and Samra, H S and Clark, A J}
}
@article {796,
	title = {Mosaic structure of plasmids from natural populations of Escherichia coli.},
	journal = {Genetics},
	volume = {143},
	year = {1996},
	month = {1996 Jul},
	pages = {1091-100},
	abstract = {The distribution of plasmids related to the fertility factor F was examined in the ECOR reference collection of Escherichia coli. Probes specific for four F-related genes were isolated and used to survey the collection by DNA hybridization. To estimate the genetic diversity of genes in F-like plasmids, DNA sequences were obtained for four plasmid genes. The phylogenetic relationships among the plasmids in the ECOR strains is very different from that of the strains themselves. This finding supports the view that plasmid transfer has been frequent within and between the major groups of ECOR. Furthermore, the sequences indicate that recombination between genes in plasmids takes place at a considerably higher frequency than that observed for chromosomal genes. The plasmid genes, and by inference the plasmids themselves, are mosaic in structure with different regions acquired from different sources. Comparison of gene sequences from a variety of naturally occurring plasmids suggested a plausible donor of some of the recombinant regions as well as implicating a chi site in the mechanism of genetic exchange. The relatively high rate of recombination in F-plasmid genes suggests that conjugational gene transfer may play a greater role in bacterial population structure than previously appreciated.},
	keywords = {Bacterial Proteins, Base Sequence, DNA Helicases, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Evolution, Molecular, Membrane Proteins, Molecular Sequence Data, Mosaicism, Nucleic Acid Hybridization, Phylogeny, Plasmids, Polymorphism, Genetic, Proteins, Recombination, Genetic, Repressor Proteins, RNA-Binding Proteins, Trans-Activators},
	issn = {0016-6731},
	author = {Boyd, E F and Hill, C W and Rich, S M and Hartl, D L}
}
@article {837,
	title = {Overlapping functions for recF and priA in cell viability and UV-inducible SOS expression are distinguished by dnaC809 in Escherichia coli K-12.},
	journal = {Mol Microbiol},
	volume = {19},
	year = {1996},
	month = {1996 Feb},
	pages = {871-80},
	abstract = {The recF and priA genes have roles in DNA repair and homologous recombination. Mutations in these genes also cause decreases in cell viability and alterations in UV-inducible sulAp-lacZ (SOS) expression. To find out if the two genes are in the same or different pathways for viability and SOS expression, the phenotypes of the double mutant strains were studied. The recF priA double mutant showed a lower viability and SOS expression level than either of the single mutants. In the case of cell viability, recF missense mutations decreased viability of a priA2::kan strain two to five-fold whereas recF null priA2::kan double mutants were not viable at all. dnaC809, a mutation that suppresses the UV-sensitive (UVs and Rec- phenotypes of priA2::kan, restored cell viability, but not UV-inducible SOS expression, to a priA recF strain. Since recF is epistatic with recO and recR (recOR) for UV resistance, recOR mutations were also tested with priA2::kan. No overlap was found between recOR and priA for viability and SOS expression. It is concluded that priA and recF have two different overlapping functions in viability and SOS expression that are distinguishable by the effects of dnaC809. The role of recF in a priA2::kan strain in cell viability is a new function for recF and unlike recF{\textquoteright}s other roles in DNA repair and recombination, is independent of recOR. A new role for priA in UV-inducible SOS expression in a recF mutant is also defined.},
	keywords = {Bacterial Proteins, DNA Repair, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Genes, Bacterial, Lac Operon, Mutation, Recombinant Fusion Proteins, Recombination, Genetic, Replication Protein A, SOS Response (Genetics), Ultraviolet Rays},
	issn = {0950-382X},
	author = {Sandler, S J}
}
@article {838,
	title = {recO and recR mutations delay induction of the SOS response in Escherichia coli.},
	journal = {Mol Gen Genet},
	volume = {246},
	year = {1995},
	month = {1995 Jan 20},
	pages = {254-8},
	abstract = {RecF, RecO and RecR, three of the important proteins of the RecF pathway of recombination, are also needed for repair of DNA damage due to UV irradiation. recF mutants are not proficient in cleaving LexA repressor in vivo following DNA damage: therefore they show a delay of induction of the SOS response. In this communication, by measuring the in vivo levels of LexA repressor using anti-LexA antibodies, we show that recO and recR mutant strains are also not proficient in LexA cleavage reactions. In addition, we show that recO and recR mutations delay induction of beta-galactosidase activity expressed from a lexA-regulated promoter following exposure of cells to UV, thus further supporting the idea that recF, recO and recR gene products are needed for induction of the SOS response.},
	keywords = {Bacterial Proteins, beta-Galactosidase, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Mutation, Promoter Regions, Genetic, Recombinant Fusion Proteins, Repressor Proteins, Serine Endopeptidases, SOS Response (Genetics), Ultraviolet Rays},
	issn = {0026-8925},
	author = {Hegde, S and Sandler, S J and Clark, A J and Madiraju, M V}
}
@article {840,
	title = {Mutational analysis of sequences in the recF gene of Escherichia coli K-12 that affect expression.},
	journal = {J Bacteriol},
	volume = {176},
	year = {1994},
	month = {1994 Jul},
	pages = {4011-6},
	abstract = {The level of translation of recF-lacZ fusions is reduced 20-fold by nucleotides 49 to 146 of recF. In this region of recF, we found a previously described ribosome-interactive sequence called epsilon and a hexapyrimidine tract located just upstream of the epsilon sequence. Mutational studies indicate that the hexapyrimidine sequence is involved in at least some of the reduced translation. When the hexapyrimidine sequence is mutant, mutating epsilon increases the level of translation maximally. We ruled out the possibility that ribosome frameshifting explains most of the effect of these two sequences on expression and suspect that multiple mechanisms may be responsible. In a separate report, we show that mutations in the hexapyrimidine tract and epsilon increase expression of the full-sized recF gene.},
	keywords = {Bacterial Proteins, Base Sequence, DNA Mutational Analysis, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Bacterial, Half-Life, Lac Operon, Molecular Sequence Data, Protein Biosynthesis, Recombinant Fusion Proteins, Regulatory Sequences, Nucleic Acid, Ribosomes},
	issn = {0021-9193},
	author = {Sandler, S J and Clark, A J}
}
@article {841,
	title = {RecOR suppression of recF mutant phenotypes in Escherichia coli K-12.},
	journal = {J Bacteriol},
	volume = {176},
	year = {1994},
	month = {1994 Jun},
	pages = {3661-72},
	abstract = {The recF, recO, and recR genes form the recFOR epistasis group for DNA repair. recF mutants are sensitive to UV irradiation and fail to properly induce the SOS response. Using plasmid derivatives that overexpress combinations of the recO+ and recR+ genes, we tested the hypothesis that high-level expression of recO+ and recR+ (recOR) in vivo will indirectly suppress the recF mutant phenotypes mentioned above. We found that overexpression of just recR+ from the plasmid will partially suppress both phenotypes. Expression of the chromosomal recO+ gene is essential for the recR+ suppression. Hence we call this RecOR suppression of recF mutant phenotypes. RecOR suppression of SOS induction is more efficient with recO+ expression from a plasmid than with recO+ expression from the chromosome. This is not true for RecOR suppression of UV sensitivity (the two are equal). Comparison of RecOR suppression with the suppression caused by recA801 and recA803 shows that RecOR suppression of UV sensitivity is more effective than recA803 suppression and that RecOR suppression of UV sensitivity, like recA801 suppression, requires recJ+. We present a model that explains the data and proposes a function for the recFOR epistasis group in the induction of the SOS response and recombinational DNA repair.},
	keywords = {Bacterial Proteins, Base Sequence, DNA Damage, DNA Repair, DNA-Binding Proteins, Epistasis, Genetic, Escherichia coli, Escherichia coli Proteins, Models, Genetic, Molecular Sequence Data, Phenotype, Plasmids, SOS Response (Genetics), Suppression, Genetic, Ultraviolet Rays},
	issn = {0021-9193},
	author = {Sandler, S J and Clark, A J}
}
@article {839,
	title = {Studies on the mechanism of reduction of UV-inducible sulAp expression by recF overexpression in Escherichia coli K-12.},
	journal = {Mol Gen Genet},
	volume = {245},
	year = {1994},
	month = {1994 Dec 15},
	pages = {741-9},
	abstract = {UV-inducible sulAp expression, an indicator of the SOS response, is reduced by recF+ overexpression in vivo. Different DNA-damaging agents and amounts of RecO and RecR were tested for their effects on this phenotype. It was found that recF+ overexpression reduced sulAp expression after DNA damage by mitomycin C or nalidixic acid, recO+ and recR+ overexpression partially suppressed the reduction of UV-induced sulAp expression caused by recF+ overexpression. The requirement for ATP binding to RecF to produce the phenotype was tested by genetically altering the putative phosphate binding cleft of recF in a way that should prevent the mutant recF protein from binding ATP. It was found that a change of lysine to glutamine at codon 36 results in a mutant recF protein (RecF4115) that is unable to reduce UV-inducible sulAp expression when overproduced. It is inferred from these results that recF overexpression may reduce UV-inducible sulAp expression by a mechanism that is sensitive to the ability of RecF to bind ATP and to the levels of RecO and RecR (RecOR) in the cell, but not to the type of DNA damage per se. Models are explored that can explain how recF+ overexpression reduces UV induction of sulAp and how RecOR overproduction might suppress this phenotype.},
	keywords = {Bacterial Proteins, Base Sequence, DNA Primers, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Bacterial, Molecular Sequence Data, Mutagenesis, Site-Directed, Restriction Mapping, RNA, Messenger, SOS Response (Genetics), Structure-Activity Relationship, Ultraviolet Rays},
	issn = {0026-8925},
	author = {Sandler, S J}
}
@article {843,
	title = {Use of high and low level overexpression plasmids to test mutant alleles of the recF gene of Escherichia coli K-12 for partial activity.},
	journal = {Genetics},
	volume = {135},
	year = {1993},
	month = {1993 Nov},
	pages = {643-54},
	abstract = {We showed that sufficient overexpression of the wild-type recF gene interfered with three normal cell functions: (1) UV induction of transcription from the LexA-protein-repressed sulA promoter, (2) UV resistance and (3) cell viability at 42 degrees. To show this, we altered a low-level overexpressing recF+ plasmid with a set of structurally neutral mutations that increased the rate of expression of recF. The resulting high-level overexpressing plasmid interfered with UV induction of the sulA promoter, as did the low-level overexpressing plasmid. It also reduced UV resistance more than its low level progenitor and decreased viability at 42 degrees, an effect not seen with the low-level plasmid. We used the high-level plasmid to test four recF structural mutations for residual activity. The structural alleles consisted of an insertion mutation, two single amino acid substitution mutations and a double amino acid substitution mutation. On the Escherichia coli chromosome the three substitution mutations acted similarly to a recF deletion in reducing UV resistance in a recB21 recC22 sbcB15 sbcC201 genetic background. By this test, therefore, all three appeared to be null alleles. Measurements of conjugational recombination revealed, however, that the three substitution mutations may have residual activity. On the high-level overexpressing plasmid all three substitution mutations definitely showed partial activity. By contrast, the insertion mutation on the high-level overexpressing plasmid showed no partial activity and can be considered a true null mutation. One of the substitutions, recF143, showed a property attributable to a leaky mutation. Another substitution, recF4101, may block selectively two of the three interference phenotypes, thus allowing us to infer a mechanism for them.},
	keywords = {Alleles, Bacterial Proteins, Base Sequence, Chromosomes, Bacterial, DNA Repair, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression, Genes, Bacterial, Molecular Sequence Data, Mutagenesis, Site-Directed, Mutation, Phenotype, Plasmids, Radiation Tolerance, Recombination, Genetic, Ultraviolet Rays},
	issn = {0016-6731},
	author = {Sandler, S J and Clark, A J}
}
@article {844,
	title = {Sequence and complementation analysis of recF genes from Escherichia coli, Salmonella typhimurium, Pseudomonas putida and Bacillus subtilis: evidence for an essential phosphate binding loop.},
	journal = {Nucleic Acids Res},
	volume = {20},
	year = {1992},
	month = {1992 Feb 25},
	pages = {839-45},
	abstract = {We have compared the recF genes from Escherichia coli K-12, Salmonella typhimurium, Pseudomonas putida, and Bacillus subtilis at the DNA and amino acid sequence levels. To do this we determined the complete nucleotide sequence of the recF gene from Salmonella typhimurium and we completed the nucleotide sequence of recF gene from Pseudomonas putida begun by Fujita et al. (1). We found that the RecF proteins encoded by these two genes contain respectively 92\% and 38\% amino acid identity with the E. coli RecF protein. Additionally, we have found that the S. typhimurium and P. putida recF genes will complement an E. coli recF mutant, but the recF gene from Bacillus subtilis [showing about 20\% identity with E. coli (2)] will not. Amino acid sequence alignment of the four proteins identified four highly conserved regions. Two of these regions are part of a putative phosphate binding loop. In one region (position 36), we changed the lysine codon (which is essential for ATPase, GTPase and kinase activity in other proteins having this phosphate binding loop) to an arginine codon. We then tested this mutation (recF4101) on a multicopy plasmid for its ability to complement a recF chromosomal mutation and on the E. coli chromosome for its effect on sensitivity to UV irradiation. The strain with recF4101 on its chromosome is as sensitive as a null recF mutant strain. The strain with the plasmid-borne mutant allele is however more UV resistant than the null mutant strain. We conclude that lysine-36 and possibly a phosphate binding loop is essential for full recF activity. Lastly we made two chimeric recF genes by exchanging the amino terminal 48 amino acids of the S. typhimurium and E. coli recF genes. Both chimeras could complement E. coli chromosomal recF mutations.},
	keywords = {Amino Acid Sequence, Bacillus subtilis, Bacterial Proteins, Base Sequence, Binding Sites, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Genes, Bacterial, Genetic Complementation Test, Molecular Sequence Data, Nucleic Acid Conformation, Phosphates, Pseudomonas putida, Salmonella typhimurium, Sequence Alignment},
	issn = {0305-1048},
	author = {Sandler, S J and Chackerian, B and Li, J T and Clark, A J}
}
