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  • 1
    Online Resource
    Online Resource
    Beneficial and detrimental genes in the cellular response to replication arrest
    Public Library of Science (PLoS) ; 2022
    In:  PLOS Genetics Vol. 18, No. 12 ( 2022-12-27), p. e1010564-
    Details
    In: PLOS Genetics, Public Library of Science (PLoS), Vol. 18, No. 12 ( 2022-12-27), p. e1010564-
    Abstract: DNA replication is essential for all living organisms. Several events can disrupt replication, including DNA damage (e.g., pyrimidine dimers, crosslinking) and so-called “roadblocks” (e.g., DNA-binding proteins or transcription). Bacteria have several well-characterized mechanisms for repairing damaged DNA and then restoring functional replication forks. However, little is known about the repair of stalled or arrested replication forks in the absence of chemical alterations to DNA. Using a library of random transposon insertions in Bacillus subtilis , we identified 35 genes that affect the ability of cells to survive exposure to an inhibitor that arrests replication elongation, but does not cause chemical alteration of the DNA. Genes identified include those involved in iron-sulfur homeostasis, cell envelope biogenesis, and DNA repair and recombination. In B . subtilis , and many bacteria, two nucleases (AddAB and RecJ) are involved in early steps in repairing replication forks arrested by chemical damage to DNA and loss of either nuclease causes increased sensitivity to DNA damaging agents. These nucleases resect DNA ends, leading to assembly of the recombinase RecA onto the single-stranded DNA. Notably, we found that disruption of recJ increased survival of cells following replication arrest, indicating that in the absence of chemical damage to DNA, RecJ is detrimental to survival. In contrast, and as expected, disruption of addA decreased survival of cells following replication arrest, indicating that AddA promotes survival. The different phenotypes of addA and recJ mutants appeared to be due to differences in assembly of RecA onto DNA. RecJ appeared to promote too much assembly of RecA filaments. Our results indicate that in the absence of chemical damage to DNA, RecA is dispensable for cells to survive replication arrest and that the stable RecA nucleofilaments favored by the RecJ pathway may lead to cell death by preventing proper processing of the arrested replication fork.
    Type of Medium: Online Resource
    ISSN: 1553-7404
    URL: Article
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    DOI: 10.1371/journal.pgen.1010564
    DOI: 10.1371/journal.pgen.1010564.g001
    DOI: 10.1371/journal.pgen.1010564.g002
    DOI: 10.1371/journal.pgen.1010564.g003
    DOI: 10.1371/journal.pgen.1010564.g004
    DOI: 10.1371/journal.pgen.1010564.g005
    DOI: 10.1371/journal.pgen.1010564.g006
    DOI: 10.1371/journal.pgen.1010564.t001
    DOI: 10.1371/journal.pgen.1010564.t002
    DOI: 10.1371/journal.pgen.1010564.t003
    DOI: 10.1371/journal.pgen.1010564.s001
    DOI: 10.1371/journal.pgen.1010564.s002
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2022
    detail.hit.zdb_id: 2186725-2
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  • 2
    Online Resource
    Online Resource
    Identification of a Single Strand Origin of Replication in the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis
    Public Library of Science (PLoS) ; 2015
    In:  PLOS Genetics Vol. 11, No. 10 ( 2015-10-6), p. e1005556-
    Details
    In: PLOS Genetics, Public Library of Science (PLoS), Vol. 11, No. 10 ( 2015-10-6), p. e1005556-
    Type of Medium: Online Resource
    ISSN: 1553-7404
    URL: Article
    URL: Article
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    DOI: 10.1371/journal.pgen.1005556
    DOI: 10.1371/journal.pgen.1005556.g001
    DOI: 10.1371/journal.pgen.1005556.g002
    DOI: 10.1371/journal.pgen.1005556.g003
    DOI: 10.1371/journal.pgen.1005556.g004
    DOI: 10.1371/journal.pgen.1005556.g005
    DOI: 10.1371/journal.pgen.1005556.g006
    DOI: 10.1371/journal.pgen.1005556.g007
    DOI: 10.1371/journal.pgen.1005556.g008
    DOI: 10.1371/journal.pgen.1005556.t001
    DOI: 10.1371/journal.pgen.1005556.t002
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2015
    detail.hit.zdb_id: 2186725-2
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  • 3
    Online Resource
    Online Resource
    Bipolar Localization of the Replication Origin Regions of Chromosomes in Vegetative and Sporulating Cells of B. subtilis
    Elsevier BV ; 1997
    In:  Cell Vol. 88, No. 5 ( 1997-03), p. 667-674
    Details
    In: Cell, Elsevier BV, Vol. 88, No. 5 ( 1997-03), p. 667-674
    Type of Medium: Online Resource
    ISSN: 0092-8674
    URL: Article
    DOI: 10.1016/S0092-8674(00)81909-1
    RVK:
    XA 36269
    RVK:
    WA 15000
    Language: English
    Publisher: Elsevier BV
    Publication Date: 1997
    detail.hit.zdb_id: 187009-9
    detail.hit.zdb_id: 2001951-8
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis
    Proceedings of the National Academy of Sciences ; 2007
    In:  Proceedings of the National Academy of Sciences Vol. 104, No. 13 ( 2007-03-27), p. 5608-5613
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 104, No. 13 ( 2007-03-27), p. 5608-5613
    Abstract: In many bacteria, there is a strong bias for genes to be encoded on the leading strand of DNA, resulting in coorientation of replication and transcription. In Bacillus subtilis , transcription of the majority of genes (75%) is cooriented with replication. By using genome-wide profiling of replication with DNA microarrays, we found that this coorientation bias reduces adverse effects of transcription on replication. We found that in wild-type cells, transcription did not appear to affect the rate of replication elongation. However, in mutants with reversed transcription bias for an extended region of the chromosome, replication elongation was slower. This reduced replication rate depended on transcription and was limited to the region in which the directions of replication and transcription are opposed. These results support the hypothesis that the strong bias to coorient transcription and replication is due to selective pressure for processive, efficient, and accurate replication.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.0608999104
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2007
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    In Vivo Effects of Sporulation Kinases on Mutant Spo0A Proteins in Bacillus subtilis
    American Society for Microbiology ; 2001
    In:  Journal of Bacteriology Vol. 183, No. 22 ( 2001-11-15), p. 6573-6578
    Details
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 183, No. 22 ( 2001-11-15), p. 6573-6578
    Abstract: The phosphorylated form of the response regulator Spo0A (Spo0A∼P) is required for the initiation of sporulation in Bacillus subtilis . Phosphate is transferred to Spo0A from at least four histidine kinases (KinA, KinB, KinC, and KinD) by a phosphotransfer pathway composed of Spo0F and Spo0B. Several mutations in spo0A allow initiation of sporulation in the absence of spo0F and spo0B , but the mechanisms by which these mutations allow bypass of spo0F and spo0B are not fully understood. We measured the ability of KinA, KinB, and KinC to activate sporulation of five spo0A mutants in the absence of Spo0F and Spo0B. We also determined the effect of Spo0E, a Spo0A∼P-specific phosphatase, on sporulation of strains containing the spo0A mutations. Our results indicate that several of the mutations relax the specificity of Spo0A, allowing Spo0A to obtain phosphate from a broader group of phosphodonors. In the course of these experiments, we observed medium-dependent effects on the sporulation of different mutants. This led us to identify a small molecule, acetoin, that can stimulate sporulation of some spo0A mutants.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    URL: Article
    DOI: 10.1128/JB.183.22.6573-6578.2001
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2001
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Control of Sporulation Gene Expression in Bacillus subtilis by the Chromosome Partitioning Proteins Soj (ParA) and Spo0J (ParB)
    American Society for Microbiology ; 2000
    In:  Journal of Bacteriology Vol. 182, No. 12 ( 2000-06-15), p. 3446-3451
    Details
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 182, No. 12 ( 2000-06-15), p. 3446-3451
    Abstract: Two chromosome partitioning proteins, Soj (ParA) and Spo0J (ParB), regulate the initiation of sporulation in Bacillus subtilis . In a spo0J null mutant, sporulation is inhibited by the action of Soj. Soj negatively regulates expression of several sporulation genes by binding to the promoter regions and inhibiting transcription. All of the genes known to be inhibited by Soj are also activated by the phosphorylated form of the transcription factor Spo0A (Spo0A∼P). We found that, in a spo0J null mutant, Soj affected sporulation, in part, by decreasing the level of Spo0A protein. Soj negatively regulated transcription of spo0A and associated with the spo0A promoter region in vivo. Expression of spo0A from a heterologous promoter in a spo0J null mutant restored Spo0A levels and partly bypassed the sporulation and gene expression defects. Soj did not appear to significantly affect phosphorylation of Spo0A. Thus, in the absence of Spo0J, Soj inhibits sporulation and sporulation gene expression by inhibiting accumulation of the activator protein Spo0A and by acting downstream of Spo0A to inhibit gene expression directly.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    URL: Article
    DOI: 10.1128/JB.182.12.3446-3451.2000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2000
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    Replication–transcription conflicts in bacteria
    Springer Science and Business Media LLC ; 2012
    In:  Nature Reviews Microbiology Vol. 10, No. 7 ( 2012-7), p. 449-458
    Details
    In: Nature Reviews Microbiology, Springer Science and Business Media LLC, Vol. 10, No. 7 ( 2012-7), p. 449-458
    Type of Medium: Online Resource
    ISSN: 1740-1526 , 1740-1534
    URL: Article
    DOI: 10.1038/nrmicro2800
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2012
    detail.hit.zdb_id: 2121463-3
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Multicopy Plasmids Affect Replisome Positioning in Bacillus subtilis
    American Society for Microbiology ; 2004
    In:  Journal of Bacteriology Vol. 186, No. 21 ( 2004-11), p. 7084-7090
    Details
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 186, No. 21 ( 2004-11), p. 7084-7090
    Abstract: The DNA replication machinery, various regions of the chromosome, and some plasmids occupy characteristic subcellular positions in bacterial cells. We visualized the location of a multicopy plasmid, pHP13, in living cells of Bacillus subtilis using an array of lac operators and LacI-green fluorescent protein (GFP). In the majority of cells, plasmids appeared to be highly mobile and randomly distributed. In a small fraction of cells, there appeared to be clusters of plasmids located predominantly at or near a cell pole. We also monitored the effects of the presence of multicopy plasmids on the position of DNA polymerase using a fusion of a subunit of DNA polymerase to GFP. Many of the plasmid-containing cells had extra foci of the replisome, and these were often found at uncharacteristic locations in the cell. Some of the replisome foci were dynamic and highly mobile, similar to what was observed for the plasmid. In contrast, replisome foci in plasmid-free cells were relatively stationary. Our results indicate that in B. subtilis , plasmid-associated replisomes are recruited to the subcellular position of the plasmid. Extending this notion to the chromosome, we postulated that the subcellular position of the chromosomally associated replisome is established by the subcellular location of oriC at the time of initiation of replication.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    URL: Article
    DOI: 10.1128/JB.186.21.7084-7090.2004
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2004
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Characterization of the Global Transcriptional Responses to Different Types of DNA Damage and Disruption of Replication in Bacillus subtilis
    American Society for Microbiology ; 2006
    In:  Journal of Bacteriology Vol. 188, No. 15 ( 2006-08), p. 5595-5605
    Details
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 188, No. 15 ( 2006-08), p. 5595-5605
    Abstract: DNA damage and perturbations in DNA replication can induce global transcriptional responses that can help organisms repair the damage and survive. RecA is known to mediate transcriptional responses to DNA damage in several bacterial species by inactivating the repressor LexA and phage repressors. To gain insight into how Bacillus subtilis responds to various types of DNA damage, we measured the effects of DNA damage and perturbations in replication on mRNA levels by using DNA microarrays. We perturbed replication either directly with p -hydroxyphenylazo-uracil (HPUra), an inhibitor of DNA polymerase, or indirectly with the DNA-damaging reagents mitomycin C (MMC) and UV irradiation. Our results indicate that the transcriptional responses to HPUra, MMC, and UV are only partially overlapping. recA is the major transcriptional regulator under all of the tested conditions, and LexA appears to directly repress the expression of 63 genes in 26 operons, including the 18 operons previously identified as LexA targets. MMC and HPUra treatments caused induction of an integrative and conjugative element (ICE Bs1 ) and resident prophages (PBSX and SPβ), which affected the expression of many host genes. Consistent with previous results, the induction of these mobile elements required recA . Induction of the phage appeared to require inactivation of LexA. Unrepaired UV damage and treatment with MMC also affected the expression of some of the genes that are controlled by DnaA. Furthermore, MMC treatment caused an increase in origin-proximal gene dosage. Our results indicate that different types of DNA damage have different effects on replication and on the global transcriptional profile.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    URL: Article
    DOI: 10.1128/JB.00342-06
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2006
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Autonomous Replication of the Conjugative Transposon Tn 916
    American Society for Microbiology ; 2016
    In:  Journal of Bacteriology Vol. 198, No. 24 ( 2016-12-15), p. 3355-3366
    Details
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 198, No. 24 ( 2016-12-15), p. 3355-3366
    Abstract: Integrative and conjugative elements (ICEs), also known as conjugative transposons, are self-transferable elements that are widely distributed among bacterial phyla and are important drivers of horizontal gene transfer. Many ICEs carry genes that confer antibiotic resistances to their host cells and are involved in the dissemination of these resistance genes. ICEs reside in host chromosomes but under certain conditions can excise to form a plasmid that is typically the substrate for transfer. A few ICEs are known to undergo autonomous replication following activation. However, it is not clear if autonomous replication is a general property of many ICEs. We found that Tn 916 , the first conjugative transposon identified, replicates autonomously via a rolling-circle mechanism. Replication of Tn 916 was dependent on the relaxase encoded by orf20 of Tn 916 . The origin of transfer of Tn 916 , oriT ( 916 ), also functioned as an origin of replication. Using immunoprecipitation and mass spectrometry, we found that the relaxase (Orf20) and the two putative helicase processivity factors (Orf22 and Orf23) encoded by Tn 916 likely interact in a complex and that the Tn 916 relaxase contains a previously unidentified conserved helix-turn-helix domain in its N-terminal region that is required for relaxase function and replication. Lastly, we identified a functional single-strand origin of replication ( sso ) in Tn 916 that we predict primes second-strand synthesis during rolling-circle replication. Together these results add to the emerging data that show that several ICEs replicate via a conserved, rolling-circle mechanism. IMPORTANCE Integrative and conjugative elements (ICEs) drive horizontal gene transfer and the spread of antibiotic resistances in bacteria. ICEs reside integrated in a host genome but can excise to create a plasmid that is the substrate for transfer to other cells. Here we show that Tn 916 , an ICE with broad host range, undergoes autonomous rolling-circle replication when in the plasmid form. We found that the origin of transfer functions as a double-stranded origin of replication and identified a single-stranded origin of replication. It was long thought that ICEs do not undergo autonomous replication. Our work adds to the evidence that ICEs replicate autonomously as part of their normal life cycle and indicates that diverse ICEs use the same replicative mechanism.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    URL: Article
    DOI: 10.1128/JB.00639-16
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2016
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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