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Bonde NJ, Kozlov AG, Cox MM, Lohman TM, Keck JL. Molecular insights into the prototypical single-stranded DNA-binding protein from E. coli. Crit Rev Biochem Mol Biol 2024; 59:99-127. [PMID: 38770626 PMCID: PMC11209772 DOI: 10.1080/10409238.2024.2330372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/11/2024] [Indexed: 05/22/2024]
Abstract
The SSB protein of Escherichia coli functions to bind single-stranded DNA wherever it occurs during DNA metabolism. Depending upon conditions, SSB occurs in several different binding modes. In the course of its function, SSB diffuses on ssDNA and transfers rapidly between different segments of ssDNA. SSB interacts with many other proteins involved in DNA metabolism, with 22 such SSB-interacting proteins, or SIPs, defined to date. These interactions chiefly involve the disordered and conserved C-terminal residues of SSB. When not bound to ssDNA, SSB can aggregate to form a phase-separated biomolecular condensate. Current understanding of the properties of SSB and the functional significance of its many intermolecular interactions are summarized in this review.
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Affiliation(s)
- Nina J. Bonde
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexander G. Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy M. Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Cox MM, Goodman MF, Keck JL, van Oijen A, Lovett ST, Robinson A. Generation and Repair of Postreplication Gaps in Escherichia coli. Microbiol Mol Biol Rev 2023; 87:e0007822. [PMID: 37212693 PMCID: PMC10304936 DOI: 10.1128/mmbr.00078-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
When replication forks encounter template lesions, one result is lesion skipping, where the stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to leave the lesion behind in a postreplication gap. Despite considerable attention in the 6 decades since postreplication gaps were discovered, the mechanisms by which postreplication gaps are generated and repaired remain highly enigmatic. This review focuses on postreplication gap generation and repair in the bacterium Escherichia coli. New information to address the frequency and mechanism of gap generation and new mechanisms for their resolution are described. There are a few instances where the formation of postreplication gaps appears to be programmed into particular genomic locations, where they are triggered by novel genomic elements.
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Affiliation(s)
- Michael M. Cox
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Myron F. Goodman
- Department of Biological Sciences, University of Southern California, University Park, Los Angeles, California, USA
- Department of Chemistry, University of Southern California, University Park, Los Angeles, California, USA
| | - James L. Keck
- Department of Biological Chemistry, University of Wisconsin—Madison School of Medicine, Madison, Wisconsin, USA
| | - Antoine van Oijen
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Susan T. Lovett
- Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Andrew Robinson
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
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3
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Mobile Element Integration Reveals a Chromosome Dimer Resolution System in Legionellales. mBio 2022; 13:e0217122. [PMID: 36314797 PMCID: PMC9765430 DOI: 10.1128/mbio.02171-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In bacteria, the mechanisms used to repair DNA lesions during genome replication include homologous recombination between sister chromosomes. This can lead to the formation of chromosome dimers if an odd number of crossover events occurs. The dimers must be resolved before cell separation to ensure genomic stability and cell viability. Dimer resolution is achieved by the broadly conserved dif/Xer system, which catalyzes one additional crossover event immediately prior to cell separation. While dif/Xer systems have been characterized or predicted in the vast majority of proteobacteria, no homologs to dif or xer have been identified in the order Legionellales. Here, we report the discovery of a distinct single-recombinase dif/Xer system in the intracellular pathogen Legionella pneumophila. The dif site was uncovered by our analysis of Legionella mobile element-1 (LME-1), which harbors a dif site mimic and integrates into the L. pneumophila genome via site-specific recombination. We demonstrate that lpg1867 (here named xerL) encodes a tyrosine recombinase that is necessary and sufficient for catalyzing recombination at the dif site and that deletion of dif or xerL causes filamentation along with extracellular and intracellular growth defects. We show that the dif/XerL system is present throughout Legionellales and that Coxiella burnetii XerL and its cognate dif site can functionally substitute for the native system in L. pneumophila. Finally, we describe an unexpected link between C. burnetii dif/Xer and the maintenance of its virulence plasmids. IMPORTANCE The maintenance of circular chromosomes depends on the ability to resolve aberrant chromosome dimers after they form. In most proteobacteria, broadly conserved Xer recombinases catalyze single crossovers at short, species-specific dif sites located near the replication terminus. Chromosomal dimerization leads to the formation of two copies of dif within the same molecule, leading to rapid site-specific recombination and conversion back into chromosome monomers. The apparent absence of chromosome dimer resolution mechanisms in Legionellales has been a mystery to date. By studying a phage-like mobile genetic element, LME-1, we have identified a previously unknown single-recombinase dif/Xer system that is not only widespread across Legionellales but whose activity is linked to virulence in two important human pathogens.
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Liu Y, Cui X, Yang R, Zhang Y, Xu Y, Liu G, Zhang B, Wang J, Wang X, Zhang W, Chen T, Zhang G. Genomic Insights into the Radiation-Resistant Capability of Sphingomonas qomolangmaensis S5-59 T and Sphingomonas glaciei S8-45 T, Two Novel Bacteria from the North Slope of Mount Everest. Microorganisms 2022; 10:microorganisms10102037. [PMID: 36296313 PMCID: PMC9611098 DOI: 10.3390/microorganisms10102037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m and 5100m above sea level. (2) Methods: The present study investigated the polyphasic features and genomic characteristics of S5-59T and S8-45T. (3) Results: The major fatty acids and the predominant respiratory menaquinone of S5-59T and S8-45T were summed as feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA sequences and average nucleotide identity values among these two strains and their reference type strains were below the species demarcation thresholds of 98.65% and 95%. Strains S5-59T and S8-45T harbored great radiation resistance. The genomic analyses showed that DNA damage repair genes, such as mutL, mutS, radA, radC, recF, recN, etc., were present in the S5-59T and S8-45T strains. Additionally, strain S5-59T possessed more genes related to DNA protection proteins. The pan-genome analysis and horizontal gene transfers revealed that strains of Sphingomonas had a consistently homologous genetic evolutionary radiation resistance. Moreover, enzymatic antioxidative proteins also served critical roles in converting ROS into harmless molecules that resulted in resistance to radiation. Further, pigments and carotenoids such as zeaxanthin and alkylresorcinols of the non-enzymatic antioxidative system were also predicted to protect them from radiation. (4) Conclusions: Type strains S5-59T (=JCM 35564T =GDMCC 1.3193T) and S8-45T (=JCM 34749T =GDMCC 1.2715T) represent two novel species of the genus Sphingomonas with the proposed name Sphingomonas qomolangmaensis sp. nov. and Sphingomonas glaciei sp. nov. The type strains, S5-59T and S8-45T, were assessed in a deeply genomic study of their radiation-resistant mechanisms and this thus resulted in a further understanding of their greater potential application for the development of anti-radiation protective drugs.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Xiaowen Cui
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, China
| | - Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou 730070, China
| | - Yiyang Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yeteng Xu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Jinxiu Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xinyue Wang
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
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Jain K, Stanage TH, Wood EA, Cox MM. The Escherichia coli serS gene promoter region overlaps with the rarA gene. PLoS One 2022; 17:e0260282. [PMID: 35427362 PMCID: PMC9012371 DOI: 10.1371/journal.pone.0260282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
Deletion of the entire gene encoding the RarA protein of Escherichia coli results in a growth defect and additional deficiencies that were initially ascribed to a lack of RarA function. Further work revealed that most of the effects reflected the presence of sequences in the rarA gene that affect expression of the downstream gene, serS. The serS gene encodes the seryl aminoacyl-tRNA synthetase. Decreases in the expression of serS can trigger the stringent response. The sequences that affect serS expression are located in the last 15 nucleotides of the rarA gene.
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Affiliation(s)
- Kanika Jain
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
| | - Tyler H. Stanage
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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6
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The rarA gene as part of an expanded RecFOR recombination pathway: Negative epistasis and synthetic lethality with ruvB, recG, and recQ. PLoS Genet 2021; 17:e1009972. [PMID: 34936656 PMCID: PMC8735627 DOI: 10.1371/journal.pgen.1009972] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/06/2022] [Accepted: 12/01/2021] [Indexed: 11/19/2022] Open
Abstract
The RarA protein, homologous to human WRNIP1 and yeast MgsA, is a AAA+ ATPase and one of the most highly conserved DNA repair proteins. With an apparent role in the repair of stalled or collapsed replication forks, the molecular function of this protein family remains obscure. Here, we demonstrate that RarA acts in late stages of recombinational DNA repair of post-replication gaps. A deletion of most of the rarA gene, when paired with a deletion of ruvB or ruvC, produces a growth defect, a strong synergistic increase in sensitivity to DNA damaging agents, cell elongation, and an increase in SOS induction. Except for SOS induction, these effects are all suppressed by inactivating recF, recO, or recJ, indicating that RarA, along with RuvB, acts downstream of RecA. SOS induction increases dramatically in a rarA ruvB recF/O triple mutant, suggesting the generation of large amounts of unrepaired ssDNA. The rarA ruvB defects are not suppressed (and in fact slightly increased) by recB inactivation, suggesting RarA acts primarily downstream of RecA in post-replication gaps rather than in double strand break repair. Inactivating rarA, ruvB and recG together is synthetically lethal, an outcome again suppressed by inactivation of recF, recO, or recJ. A rarA ruvB recQ triple deletion mutant is also inviable. Together, the results suggest the existence of multiple pathways, perhaps overlapping, for the resolution or reversal of recombination intermediates created by RecA protein in post-replication gaps within the broader RecF pathway. One of these paths involves RarA.
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7
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Cataldo PG, Klemm P, Thüring M, Saavedra L, Hebert EM, Hartmann RK, Lechner M. Insights into 6S RNA in lactic acid bacteria (LAB). BMC Genom Data 2021; 22:29. [PMID: 34479493 PMCID: PMC8414754 DOI: 10.1186/s12863-021-00983-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute a group of microorganisms with strong biotechnological relevance, often exploited as starter cultures for industrial products through fermentation. Some strains are used as probiotics while others represent potential pathogens. Occasional reports of 6S RNA within this group already indicate striking metabolic implications. A conceivable idea is that LAB with 6S RNA defects may metabolize nutrients faster, as inferred from studies of Echerichia coli. This may accelerate fermentation processes with the potential to reduce production costs. Similarly, elevated levels of secondary metabolites might be produced. Evidence for this possibility comes from preliminary findings regarding the production of surfactin in Bacillus subtilis, which has functions similar to those of bacteriocins. The prerequisite for its potential biotechnological utility is a general characterization of 6S RNA in LAB. RESULTS We provide a genomic annotation of 6S RNA throughout the Lactobacillales order. It laid the foundation for a bioinformatic characterization of common 6S RNA features. This covers secondary structures, synteny, phylogeny, and product RNA start sites. The canonical 6S RNA structure is formed by a central bulge flanked by helical arms and a template site for product RNA synthesis. 6S RNA exhibits strong syntenic conservation. It is usually flanked by the replication-associated recombination protein A and the universal stress protein A. A catabolite responsive element was identified in over a third of all 6S RNA genes. It is known to modulate gene expression based on the available carbon sources. The presence of antisense transcripts could not be verified as a general trait of LAB 6S RNAs. CONCLUSIONS Despite a large number of species and the heterogeneity of LAB, the stress regulator 6S RNA is well-conserved both from a structural as well as a syntenic perspective. This is the first approach to describe 6S RNAs and short 6S RNA-derived transcripts beyond a single species, spanning a large taxonomic group covering multiple families. It yields universal insights into this regulator and complements the findings derived from other bacterial model organisms.
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Affiliation(s)
- Pablo Gabriel Cataldo
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, San Miguel de Tucumán, 4000, Argentina
| | - Paul Klemm
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, Marburg, 35032, Germany
| | - Marietta Thüring
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, Marburg, 35032, Germany
| | - Lucila Saavedra
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, San Miguel de Tucumán, 4000, Argentina
| | - Elvira Maria Hebert
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, San Miguel de Tucumán, 4000, Argentina
| | - Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, Marburg, 35032, Germany
| | - Marcus Lechner
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, Marburg, 35032, Germany. .,Philipps-Universität Marburg, Center for Synthetic Microbiology (Synmikro), Hans-Meerwein-Straße 6, Marburg, 35043, Germany.
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Abstract
Since the nucleoid was isolated from bacteria in the 1970s, two fundamental questions emerged and are still in the spotlight: how bacteria organize their chromosomes to fit inside the cell and how nucleoid organization enables essential biological processes. During the last decades, knowledge of bacterial chromosome organization has advanced considerably, and today, such chromosomes are considered to be highly organized and dynamic structures that are shaped by multiple factors in a multiscale manner. Here we review not only the classical well-known factors involved in chromosome organization but also novel components that have recently been shown to dynamically shape the 3D structuring of the bacterial genome. We focus on the different functional elements that control short-range organization and describe how they collaborate in the establishment of the higher-order folding and disposition of the chromosome. Recent advances have opened new avenues for a deeper understanding of the principles and mechanisms of chromosome organization in bacteria. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France;
| | - Ivan Junier
- Université Grenoble Alpes, CNRS, TIMC-IMAG, 38000 Grenoble, France
| | - Frédéric Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France;
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Jain K, Wood EA, Romero ZJ, Cox MM. RecA-independent recombination: Dependence on the Escherichia coli RarA protein. Mol Microbiol 2021; 115:1122-1137. [PMID: 33247976 PMCID: PMC8160026 DOI: 10.1111/mmi.14655] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/29/2020] [Accepted: 11/20/2020] [Indexed: 11/30/2022]
Abstract
Most, but not all, homologous genetic recombination in bacteria is mediated by the RecA recombinase. The mechanistic origin of RecA-independent recombination has remained enigmatic. Here, we demonstrate that the RarA protein makes a major enzymatic contribution to RecA-independent recombination. In particular, RarA makes substantial contributions to intermolecular recombination and to recombination events involving relatively short (<200 bp) homologous sequences, where RecA-mediated recombination is inefficient. The effects are seen here in plasmid-based recombination assays and in vivo cloning processes. Vestigial levels of recombination remain even when both RecA and RarA are absent. Additional pathways for RecA-independent recombination, possibly mediated by helicases, are suppressed by exonucleases ExoI and RecJ. Translesion DNA polymerases may also contribute. Our results provide additional substance to a previous report of a functional overlap between RecA and RarA.
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Affiliation(s)
- Kanika Jain
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachary J Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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10
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The Role of Replication Clamp-Loader Protein HolC of Escherichia coli in Overcoming Replication/Transcription Conflicts. mBio 2021; 12:mBio.00184-21. [PMID: 33688004 PMCID: PMC8092217 DOI: 10.1128/mbio.00184-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, DNA replication is catalyzed by an assembly of proteins, the DNA polymerase III holoenzyme. This complex includes the polymerase and proofreading subunits, the processivity clamp, and clamp loader complex. The holC gene encodes an accessory protein (known as χ) to the core clamp loader complex and is the only protein of the holoenzyme that binds to single-strand DNA binding protein, SSB. HolC is not essential for viability, although mutants show growth impairment, genetic instability, and sensitivity to DNA damaging agents. In this study, we isolate spontaneous suppressor mutants in a ΔholC strain and identify these by whole-genome sequencing. Some suppressors are alleles of RNA polymerase, suggesting that transcription is problematic for holC mutant strains, or alleles of sspA, encoding stringent starvation protein. Using a conditional holC plasmid, we examine factors affecting transcription elongation and termination for synergistic or suppressive effects on holC mutant phenotypes. Alleles of RpoA (α), RpoB (β), and RpoC (β') RNA polymerase holoenzyme can partially suppress loss of HolC. In contrast, mutations in transcription factors DksA and NusA enhanced the inviability of holC mutants. HolC mutants showed enhanced sensitivity to bicyclomycin, a specific inhibitor of Rho-dependent termination. Bicyclomycin also reverses suppression of holC by rpoA, rpoC, and sspA An inversion of the highly expressed rrnA operon exacerbates the growth defects of holC mutants. We propose that transcription complexes block replication in holC mutants and that Rho-dependent transcriptional termination and DksA function are particularly important to sustain viability and chromosome integrity.IMPORTANCE Transcription elongation complexes present an impediment to DNA replication. We provide evidence that one component of the replication clamp loader complex, HolC, of Escherichia coli is required to overcome these blocks. This genetic study of transcription factor effects on holC growth defects implicates Rho-dependent transcriptional termination and DksA function as critical. It also implicates, for the first time, a role of SspA, stringent starvation protein, in avoidance or tolerance of replication/replication conflicts. We speculate that HolC helps avoid or resolve collisions between replication and transcription complexes, which become toxic in HolC's absence.
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11
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Sutera VA, Weeks SJ, Dudenhausen EE, Baggett HBR, Shaw MC, Brand KA, Glass DJ, Bloom LB, Lovett ST. Alternative complexes formed by the Escherichia coli clamp loader accessory protein HolC (x) with replication protein HolD (ψ) and repair protein YoaA. DNA Repair (Amst) 2021; 100:103006. [PMID: 33582602 DOI: 10.1016/j.dnarep.2020.103006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 10/22/2022]
Abstract
Efficient and faithful replication of DNA is essential for all organisms. However, the replication fork frequently encounters barriers that need to be overcome to ensure cell survival and genetic stability. Cells must carefully balance and regulate replication vs. repair reactions. In Escherichia coli, the replisome consists of the DNA polymerase III holoenzyme, including DNA polymerase, proofreading exonuclease, processivity clamp and clamp loader, as well as a fork helicase, DnaB and primase, DnaG. We provide evidence here that one component of the clamp loader complex, HolC (or χ) plays a dual role via its ability to form 2 mutually exclusive complexes: one with HolD (or ψ) that recruits the clamp-loader and hence the DNA polymerase holoenzyme and another with helicase-like YoaA protein, a DNA-damage inducible repair protein. By yeast 2 hybrid analysis, we show that two residues of HolC, F64 and W57, at the interface in the structure with HolD, are required for interaction with HolD and for interaction with YoaA. Mutation of these residues does not interfere with HolC's interaction with single-strand DNA binding protein, SSB. In vivo, these mutations fail to complement the poor growth and sensitivity to azidothymidine, a chain-terminating replication inhibitor. In support of the notion that these are exclusive complexes, co-expression of HolC, HolD and YoaA, followed by pulldown of YoaA, yields a complex with HolC but not HolD. YoaA fails to pulldown HolC-F64A. We hypothesize that HolC, by binding with SSB, can recruit the DNA polymerase III holoenzyme through HolD, or an alternative repair complex with YoaA helicase.
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Affiliation(s)
- Vincent A Sutera
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South St., Waltham, MA, 02453, United States
| | - Savannah J Weeks
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32610-0245, United States
| | - Elizabeth E Dudenhausen
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32610-0245, United States
| | - Helen B Rappe Baggett
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South St., Waltham, MA, 02453, United States
| | - McKay C Shaw
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South St., Waltham, MA, 02453, United States
| | - Kirsten A Brand
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South St., Waltham, MA, 02453, United States
| | - David J Glass
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South St., Waltham, MA, 02453, United States
| | - Linda B Bloom
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32610-0245, United States
| | - Susan T Lovett
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South St., Waltham, MA, 02453, United States.
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12
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Romero H, Serrano E, Hernández-Tamayo R, Carrasco B, Cárdenas PP, Ayora S, Graumann PL, Alonso JC. Bacillus subtilis RarA Acts as a Positive RecA Accessory Protein. Front Microbiol 2020; 11:92. [PMID: 32117122 PMCID: PMC7031210 DOI: 10.3389/fmicb.2020.00092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/16/2020] [Indexed: 01/15/2023] Open
Abstract
Ubiquitous RarA AAA+ ATPases play crucial roles in the cellular response to blocked replication forks in pro- and eukaryotes. Here, we provide evidence that absence of RarA reduced the viability of ΔrecA, ΔrecO, and recF15 cells during unperturbed growth. The rarA gene was epistatic to recO and recF genes in response to H2O2- or MMS-induced DNA damage. Conversely, the inactivation of rarA partially suppressed the HR defect of mutants lacking end-resection (ΔaddAB, ΔrecJ, ΔrecQ, ΔrecS) or branch migration (ΔruvAB, ΔrecG, ΔradA) activity. RarA contributes to RecA thread formation, that are thought to be the active forms of RecA during homology search. The absence of RarA reduced RecA accumulation, and the formation of visible RecA threads in vivo upon DNA damage. When ΔrarA was combined with mutations in genuine RecA accessory genes, RecA accumulation was further reduced in ΔrarA ΔrecU and ΔrarA ΔrecX double mutant cells, and was blocked in ΔrarA recF15 cells. These results suggest that RarA contributes to the assembly of RecA nucleoprotein filaments onto single-stranded DNA, and possibly antagonizes RecA filament disassembly.
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Affiliation(s)
- Hector Romero
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Paula P. Cárdenas
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Peter L. Graumann
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Juan C. Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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13
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Ramirez MS, Iriarte A, Reyes-Lamothe R, Sherratt DJ, Tolmasky ME. Small Klebsiella pneumoniae Plasmids: Neglected Contributors to Antibiotic Resistance. Front Microbiol 2019; 10:2182. [PMID: 31616398 PMCID: PMC6764390 DOI: 10.3389/fmicb.2019.02182] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Klebsiella pneumoniae is the causative agent of community- and, more commonly, hospital-acquired infections. Infections caused by this bacterium have recently become more dangerous due to the acquisition of multiresistance to antibiotics and the rise of hypervirulent variants. Plasmids usually carry genes coding for resistance to antibiotics or virulence factors, and the recent sequence of complete K. pneumoniae genomes showed that most strains harbor many of them. Unlike large plasmids, small, usually high copy number plasmids, did not attract much attention. However, these plasmids may include genes coding for specialized functions, such as antibiotic resistance, that can be expressed at high levels due to gene dosage effect. These genes may be part of mobile elements that not only facilitate their dissemination but also participate in plasmid evolution. Furthermore, high copy number plasmids may also play a role in evolution by allowing coexistence of mutated and non-mutated versions of a gene, which helps to circumvent the constraints imposed by trade-offs after certain genes mutate. Most K. pneumoniae plasmids 25-kb or smaller replicate by the ColE1-type mechanism and many of them are mobilizable. The transposon Tn1331 and derivatives were found in a high percentage of these plasmids. Another transposon that was found in representatives of this group is the bla KPC-containing Tn4401. Common resistance determinants found in these plasmids were aac(6')-Ib and genes coding for β-lactamases including carbapenemases.
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Affiliation(s)
- Maria S. Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Sciences, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, United States
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Universidad de la República de Uruguay, Montevideo, Uruguay
| | | | - David J. Sherratt
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Sciences, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, United States
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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14
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Midgley-Smith SL, Dimude JU, Rudolph CJ. A role for 3' exonucleases at the final stages of chromosome duplication in Escherichia coli. Nucleic Acids Res 2019; 47:1847-1860. [PMID: 30544222 PMCID: PMC6393302 DOI: 10.1093/nar/gky1253] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/25/2018] [Accepted: 12/06/2018] [Indexed: 11/13/2022] Open
Abstract
Chromosome duplication initiates via the assembly of replication fork complexes at defined origins, from where they proceed in opposite directions until they fuse with a converging fork. Recent work highlights that the completion of DNA replication is highly complex in both pro- and eukaryotic cells. In this study we have investigated how 3' and 5' exonucleases contribute towards the successful termination of chromosome duplication in Escherichia coli. We show that the absence of 3' exonucleases can trigger levels of over-replication in the termination area robust enough to allow successful chromosome duplication in the absence of oriC firing. Over-replication is completely abolished if replication fork complexes are prevented from fusing by chromosome linearization. Our data strongly support the idea that 3' flaps are generated as replication fork complexes fuse. In the absence of 3' exonucleases, such as ExoI, these 3' flaps can be converted into 5' flaps, which are degraded by 5' exonucleases, such as ExoVII and RecJ. Our data support the idea that multiple protein activities are required to process fork fusion intermediates. They highlight the complexity of fork fusions and further support the idea that the termination area evolved to contain fork fusion-mediated pathologies.
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Affiliation(s)
- Sarah L Midgley-Smith
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Juachi U Dimude
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Christian J Rudolph
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
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15
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Midgley-Smith SL, Dimude JU, Taylor T, Forrester NM, Upton AL, Lloyd RG, Rudolph CJ. Chromosomal over-replication in Escherichia coli recG cells is triggered by replication fork fusion and amplified if replichore symmetry is disturbed. Nucleic Acids Res 2019; 46:7701-7715. [PMID: 29982635 PMCID: PMC6125675 DOI: 10.1093/nar/gky566] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/13/2018] [Indexed: 01/04/2023] Open
Abstract
Chromosome duplication initiates via the assembly of replication forks at defined origins. Forks proceed in opposite directions until they fuse with a converging fork. Recent work highlights that fork fusions are highly choreographed both in pro- and eukaryotic cells. The circular Escherichia coli chromosome is replicated from a single origin (oriC), and a single fork fusion takes place in a specialised termination area opposite oriC that establishes a fork trap mediated by Tus protein bound at ter sequences that allows forks to enter but not leave. Here we further define the molecular details of fork fusions and the role of RecG helicase in replication termination. Our data support the idea that fork fusions have the potential to trigger local re-replication of the already replicated DNA. In ΔrecG cells this potential is realised in a substantial fraction of cells and is dramatically elevated when one fork is trapped for some time before the converging fork arrives. They also support the idea that the termination area evolved to contain such over-replication and we propose that the stable arrest of replication forks at ter/Tus complexes is an important feature that limits the likelihood of problems arising as replication terminates.
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Affiliation(s)
- Sarah L Midgley-Smith
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Juachi U Dimude
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Toni Taylor
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Nicole M Forrester
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Amy L Upton
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Robert G Lloyd
- Medical School, Queen's Medical Centre, Nottingham University, Nottingham NG7 2UH, UK
| | - Christian J Rudolph
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
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16
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Tomaska L, Nosek J, Kar A, Willcox S, Griffith JD. A New View of the T-Loop Junction: Implications for Self-Primed Telomere Extension, Expansion of Disease-Related Nucleotide Repeat Blocks, and Telomere Evolution. Front Genet 2019; 10:792. [PMID: 31475042 PMCID: PMC6702307 DOI: 10.3389/fgene.2019.00792] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022] Open
Abstract
Telomere loops (t-loops) are formed at the ends of chromosomes in species ranging from humans to worms, plants, and with genetic manipulation, some yeast. Recent in vitro studies demonstrated that transcription of telomeric DNA leads to highly efficient t-loop formation. It was also shown that both DNA termini are inserted into the preceding DNA to generate a highly stable t-loop junction. Furthermore, some telomeric RNA remains present at the junction, potentially acting as a plug to further protect and stabilize the t-loop. Modeling the loop junction reveals two mechanisms by which the canonical chromosomal replication factors could extend the telomere in the absence of telomerase. One mechanism would utilize the annealed 3’ terminus as a de novo replication origin. In vitro evidence for the ability of the t-loop to prime telomere extension using the T7 replication factors is presented. A second mechanism would involve resolution of the Holliday junction present in the t-loop bubble by factors such as GEN1 to generate a rolling circle template at the extreme terminus of the telomere. This could lead to large expansions of the telomeric tract. Here, we propose that telomeres evolved as terminal elements containing long arrays of short nucleotide repeats due to the ability of such arrays to fold back into loops and self-prime their replicative extension. In this view, telomerase may have evolved later to provide a more precise mechanism of telomere maintenance. Both pathways have direct relevance to the alternative lengthening of telomeres (ALT) pathway. This view also provides a possible mechanism for the very large repeat expansions observed in nucleotide repeat diseases such as Fragile X syndrome, myotonic dystrophy, familial amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). The evolution of telomeres is discussed in the framework of these models.
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Affiliation(s)
- Lubomir Tomaska
- Departments of Genetics and Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jozef Nosek
- Departments of Genetics and Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Anirban Kar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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17
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Wang J, Liu Y, Liu Y, Du K, Xu S, Wang Y, Krupovic M, Chen X. A novel family of tyrosine integrases encoded by the temperate pleolipovirus SNJ2. Nucleic Acids Res 2019; 46:2521-2536. [PMID: 29361162 PMCID: PMC5861418 DOI: 10.1093/nar/gky005] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/08/2018] [Indexed: 01/19/2023] Open
Abstract
Genomes of halophilic archaea typically contain multiple loci of integrated mobile genetic elements (MGEs). Despite the abundance of these elements, however, mechanisms underlying their site-specific integration and excision have not been investigated. Here, we identified and characterized a novel recombination system encoded by the temperate pleolipovirus SNJ2, which infects haloarchaeon Natrinema sp. J7-1. SNJ2 genome is inserted into the tRNAMet gene and flanked by 14 bp direct repeats corresponding to attachment core sites. We showed that SNJ2 encodes an integrase (IntSNJ2) that excises the proviral genome from its host cell chromosome, but requires two small accessory proteins, Orf2 and Orf3, for integration. These proteins were co-transcribed with IntSNJ2 to form an operon. Homology searches showed that IntSNJ2-type integrases are widespread in haloarchaeal genomes and are associated with various integrated MGEs. Importantly, we confirmed that SNJ2-like recombination systems are encoded by haloarchaea from three different genera and are critical for integration and excision. Finally, phylogenetic analysis suggested that IntSNJ2-type recombinases belong to a novel family of archaeal integrases distinct from previously characterized recombinases, including those from the archaeal SSV- and pNOB8-type families.
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Affiliation(s)
- Jiao Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yingchun Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ying Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, Paris 75015, France
| | - Kaixin Du
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shuqi Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yuchen Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mart Krupovic
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, Paris 75015, France
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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18
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Wong SM, Jackson MD, Akerley BJ. Suppression of Alternative Lipooligosaccharide Glycosyltransferase Activity by UDP-Galactose Epimerase Enhances Murine Lung Infection and Evasion of Serum IgM. Front Cell Infect Microbiol 2019; 9:160. [PMID: 31157175 PMCID: PMC6530457 DOI: 10.3389/fcimb.2019.00160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/29/2019] [Indexed: 01/17/2023] Open
Abstract
In pathogens that produce lipooligosaccharide (LOS), sugar residues within the surface-exposed LOS outer core mediate interactions with components of the host immune system, promoting bacterial infection. Many LOS structures are controlled by phase variation mediated by random slipped-strand base mispairing, which can reversibly switch gene expression on or off. Phase variation diversifies the LOS, however its adaptive role is not well-understood. Nontypeable Haemophilus influenzae (NTHi) is an important pathogen that causes a range of illnesses in the upper and lower respiratory tract. In NTHi a phase variable galactosyltransferase encoded by lic2A initiates galactose chain extension of the LOS outer core. The donor substrate for Lic2A, UDP-galactose, is generated from UDP-glucose by UDP-galactose epimerase encoded by galE. Our previous fitness profiling of H. influenzae mutants in a murine lung model showed that the galE mutant had a severe survival defect, while the lic2A mutant's defect was modest, leading us to postulate that unidentified factors act as suppressors of potential defects in a lic2A mutant. Herein we conducted a genome-wide genetic interaction screen to identify genes epistatic on lic2A for survival in the murine lung. An unexpected finding was that galE mutants exhibited restored virulence properties in a lic2A mutant background. We identified an alternative antibody epitope generated by Lic2A in the galE mutant that increased sensitivity to classical complement mediated killing in human serum. Deletion of lic2A or restoration of UDP-galactose synthesis alleviated the galE mutant's virulence defects. These studies indicate that when deprived of its galactosyl substrate, Lic2A acquires an alternative activity leading to increased recognition of NTHi by IgM and decreased survival in the lung model. Biofilm formation was increased by deletion of galE and by increased availability of UDP-GlcNAc precursors that can compete with UDP-galactose production. NTHi's ability to reversibly inactivate lic2A by phase-variation may influence survival in niches of infection in which UDP-Galactose levels are limiting.
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Affiliation(s)
- Sandy M Wong
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Mary Darby Jackson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Brian J Akerley
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
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19
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Romero H, Torres R, Hernández-Tamayo R, Carrasco B, Ayora S, Graumann PL, Alonso JC. Bacillus subtilis RarA acts at the interplay between replication and repair-by-recombination. DNA Repair (Amst) 2019; 78:27-36. [PMID: 30954900 DOI: 10.1016/j.dnarep.2019.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 02/20/2019] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
Abstract
Bacterial RarA is thought to play crucial roles in the cellular response to blocked replication forks. We show that lack of Bacillus subtilis RarA renders cells very sensitive to H2O2, but not to methyl methane sulfonate or 4-nitroquinoline-1-oxide. RarA is epistatic to RecA in response to DNA damage. Inactivation of rarA partially suppressed the DNA repair defect of mutants lacking translesion synthesis polymerases. RarA may contribute to error-prone DNA repair as judged by the reduced frequency of rifampicin-resistant mutants in ΔrarA and in ΔpolY1 ΔrarA cells. The absence of RarA strongly reduced the viability of dnaD23ts and dnaB37ts cells upon partial thermal inactivation, suggesting that ΔrarA cells are deficient in replication fork assembly. A ΔrarA mutation also partially reduced the viability of dnaC30ts and dnaX51ts cells and slightly improved the viability of dnaG40ts cells at semi-permissive temperature. These results suggest that RarA links re-initiation of DNA replication with repair-by-recombination by controlling the access of the replication machinery to a collapsed replication fork.
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Affiliation(s)
- Hector Romero
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain; SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043, Marburg, Germany; Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain
| | - Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043, Marburg, Germany; Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain
| | - Peter L Graumann
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043, Marburg, Germany; Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032, Marburg, Germany.
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain.
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20
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Romero H, Rösch TC, Hernández-Tamayo R, Lucena D, Ayora S, Alonso JC, Graumann PL. Single molecule tracking reveals functions for RarA at replication forks but also independently from replication during DNA repair in Bacillus subtilis. Sci Rep 2019; 9:1997. [PMID: 30760776 PMCID: PMC6374455 DOI: 10.1038/s41598-018-38289-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/18/2018] [Indexed: 12/19/2022] Open
Abstract
RarA is a widely conserved protein proposed to be involved in recombination-dependent replication. We present a cell biological approach to identify functional connections between RarA and other proteins using single molecule tracking. We found that 50% of RarA molecules were static, mostly close to replication forks and likely DNA-bound, while the remaining fraction was highly dynamic throughout the cells. RarA alternated between static and dynamic states. Exposure to H2O2 increased the fraction of dynamic molecules, but not treatment with mitomycin C or with methyl methanesulfonate, which was exacerbated by the absence of RecJ, RecD2, RecS and RecU proteins. The ratio between static and dynamic RarA also changed in replication temperature-sensitive mutants, but in opposite manners, dependent upon inhibition of DnaB or of DnaC (pre)primosomal proteins, revealing an intricate function related to DNA replication restart. RarA likely acts in the context of collapsed replication forks, as well as in conjunction with a network of proteins that affect the activity of the RecA recombinase. Our novel approach reveals intricate interactions of RarA, and is widely applicable for in vivo protein studies, to underpin genetic or biochemical connections, and is especially helpful for investigating proteins whose absence does not lead to any detectable phenotype.
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Affiliation(s)
- Hector Romero
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
- Department Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Cantoblanco, Madrid, Spain
| | - Thomas C Rösch
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Daniella Lucena
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Silvia Ayora
- Department Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Cantoblanco, Madrid, Spain
| | - Juan C Alonso
- Department Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Cantoblanco, Madrid, Spain.
| | - Peter L Graumann
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany.
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany.
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21
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Carrasco B, Seco EM, López-Sanz M, Alonso JC, Ayora S. Bacillus subtilis RarA modulates replication restart. Nucleic Acids Res 2018; 46:7206-7220. [PMID: 29947798 PMCID: PMC6101539 DOI: 10.1093/nar/gky541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/05/2018] [Indexed: 02/01/2023] Open
Abstract
The ubiquitous RarA/Mgs1/WRNIP protein plays a crucial, but poorly understood role in genome maintenance. We show that Bacillus subtilis RarA, in the apo form, preferentially binds single-stranded (ss) over double-stranded (ds) DNA. SsbA bound to ssDNA loads RarA, and for such recruitment the amphipathic C-terminal domain of SsbA is required. RarA is a DNA-dependent ATPase strongly stimulated by ssDNA–dsDNA junctions and SsbA, or by dsDNA ends. RarA, which may interact with PriA, does not stimulate PriA DNA unwinding. In a reconstituted PriA-dependent DNA replication system, RarA inhibited initiation, but not chain elongation. The RarA effect was not observed in the absence of SsbA, or when the host-encoded preprimosome and the DNA helicase are replaced by proteins from the SPP1 phage with similar function. We propose that RarA assembles at blocked forks to maintain genome integrity. Through its interaction with SsbA and with a preprimosomal component, RarA might impede the assembly of the replicative helicase, to prevent that recombination intermediates contribute to pathological DNA replication restart.
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Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - Elena M Seco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - María López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
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22
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Stanage TH, Page AN, Cox MM. DNA flap creation by the RarA/MgsA protein of Escherichia coli. Nucleic Acids Res 2017; 45:2724-2735. [PMID: 28053120 PMCID: PMC5389604 DOI: 10.1093/nar/gkw1322] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/19/2016] [Indexed: 11/24/2022] Open
Abstract
We identify a novel activity of the RarA (also MgsA) protein of Escherichia coli, demonstrating that this protein functions at DNA ends to generate flaps. A AAA+ ATPase in the clamp loader clade, RarA protein is part of a highly conserved family of DNA metabolism proteins. We demonstrate that RarA binds to double-stranded DNA in its ATP-bound state and single-stranded DNA in its apo state. RarA ATPase activity is stimulated by single-stranded DNA gaps and double-stranded DNA ends. At these double-stranded DNA ends, RarA couples the energy of ATP binding and hydrolysis to separating the strands of duplex DNA, creating flaps. We hypothesize that the creation of a flap at the site of a leading strand discontinuity could, in principle, allow DnaB and the associated replisome to continue DNA synthesis without impediment, with leading strand re-priming by DnaG. Replication forks could thus be rescued in a manner that does not involve replisome disassembly or reassembly, albeit with loss of one of the two chromosomal products of a replication cycle.
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Affiliation(s)
- Tyler H Stanage
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Asher N Page
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
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23
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Michel B, Sinha AK. The inactivation of rfaP, rarA or sspA gene improves the viability of the Escherichia coli DNA polymerase III holD mutant. Mol Microbiol 2017; 104:1008-1026. [PMID: 28342235 DOI: 10.1111/mmi.13677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 12/11/2022]
Abstract
The Escherichia coli holD mutant is poorly viable because the stability of holoenzyme polymerase III (Pol III HE) on DNA is compromised. Consequently, the SOS response is induced and the SOS polymerases DinB and Pol II further hinder replication. Mutations that restore the holD mutant viability belong to two classes, those that stabilize Pol III on DNA and those that prevent the deleterious effects of DinB over-production. We identified a dnaX mutation and the inactivation of rfaP and sspA genes as belonging to the first class of holD mutant suppressors. dnaX encodes a Pol III clamp loader subunit that interacts with HolD. rfaP encodes a lipopolysaccharide kinase that acts in outer membrane biogenesis. Its inactivation improves the holD mutant growth in part by affecting potassium import, previously proposed to stabilize Pol III HE on DNA by increasing electrostatic interactions. sspA encodes a global transcriptional regulator and growth of the holD mutant in its absence suggests that SspA controls genes that affect protein-DNA interactions. The inactivation of rarA belongs to the second class of suppressor mutations. rarA inactivation has a weak effect but is additive with other suppressor mutations. Our results suggest that RarA facilitates DinB binding to abandoned forks.
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Affiliation(s)
- Bénédicte Michel
- Genome Biology Department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Anurag Kumar Sinha
- Genome Biology Department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
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24
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Castillo F, Benmohamed A, Szatmari G. Xer Site Specific Recombination: Double and Single Recombinase Systems. Front Microbiol 2017; 8:453. [PMID: 28373867 PMCID: PMC5357621 DOI: 10.3389/fmicb.2017.00453] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/03/2017] [Indexed: 12/20/2022] Open
Abstract
The separation and segregation of newly replicated bacterial chromosomes can be constrained by the formation of circular chromosome dimers caused by crossing over during homologous recombination events. In Escherichia coli and most bacteria, dimers are resolved to monomers by site-specific recombination, a process performed by two Chromosomally Encoded tyrosine Recombinases (XerC and XerD). XerCD recombinases act at a 28 bp recombination site dif, which is located at the replication terminus region of the chromosome. The septal protein FtsK controls the initiation of the dimer resolution reaction, so that recombination occurs at the right time (immediately prior to cell division) and at the right place (cell division septum). XerCD and FtsK have been detected in nearly all sequenced eubacterial genomes including Proteobacteria, Archaea, and Firmicutes. However, in Streptococci and Lactococci, an alternative system has been found, composed of a single recombinase (XerS) genetically linked to an atypical 31 bp recombination site (difSL). A similar recombination system has also been found in 𝜀-proteobacteria such as Campylobacter and Helicobacter, where a single recombinase (XerH) acts at a resolution site called difH. Most Archaea contain a recombinase called XerA that acts on a highly conserved 28 bp sequence dif, which appears to act independently of FtsK. Additionally, several mobile elements have been found to exploit the dif/Xer system to integrate their genomes into the host chromosome in Vibrio cholerae, Neisseria gonorrhoeae, and Enterobacter cloacae. This review highlights the versatility of dif/Xer recombinase systems in prokaryotes and summarizes our current understanding of homologs of dif/Xer machineries.
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Affiliation(s)
- Fabio Castillo
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
| | | | - George Szatmari
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
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25
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Puentes B, Balado M, Bermúdez-Crespo J, Osorio CR, Lemos ML. A proteomic analysis of the iron response of Photobacterium damselae subsp. damselae reveals metabolic adaptations to iron levels changes and novel potential virulence factors. Vet Microbiol 2017; 201:257-264. [PMID: 28284618 DOI: 10.1016/j.vetmic.2017.01.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/13/2016] [Accepted: 01/23/2017] [Indexed: 11/29/2022]
Abstract
Photobacterium damselae subsp. damselae (Pdd) is a marine bacterium that can infect numerous species of marine fish as well as other species including humans. Low iron availability is one of the signs that bacterial pathogens can detect in order to begin colonizing their host, and the reduction of iron levels is a nonspecific host defense strategy that prevents bacterial proliferation. In this work a proteomic approach was used to study the gene expression adaptations of a Pdd strain in response to iron availability. A comparative analysis of induced proteins in both high- and low-iron conditions showed profound cellular metabolic adaptations that result, for instance, in amino acid requirement. It also provided important information about the changes that occur in the energetic metabolism induced by the surrounding iron levels, allowing for the identification of novel potential virulence factors. Among others, genes involved in the synthesis and transport of a vibrioferrin-like siderophore were identified for the first time. In addition to plasmid pPHDD1-encoded Dly and HlyA hemolysins, a pPHDD1-borne operon, which may encode a transferrin receptor, was also found. This operon identification suggests that this virulence plasmid could encode so-far unknown additional virulence factors other than hemolysins.
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Affiliation(s)
- Beatriz Puentes
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - Miguel Balado
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - José Bermúdez-Crespo
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - Carlos R Osorio
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - Manuel L Lemos
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain.
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26
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Bebel A, Karaca E, Kumar B, Stark WM, Barabas O. Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending. eLife 2016; 5. [PMID: 28009253 PMCID: PMC5241119 DOI: 10.7554/elife.19706] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/21/2016] [Indexed: 02/06/2023] Open
Abstract
Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicobacter pylori XerH with its recombination site DNA difH, representing pre-cleavage and post-cleavage synaptic intermediates in the recombination pathway. The structures reveal that activation of DNA strand cleavage and rejoining involves large conformational changes and DNA bending, suggesting how interaction with the cell division protein FtsK may license recombination at the septum. Together with biochemical and in vivo analysis, our structures also reveal how a small sequence asymmetry in difH defines protein conformation in the synaptic complex and orchestrates the order of DNA strand exchanges. Our results provide insights into the catalytic mechanism of Xer recombination and a model for regulation of recombination activity during cell division. DOI:http://dx.doi.org/10.7554/eLife.19706.001 Similar to humans, bacteria store their genetic material in the form of DNA and arrange it into structures called chromosomes. In fact, most bacteria have a single circular chromosome. Bacteria multiply by simply dividing in two, and before that happens they must replicate their DNA so that each of the newly formed cells receives one copy of the chromosome. Occasionally, mistakes during the DNA replication process can cause the two chromosomes to become tangled with each other; this prevents them from separating into the newly formed cells. For instance, the chromosomes can become physically connected like links in a chain, or merge into one long string. This kind of tangling can result in cell death, so bacteria encode enzymes called Xer recombinases that can untangle chromosomes. These enzymes separate the chromosomes by cutting and rejoining the DNA strands in a process known as Xer recombination. Although Xer recombinases have been studied in quite some detail, many questions remain unanswered about how they work. How do Xer recombinases interact with DNA? How do they ensure they only work on tangled chromosomes? And how does a protein called FtsK ensure that Xer recombination takes place at the correct time and place? Bebel et al. have now studied the Xer recombinase from a bacterium called Helicobacter pylori, which causes stomach ulcers, using a technique called X-ray crystallography. This enabled the three-dimensional structure of the Xer recombinase to be visualized as it interacted with DNA to form a Xer-DNA complex. Structures of the enzyme before and after it cut the DNA show that Xer-DNA complexes first assemble in an inactive state and are then activated by large conformational changes that make the DNA bend. Bebel et al. propose that the FtsK protein might trigger these changes and help to bend the DNA as it activates Xer recombination. Further work showed that the structures could be used to model and understand Xer recombinases from other species of bacteria. The next step is to analyze how FtsK activates Xer recombinases and to see if this process is universal amongst bacteria. Understanding how this process can be interrupted could help to develop new drugs that can kill harmful bacteria. DOI:http://dx.doi.org/10.7554/eLife.19706.002
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Affiliation(s)
- Aleksandra Bebel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ezgi Karaca
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Banushree Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - W Marshall Stark
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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27
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Abstract
Cre-lox of bacteriophage P1 has become one of the most widely used tools for genetic engineering in eukaryotes. The origins of this tool date to more than 30 years ago when Nat L. Sternberg discovered the recombinase, Cre, and its specific locus of crossover, lox, while studying the maintenance of bacteriophage P1 as a stable plasmid. Recombinations mediated by Cre assist in cyclization of the DNA of infecting phage and in resolution of prophage multimers created by generalized recombination. Early in vitro work demonstrated that, although it shares similarities with the well-characterized bacteriophage λ integration, Cre-lox is in many ways far simpler in its requirements for carrying out recombination. These features would prove critical for its development as a powerful and versatile tool in genetic engineering. We review the history of the discovery and characterization of Cre-lox and touch upon the present direction of Cre-lox research.
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Affiliation(s)
- Michael Yarmolinsky
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892;
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28
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Dimude JU, Midgley-Smith SL, Stein M, Rudolph CJ. Replication Termination: Containing Fork Fusion-Mediated Pathologies in Escherichia coli. Genes (Basel) 2016; 7:genes7080040. [PMID: 27463728 PMCID: PMC4999828 DOI: 10.3390/genes7080040] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/12/2016] [Accepted: 07/19/2016] [Indexed: 01/18/2023] Open
Abstract
Duplication of bacterial chromosomes is initiated via the assembly of two replication forks at a single defined origin. Forks proceed bi-directionally until they fuse in a specialised termination area opposite the origin. This area is flanked by polar replication fork pause sites that allow forks to enter but not to leave. The precise function of this replication fork trap has remained enigmatic, as no obvious phenotypes have been associated with its inactivation. However, the fork trap becomes a serious problem to cells if the second fork is stalled at an impediment, as replication cannot be completed, suggesting that a significant evolutionary advantage for maintaining this chromosomal arrangement must exist. Recently, we demonstrated that head-on fusion of replication forks can trigger over-replication of the chromosome. This over-replication is normally prevented by a number of proteins including RecG helicase and 3’ exonucleases. However, even in the absence of these proteins it can be safely contained within the replication fork trap, highlighting that multiple systems might be involved in coordinating replication fork fusions. Here, we discuss whether considering the problems associated with head-on replication fork fusion events helps us to better understand the important role of the replication fork trap in cellular metabolism.
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Affiliation(s)
- Juachi U Dimude
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
| | - Sarah L Midgley-Smith
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
| | - Monja Stein
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
| | - Christian J Rudolph
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
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29
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XerC Contributes to Diverse Forms of Staphylococcus aureus Infection via agr-Dependent and agr-Independent Pathways. Infect Immun 2016; 84:1214-1225. [PMID: 26857575 DOI: 10.1128/iai.01462-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/02/2016] [Indexed: 02/06/2023] Open
Abstract
We demonstrate that mutation of xerC, which reportedly encodes a homologue of an Escherichia coli recombinase, limits biofilm formation in the methicillin-resistant Staphylococcus aureus strain LAC and the methicillin-sensitive strain UAMS-1. This was not due to the decreased production of the polysaccharide intracellular adhesin (PIA) in either strain because the amount of PIA was increased in a UAMS-1xerC mutant and undetectable in both LAC and its isogenic xerC mutant. Mutation of xerC also resulted in the increased production of extracellular proteases and nucleases in both LAC and UAMS-1, and limiting the production of either class of enzymes increased biofilm formation in the isogenic xerC mutants. More importantly, the limited capacity to form a biofilm was correlated with increased antibiotic susceptibility in both strains in the context of an established biofilm in vivo. Mutation of xerC also attenuated virulence in a murine bacteremia model, as assessed on the basis of the bacterial loads in internal organs and overall lethality. It also resulted in the decreased accumulation of alpha toxin and the increased accumulation of protein A. These findings suggest that xerC may impact the functional status of agr. This was confirmed by demonstrating the reduced accumulation of RNAIII and AgrA in LAC and UAMS-1xerC mutants. However, this cannot account for the biofilm-deficient phenotype of xerC mutants because mutation of agr did not limit biofilm formation in either strain. These results demonstrate that xerC contributes to biofilm-associated infections and acute bacteremia and that this is likely due to agr-independent and -dependent pathways, respectively.
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30
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Xer Site-Specific Recombination: Promoting Vertical and Horizontal Transmission of Genetic Information. Microbiol Spectr 2016; 2. [PMID: 26104463 DOI: 10.1128/microbiolspec.mdna3-0056-2014] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Two related tyrosine recombinases, XerC and XerD, are encoded in the genome of most bacteria where they serve to resolve dimers of circular chromosomes by the addition of a crossover at a specific site, dif. From a structural and biochemical point of view they belong to the Cre resolvase family of tyrosine recombinases. Correspondingly, they are exploited for the resolution of multimers of numerous plasmids. In addition, they are exploited by mobile DNA elements to integrate into the genome of their host. Exploitation of Xer is likely to be advantageous to mobile elements because the conservation of the Xer recombinases and of the sequence of their chromosomal target should permit a quite easy extension of their host range. However, it requires means to overcome the cellular mechanisms that normally restrict recombination to dif sites harbored by a chromosome dimer and, in the case of integrative mobile elements, to convert dedicated tyrosine resolvases into integrases.
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31
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Abstract
One of the disadvantages of circular plasmids and chromosomes is their high sensitivity to rearrangements caused by homologous recombination. Odd numbers of crossing-over occurring during or after replication of a circular replicon result in the formation of a dimeric molecule in which the two copies of the replicon are fused. If they are not converted back to monomers, the dimers of replicons may fail to correctly segregate at the time of cell division. Resolution of multimeric forms of circular plasmids and chromosomes is mediated by site-specific recombination, and the enzymes that catalyze this type of reaction fall into two families of proteins: the serine and tyrosine recombinase families. Here we give an overview of the variety of site-specific resolution systems found on circular plasmids and chromosomes.
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32
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Abstract
About a decade ago, I proposed that t-loops, the lariat structures adopted by many eukaryotic telomeres, could explain how the transition from circular to linear chromosomes was successfully negotiated by early eukaryotes. Here I reconsider this loopy hypothesis in the context of the idea that eukaryotes evolved through a period of genome invasion by Group II introns.
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Affiliation(s)
- Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University , New York, NY, USA
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33
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Quantitative genomic analysis of RecA protein binding during DNA double-strand break repair reveals RecBCD action in vivo. Proc Natl Acad Sci U S A 2015; 112:E4735-42. [PMID: 26261330 PMCID: PMC4553759 DOI: 10.1073/pnas.1424269112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Understanding molecular mechanisms in the context of living cells requires the development of new methods of in vivo biochemical analysis to complement established in vitro biochemistry. A critically important molecular mechanism is genetic recombination, required for the beneficial reassortment of genetic information and for DNA double-strand break repair (DSBR). Central to recombination is the RecA (Rad51) protein that assembles into a spiral filament on DNA and mediates genetic exchange. Here we have developed a method that combines chromatin immunoprecipitation with next-generation sequencing (ChIP-Seq) and mathematical modeling to quantify RecA protein binding during the active repair of a single DSB in the chromosome of Escherichia coli. We have used quantitative genomic analysis to infer the key in vivo molecular parameters governing RecA loading by the helicase/nuclease RecBCD at recombination hot-spots, known as Chi. Our genomic analysis has also revealed that DSBR at the lacZ locus causes a second RecBCD-mediated DSBR event to occur in the terminus region of the chromosome, over 1 Mb away.
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34
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Huo YJ, Qiao L, Zheng XW, Cui C, Ma YF, Lu F. MreBCD-associated Cytoskeleton is Required for Proper Segregation of the Chromosomal Terminus during the Division Cycle of Escherichia Coli. Chin Med J (Engl) 2015; 128:1209-14. [PMID: 25947405 PMCID: PMC4831549 DOI: 10.4103/0366-6999.156131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background: In prokaryotic organisms, the mechanism responsible for the accurate partition of newly replicated chromosomes into daughter cells is incompletely understood. Segregation of the replication terminus of the circular prokaryotic chromosome poses special problems that have not previously been addressed. The aim of this study was to investigate the roles of several protein components (MreB, MreC, and MreD) of the prokaryotic cytoskeleton for the faithful transmission of the chromosomal terminus into daughter cells. Methods: Strain LQ1 (mreB::cat), LQ2 (mreC::cat), and LQ3 (mreD::cat) were constructed using the Red recombination system. LQ11/pLAU53, LQ12/pLAU53, LQ13/pLAU53, LQ14/pLAU53, and LQ15/pLAU53 strains were generated by P1transduction of (tetO)240-Gm and (lacO)240-Km cassettes from strains IL2 and IL29. Fluorescence microscopy was performed to observe localization pattern of fluorescently-labeled origin and terminus foci in wild-type and mutant cells. SOS induction was monitored as gfp fluorescence from PsulA-gfp in log phase cells grown in Luria-Bertani medium at 37°C by measurement of emission at 525 nm with excitation at 470 nm in a microplate fluorescence reader. Results: Mutational deletion of the mreB, mreC, or mreD genes was associated with selective loss of the terminus region in approximately 40% of the cells within growing cultures. This was accompanied by significant induction of the SOS DNA damage response, suggesting that deletion of terminus sequences may have occurred by chromosomal cleavage, presumably caused by ingrowth of the division septum prior to segregation of the replicated terminal. Conclusions: These results imply a role for the MreBCD cytoskeleton in the resolution of the final products of terminus replication and/or in the specific movement of newly replicated termini away from midcell prior to completion of septal ingrowth. This would identify a previously unrecognized stage in the overall process of chromosome segregation.
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Affiliation(s)
| | | | | | | | | | - Feng Lu
- Henan Engineering Laboratory of Antibody Medicine, Medical School of Henan University, Kaifeng, Henan 475001, China
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35
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Kono N, Arakawa K, Sato M, Yoshikawa H, Tomita M, Itaya M. Undesigned selection for replication termination of bacterial chromosomes. J Mol Biol 2014; 426:2918-27. [PMID: 24946150 DOI: 10.1016/j.jmb.2014.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/09/2014] [Accepted: 06/09/2014] [Indexed: 11/15/2022]
Abstract
The oriC DNA replication origin in bacterial chromosomes, the location of which appears to be physically identified, is genetically regulated by relevant molecular machinery. In contrast, the location of the terminus remains obscure for many bacterial replicons, except for terC, the proposed and well-studied chromosome termination site in certain bacteria. The terC locus, which is composed of specific sequences for its binding protein, is located at a site opposite from oriC, exhibiting a symmetric structure around the oriC-terC axis. Here, we investigated Bacillus subtilis 168 strains whose axes were hindered and found that the native terC function was robust. However, eradication of terminus region specific binding protein resulted in the natural terC sites not being used for termination; instead, new termini were selected at a location exactly opposite to oriC. We concluded that replication generally terminates at the loci where the two approaching replisomes meet. This site was automatically selected, and two replisomes moving at the same rate supported symmetrical chromosome structures relative to oriC. The rule, which was even validated by artificial chromosomes irrespective of oriC, should be general for replicons administered by two replisomes.
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Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, Yamagata 997-0017, Japan.
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Yamagata 997-0017, Japan
| | - Mitsuru Sato
- Institute for Advanced Biosciences, Keio University, Yamagata 997-0017, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Yamagata 997-0017, Japan
| | - Mitsuhiro Itaya
- Institute for Advanced Biosciences, Keio University, Yamagata 997-0017, Japan.
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36
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Warth L, Altenbuchner J. The tyrosine recombinase MrpA and its target sequence: a mutational analysis of the recombination site mrpS resulting in a new left element/right element (LE/RE) deletion system. Arch Microbiol 2013; 195:617-36. [PMID: 23861149 DOI: 10.1007/s00203-013-0910-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 06/06/2013] [Accepted: 06/22/2013] [Indexed: 11/28/2022]
Abstract
MrpA is the multimer resolution protein of the Streptomyces coelicolor A3(2) plasmid SCP2*. Previously, MrpA was found to be a site-specific tyrosine recombinase that acts with the 36-bp recombination site mrpS. The present report gives a comprehensive characterization of the composition as well as the position of the spacer and MrpA binding sites within mrpS. Experiments revealed a spacer consisting of 6 remarkably variable nucleotides in the middle of the mrpS-site. A reduction in the spacer to 5 nucleotides abolished recombination. Investigation of the MrpA binding sites showed the importance of its 15 nucleotides on an effective recombination. Among almost randomly exchangeable nucleotides, two nucleotides were identified as essential for MrpA binding. Alteration of either of these nucleotides led to a reduction in MrpA binding down to 2 % or even to no binding. Based on these results, a new left element/right element (LE/RE) deletion system was developed. The constructed heteromeric mrpS-sites are efficiently resolved by MrpA. The resulting double mutated (LE/RE) site can no longer be used as a recombination site by MrpA. The system has been successfully applied for the generation of multiple-targeted deletions in the genome of E. coli.
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Affiliation(s)
- Lydia Warth
- Institut für Industrielle Genetik, Universität Stuttgart, Germany
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37
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Pereira AR, Reed P, Veiga H, Pinho MG. The Holliday junction resolvase RecU is required for chromosome segregation and DNA damage repair in Staphylococcus aureus. BMC Microbiol 2013; 13:18. [PMID: 23356868 PMCID: PMC3584850 DOI: 10.1186/1471-2180-13-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 01/17/2013] [Indexed: 11/24/2022] Open
Abstract
Background The Staphylococcus aureus RecU protein is homologous to a Bacillus subtilis Holliday junction resolvase. Interestingly, RecU is encoded in the same operon as PBP2, a penicillin-binding protein required for cell wall synthesis and essential for the full expression of resistance in Methicillin Resistant S. aureus strains. In this work we have studied the role of RecU in the clinical pathogen S. aureus. Results Depletion of RecU in S. aureus results in the appearance of cells with compact nucleoids, septa formed over the DNA and anucleate cells. RecU-depleted cells also show increased septal recruitment of the DNA translocase SpoIIIE, presumably to resolve chromosome segregation defects. Additionally cells are more sensitive to DNA damaging agents such as mitomycin C or UV radiation. Expression of RecU from the ectopic chromosomal spa locus showed that co-expression of RecU and PBP2 was not necessary to ensure correct cell division, a process that requires tight coordination between chromosome segregation and septal cell wall synthesis. Conclusions RecU is required for correct chromosome segregation and DNA damage repair in S. aureus. Co-expression of recU and pbp2 from the same operon is not required for normal cell division.
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Affiliation(s)
- Ana R Pereira
- Laboratory of Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av, da República, Oeiras 2780-157, Portugal
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Fission yeast RecQ helicase Rqh1 is required for the maintenance of circular chromosomes. Mol Cell Biol 2013; 33:1175-87. [PMID: 23297345 DOI: 10.1128/mcb.01713-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Protection of telomeres protein 1 (Pot1) binds to single-stranded telomere overhangs and protects chromosome ends. RecQ helicases regulate homologous recombination at multiple stages, including resection, strand displacement, and resolution. Fission yeast pot1 and RecQ helicase rqh1 double mutants are synthetically lethal, but the mechanism is not fully understood. Here, we show that the synthetic lethality of pot1Δ rqh1Δ double mutants is due to inappropriate homologous recombination, as it is suppressed by the deletion of rad51(+). The expression of Rad51 in the pot1Δ rqh1Δ rad51Δ triple mutant, which has circular chromosomes, is lethal. Reduction of the expression of Rqh1 in a pot1 disruptant with circular chromosomes caused chromosome missegregation, and this defect was partially suppressed by the deletion of rad51(+). Taken together, our results suggest that Rqh1 is required for the maintenance of circular chromosomes when homologous recombination is active. Crossovers between circular monomeric chromosomes generate dimers that cannot segregate properly in Escherichia coli. We propose that Rqh1 inhibits crossovers between circular monomeric chromosomes to suppress the generation of circular dimers.
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Abstract
Homologous recombination is an ubiquitous process that shapes genomes and repairs DNA damage. The reaction is classically divided into three phases: presynaptic, synaptic, and postsynaptic. In Escherichia coli, the presynaptic phase involves either RecBCD or RecFOR proteins, which act on DNA double-stranded ends and DNA single-stranded gaps, respectively; the central synaptic steps are catalyzed by the ubiquitous DNA-binding protein RecA; and the postsynaptic phase involves either RuvABC or RecG proteins, which catalyze branch-migration and, in the case of RuvABC, the cleavage of Holliday junctions. Here, we review the biochemical properties of these molecular machines and analyze how, in light of these properties, the phenotypes of null mutants allow us to define their biological function(s). The consequences of point mutations on the biochemical properties of recombination enzymes and on cell phenotypes help refine the molecular mechanisms of action and the biological roles of recombination proteins. Given the high level of conservation of key proteins like RecA and the conservation of the principles of action of all recombination proteins, the deep knowledge acquired during decades of studies of homologous recombination in bacteria is the foundation of our present understanding of the processes that govern genome stability and evolution in all living organisms.
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Abstract
The role of bacteriophages as natural vectors for some of the most potent bacterial toxins is well recognized and includes classical type I membrane-acting superantigens, type II pore-forming lysins, and type III exotoxins, such as diphtheria and botulinum toxins. Among Gram-negative pathogens, a novel class of bacterial virulence factors called effector proteins (EPs) are phage encoded among pathovars of Escherichia coli, Shigella spp., and Salmonella enterica. This chapter gives an overview of the different types of virulence factors encoded within phage genomes based on their role in bacterial pathogenesis. It also discusses phage-pathogenicity island interactions uncovered from studies of phage-encoded EPs. A detailed examination of the filamentous phage CTXφ that encodes cholera toxin is given as the sole example to date of a single-stranded DNA phage that encodes a bacterial toxin.
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Page AN, George NP, Marceau AH, Cox MM, Keck JL. Structure and biochemical activities of Escherichia coli MgsA. J Biol Chem 2011; 286:12075-85. [PMID: 21297161 PMCID: PMC3069411 DOI: 10.1074/jbc.m110.210187] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 01/14/2011] [Indexed: 11/06/2022] Open
Abstract
Bacterial "maintenance of genome stability protein A" (MgsA) and related eukaryotic enzymes play important roles in cellular responses to stalled DNA replication processes. Sequence information identifies MgsA enzymes as members of the clamp loader clade of AAA+ proteins, but structural information defining the family has been limited. Here, the x-ray crystal structure of Escherichia coli MgsA is described, revealing a homotetrameric arrangement for the protein that distinguishes it from other clamp loader clade AAA+ proteins. Each MgsA protomer is composed of three elements as follows: ATP-binding and helical lid domains (conserved among AAA+ proteins) and a tetramerization domain. Although the tetramerization domains bury the greatest amount of surface area in the MgsA oligomer, each of the domains participates in oligomerization to form a highly intertwined quaternary structure. Phosphate is bound at each AAA+ ATP-binding site, but the active sites do not appear to be in a catalytically competent conformation due to displacement of Arg finger residues. E. coli MgsA is also shown to form a complex with the single-stranded DNA-binding protein through co-purification and biochemical studies. MgsA DNA-dependent ATPase activity is inhibited by single-stranded DNA-binding protein. Together, these structural and biochemical observations provide insights into the mechanisms of MgsA family AAA+ proteins.
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Affiliation(s)
- Asher N. Page
- From the Department of Biochemistry, University of Wisconsin and
| | - Nicholas P. George
- the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Aimee H. Marceau
- the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Michael M. Cox
- From the Department of Biochemistry, University of Wisconsin and
| | - James L. Keck
- the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
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42
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Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol 2011; 79:484-502. [PMID: 21219465 PMCID: PMC3071548 DOI: 10.1111/j.1365-2958.2010.07465.x] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes. Cas1 is a CRISPR-associated protein that is common to all CRISPR-containing prokaryotes but its function remains obscure. Here we show that the purified Cas1 protein of Escherichia coli (YgbT) exhibits nuclease activity against single-stranded and branched DNAs including Holliday junctions, replication forks and 5'-flaps. The crystal structure of YgbT and site-directed mutagenesis have revealed the potential active site. Genome-wide screens show that YgbT physically and genetically interacts with key components of DNA repair systems, including recB, recC and ruvB. Consistent with these findings, the ygbT deletion strain showed increased sensitivity to DNA damage and impaired chromosomal segregation. Similar phenotypes were observed in strains with deletion of CRISPR clusters, suggesting that the function of YgbT in repair involves interaction with the CRISPRs. These results show that YgbT belongs to a novel, structurally distinct family of nucleases acting on branched DNAs and suggest that, in addition to antiviral immunity, at least some components of the CRISPR-Cas system have a function in DNA repair.
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Affiliation(s)
- Mohan Babu
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Natalia Beloglazova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Robert Flick
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Chris Graham
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Tatiana Skarina
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
| | - Alla Gagarinova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Oxana Pogoutse
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Greg Brown
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Andrew Binkowski
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
| | - Sadhna Phanse
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Alexei Savchenko
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Jack Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Aled M. Edwards
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Alexander F. Yakunin
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
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Tomioka N, Morita K, Kobayashi N, Tada M, Itoh T, Saitoh S, Kondo M, Takahashi N, Kataoka A, Nakanishi K, Takahashi M, Kamiyama T, Ozaki M, Hirano T, Todo S. Array comparative genomic hybridization analysis revealed four genomic prognostic biomarkers for primary gastric cancers. ACTA ACUST UNITED AC 2010; 201:6-14. [PMID: 20633762 DOI: 10.1016/j.cancergencyto.2010.04.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Revised: 03/29/2010] [Accepted: 04/21/2010] [Indexed: 12/14/2022]
Abstract
Unlike the case with some other solid tumors, whole genome array screening has not revealed prognostic genetic aberrations in primary gastric cancer. Comparative genomic hybridization (CGH) using bacterial artificial chromosome (BAC) arrays for 56 primary gastric cancers resulted in identification of four prognostic loci in this study: 6q21 (harboring FOXO3A; previously FKHRL1), 9q32 (UGCG), 17q21.1 approximately q21.2 (CASC3), and 17q21.32 (HOXB3 through HOXB9). If any one of these four loci was deleted, the prognosis of the patient was significantly worse (P = 0.0019). This was true even for advanced tumors (stage IIIA, IIB, or IV, n = 39) (P = 0.0113), whereas only 1 of the 17 patients with less advanced tumors (stage IA, IB, or II; n = 17) died of disease after surgery. Multivariate analysis according to the status of four BACs or pathological stage based on the Japanese Classification of Gastric Carcinoma (stages IA, IB, and II vs. stages IIIA, IIIB, and IV) demonstrated that the BAC clone status was also an independent prognostic factor (P = 0.006). These findings may help predict which patients with malignant potential need more intensive therapy, or may point to new therapeutic approaches especially for advanced tumors. The parameter here termed the integrated genomic prognostic biomarker may therefore be of clinical utility as a prognostic biomarker.
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Affiliation(s)
- Nobumoto Tomioka
- Department of General Surgery, Hokkaido University Graduate School of Medicine, N-15 W-7 Kita-ku, Sapporo, Japan.
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Imanian B, Pombert JF, Keeling PJ. The complete plastid genomes of the two 'dinotoms' Durinskia baltica and Kryptoperidinium foliaceum. PLoS One 2010; 5:e10711. [PMID: 20502706 PMCID: PMC2873285 DOI: 10.1371/journal.pone.0010711] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 04/23/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In one small group of dinoflagellates, photosynthesis is carried out by a tertiary endosymbiont derived from a diatom, giving rise to a complex cell that we collectively refer to as a 'dinotom'. The endosymbiont is separated from its host by a single membrane and retains plastids, mitochondria, a large nucleus, and many other eukaryotic organelles and structures, a level of complexity suggesting an early stage of integration. Although the evolution of these endosymbionts has attracted considerable interest, the plastid genome has not been examined in detail, and indeed no tertiary plastid genome has yet been sequenced. METHODOLOGY/PRINCIPAL FINDINGS Here we describe the complete plastid genomes of two closely related dinotoms, Durinskia baltica and Kryptoperidinium foliaceum. The D. baltica (116470 bp) and K. foliaceum (140426 bp) plastid genomes map as circular molecules featuring two large inverted repeats that separate distinct single copy regions. The organization and gene content of the D. baltica plastid closely resemble those of the pennate diatom Phaeodactylum tricornutum. The K. foliaceum plastid genome is much larger, has undergone more reorganization, and encodes a putative tyrosine recombinase (tyrC) also found in the plastid genome of the heterokont Heterosigma akashiwo, and two putative serine recombinases (serC1 and serC2) homologous to recombinases encoded by plasmids pCf1 and pCf2 in another pennate diatom, Cylindrotheca fusiformis. The K. foliaceum plastid genome also contains an additional copy of serC1, two degenerate copies of another plasmid-encoded ORF, and two non-coding regions whose sequences closely resemble portions of the pCf1 and pCf2 plasmids. CONCLUSIONS/SIGNIFICANCE These results suggest that while the plastid genomes of two dinotoms share very similar gene content and genome organization with that of the free-living pennate diatom P. tricornutum, the K. folicaeum plastid genome has absorbed two exogenous plasmids. Whether this took place before or after the tertiary endosymbiosis is not clear.
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Affiliation(s)
- Behzad Imanian
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jean-François Pombert
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Efficiency and specificity of CTXphi chromosomal integration: dif makes all the difference. Proc Natl Acad Sci U S A 2010; 107:3951-2. [PMID: 20197438 DOI: 10.1073/pnas.1000310107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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46
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A role for recombination in centromere function. Trends Genet 2010; 26:209-13. [PMID: 20382440 DOI: 10.1016/j.tig.2010.02.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 11/20/2022]
Abstract
Centromeres are essential for chromosome segregation during both mitosis and meiosis. There are no obvious or conserved DNA sequence motif determinants for centromere function, but the complex centromeres found in the majority of eukaryotes studied to date consist of repetitive DNA sequences. A striking feature of these repeats is that they maintain a high level of inter-repeat sequence identity within the centromere. This observation is suggestive of a recombination mechanism that operates at centromeres. Here we postulate that inter-repeat homologous recombination plays an intrinsic role in centromere function by forming covalently closed DNA loops. Moreover, the model provides an explanation of why both inverted and direct repeats are maintained and how they contribute to centromere function.
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Chittela RK, Sainis JK. Plant DNA recombinases: a long way to go. J Nucleic Acids 2009; 2010. [PMID: 20798837 PMCID: PMC2925088 DOI: 10.4061/2010/646109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 09/08/2009] [Indexed: 01/12/2023] Open
Abstract
DNA homologous recombination is fundamental process by which two homologous DNA molecules exchange the genetic information for the generation of genetic diversity and maintain the genomic integrity. DNA recombinases, a special group of proteins bind to single stranded DNA (ssDNA) nonspecifically and search the double stranded DNA (dsDNA) molecule for a stretch of DNA that is homologous with the bound ssDNA. Recombinase A (RecA) has been well characterized at genetic, biochemical, as well as structural level from prokaryotes. Two homologues of RecA called Rad51 and Dmc1 have been detected in yeast and higher eukaryotes and are known to mediate the homologous recombination in eukaryotes. The biochemistry and mechanism of action of recombinase is important in understanding the process of homologous recombination. Even though considerable progress has been made in yeast and human recombinases, understanding of the plant recombination and recombinases is at nascent stage. Since crop plants are subjected to different breeding techniques, it is important to know the homologous recombination process. This paper focuses on the properties of eukaryotes recombinases and recent developments in the field of plant recombinases Dmc1 and Rad51.
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Affiliation(s)
- Rajani Kant Chittela
- Plant Biochemistry Section, Molecular Biology Division, Bhabha Atomic Research Center, Trombay, Mumbai 400 085, India
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Wardrope L, Okely E, Leach D. Resolution of joint molecules by RuvABC and RecG following cleavage of the Escherichia coli chromosome by EcoKI. PLoS One 2009; 4:e6542. [PMID: 19657385 PMCID: PMC2716532 DOI: 10.1371/journal.pone.0006542] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 07/02/2009] [Indexed: 11/28/2022] Open
Abstract
DNA double-strand breaks can be repaired by homologous recombination involving the formation and resolution of Holliday junctions. In Escherichia coli, the RuvABC resolvasome and the RecG branch-migration enzyme have been proposed to act in alternative pathways for the resolution of Holliday junctions. Here, we have studied the requirements for RuvABC and RecG in DNA double-strand break repair after cleavage of the E. coli chromosome by the EcoKI restriction enzyme. We show an asymmetry in the ability of RuvABC and RecG to deal with joint molecules in vivo. We detect linear DNA products compatible with the cleavage-ligation of Holliday junctions by the RuvABC pathway but not by the RecG pathway. Nevertheless we show that the XerCD-mediated pathway of chromosome dimer resolution is required for survival regardless of whether the RuvABC or the RecG pathway is active, suggesting that crossing-over is a common outcome irrespective of the pathway utilised. This poses a problem. How can cells resolve joint molecules, such as Holliday junctions, to generate crossover products without cleavage-ligation? We suggest that the mechanism of bacterial DNA replication provides an answer to this question and that RecG can facilitate replication through Holliday junctions.
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Affiliation(s)
- Laura Wardrope
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Ewa Okely
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - David Leach
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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DNA double strand break repair and crossing over mediated by RuvABC resolvase and RecG translocase. DNA Repair (Amst) 2008; 7:1517-30. [PMID: 18606573 DOI: 10.1016/j.dnarep.2008.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 05/02/2008] [Accepted: 05/16/2008] [Indexed: 10/21/2022]
Abstract
DNA double-strand breaks threaten the stability of the genome, and yet are induced deliberately during meiosis in order to provoke homologous recombination and generate the crossovers needed to promote faithful chromosome transmission. Crossovers are secured via biased resolution of the double Holliday junction intermediates formed when both ends of the broken chromosome engage an intact homologue. To investigate whether the enzymes catalysing branch migration and resolution of Holliday junctions are directed to favour production of either crossover or noncrossover products, we engineered a genetic system based on DNA breakage induced by the I-SceI endonuclease to detect analogous exchanges in Escherichia coli where the enzymology of recombination is more fully understood. Analysis of the recombinants generated revealed approximately equal numbers of crossover and noncrossover products, regardless of whether repair is mediated via RecG, RuvABC, or the RusA resolvase. We conclude that there little or no control of crossing over at the level of Holliday junction resolution. Thus, if similar resolvases function during meiosis, additional factors must act to bias recombination in favour of crossover progeny.
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UvrD and UvrD252 counteract RecQ, RecJ, and RecFOR in a rep mutant of Escherichia coli. J Bacteriol 2008; 190:5995-6001. [PMID: 18567657 DOI: 10.1128/jb.00620-08] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rep and UvrD are two related Escherichia coli helicases, and inactivating both is lethal. Based on the observation that the synthetic lethality of rep and uvrD inactivation is suppressed in the absence of the recombination presynaptic proteins RecF, RecO, or RecR, it was proposed that UvrD is essential in the rep mutant to counteract a deleterious RecFOR-dependent RecA binding. We show here that the synthetic lethality of rep and uvrD mutations is also suppressed by recQ and recJ inactivation but not by rarA inactivation. Furthermore, it is independent of the action of UvrD in nucleotide excision repair and mismatch repair. These observations support the idea that UvrD counteracts a deleterious RecA binding to forks blocked in the rep mutant. An ATPase-deficient mutant of UvrD [uvrD(R284A)] is dominant negative in a rep mutant, but only in the presence of all RecQJFOR proteins, suggesting that the UvrD(R284A) mutant protein is deleterious when it counteracts one of these proteins. In contrast, the uvrD252 mutant (G30D), which exhibits a strongly decreased ATPase activity, is viable in a rep mutant, where it allows replication fork reversal. We conclude that the residual ATPase activity of UvrD252 prevents a negative effect on the viability of the rep mutant and allows UvrD to counteract the action of RecQ, RecJ, and RecFOR at forks blocked in the rep mutant. Models for the action of UvrD at blocked forks are proposed.
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