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Song N, De Greve H, Wang Q, Hernalsteens JP, Li Z. Plasmid parB contributes to uropathogenic Escherichia coli colonization in vivo by acting on biofilm formation and global gene regulation. Front Mol Biosci 2022; 9:1053888. [PMID: 36589237 PMCID: PMC9800825 DOI: 10.3389/fmolb.2022.1053888] [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] [Received: 09/26/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
The endogenous plasmid pUTI89 harbored by the uropathogenic Escherichia coli (UPEC) strain UTI89 plays an important role in the acute stage of infection. The partitioning gene parB is important for stable inheritance of pUTI89. However, the function of partitioning genes located on the plasmid in pathogenesis of UPEC still needs to be further investigated. In the present study, we observed that disruption of the parB gene leads to a deficiency in biofilm formation in vitro. Moreover, in a mixed infection with the wild type strain and the parB mutant, in an ascending UTI mouse model, the mutant displayed a lower bacterial burden in the bladder and kidneys, not only at the acute infection stage but also extending to 72 hours post infection. However, in the single infection test, the reduced colonization ability of the parB mutant was only observed at six hpi in the bladder, but not in the kidneys. The colonization capacity in vivo of the parB-complemented strain was recovered. qRT-PCR assay suggested that ParB could be a global regulator, influencing the expression of genes located on both the endogenous plasmid and chromosome, while the gene parA or the operon parAB could not. Our study demonstrates that parB contributes to the virulence of UPEC by influencing biofilm formation and proposes that the parB gene of the endogenous plasmid could regulate gene expression globally.
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Affiliation(s)
- Ningning Song
- School of Life Science and Technology, Weifang Medical University, Weifang, China,Department of Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Henri De Greve
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Quanjun Wang
- SAFE Pharmaceutical Technology Co, Ltd., Beijing, China
| | - Jean-Pierre Hernalsteens
- Department of Biology, Vrije Universiteit Brussel, Brussels, Belgium,*Correspondence: Jean-Pierre Hernalsteens, , Zhaoli Li,
| | - Zhaoli Li
- Department of Biology, Vrije Universiteit Brussel, Brussels, Belgium,SAFE Pharmaceutical Technology Co, Ltd., Beijing, China,*Correspondence: Jean-Pierre Hernalsteens, , Zhaoli Li,
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2
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Volante A, Alonso JC, Mizuuchi K. Distinct architectural requirements for the parS centromeric sequence of the pSM19035 plasmid partition machinery. eLife 2022; 11:79480. [PMID: 36062913 PMCID: PMC9499535 DOI: 10.7554/elife.79480] [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: 04/14/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Three-component ParABS partition systems ensure stable inheritance of many bacterial chromosomes and low-copy-number plasmids. ParA localizes to the nucleoid through its ATP-dependent nonspecific DNA-binding activity, whereas centromere-like parS-DNA and ParB form partition complexes that activate ParA-ATPase to drive the system dynamics. The essential parS sequence arrangements vary among ParABS systems, reflecting the architectural diversity of their partition complexes. Here, we focus on the pSM19035 plasmid partition system that uses a ParBpSM of the ribbon-helix-helix (RHH) family. We show that parSpSM with four or more contiguous ParBpSM-binding sequence repeats is required to assemble a stable ParApSM-ParBpSM complex and efficiently activate the ParApSM-ATPase, stimulating complex disassembly. Disruption of the contiguity of the parSpSM sequence array destabilizes the ParApSM-ParBpSM complex and prevents efficient ATPase activation. Our findings reveal the unique architecture of the pSM19035 partition complex and how it interacts with nucleoid-bound ParApSM-ATP.
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Affiliation(s)
- Andrea Volante
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, United States
| | - Juan Carlos Alonso
- Department of Microbial Biotechnology, National Center for Biotechnology, Madrid, Spain
| | - Kiyoshi Mizuuchi
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, United States
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Chromosome Segregation in Bacillus subtilis Follows an Overall Pattern of Linear Movement and Is Highly Robust against Cell Cycle Perturbations. mSphere 2020; 5:5/3/e00255-20. [PMID: 32554717 PMCID: PMC7300352 DOI: 10.1128/msphere.00255-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We have followed the segregation of origin regions on the Bacillus subtilis chromosome in the fastest practically achievable temporal manner, for a large fraction of the cell cycle. We show that segregation occurred in highly variable patterns but overall in an almost linear manner throughout the cell cycle. Segregation was slowed down, but not arrested, by treatment of cells that led to transient blocks in DNA replication, showing that segregation is highly robust against cell cycle perturbation. Computer simulations based on entropy-driven separation of newly synthesized DNA polymers can recapitulate sudden bursts of movement and segregation patterns compatible with the observed in vivo patterns, indicating that for Bacillus, segregation patterns may include entropic forces helping to separate chromosomes during the cell cycle. Although several proteins have been identified that facilitate chromosome segregation in bacteria, no clear analogue of the mitotic machinery in eukaryotic cells has been identified. In order to investigate if recognizable patterns of segregation exist during the cell cycle, we tracked the segregation of duplicated origin regions in Bacillus subtilis for 60 min in the fastest practically achievable resolution, achieving 10-s intervals. We found that while separation occurred in random patterns, often including backwards movement, overall, segregation of loci near the origins of replication was linear for the entire cell cycle. Thus, the process of partitioning can be best described as directed motion. Simulations with entropy-driven separation of polymers synthesized by two polymerases show sudden bursts of movement and segregation patterns compatible with the observed in vivo patterns, showing that for Bacillus, segregation patterns can be modeled based on entropic forces. To test if obstacles for replication forks lead to an alteration of the partitioning pattern, we challenged cells with chemicals inducing DNA damage or blocking of topoisomerase activity. Both treatments led to a moderate slowing down of separation, but linear segregation was retained, showing that chromosome segregation is highly robust against cell cycle perturbation. IMPORTANCE We have followed the segregation of origin regions on the Bacillus subtilis chromosome in the fastest practically achievable temporal manner, for a large fraction of the cell cycle. We show that segregation occurred in highly variable patterns but overall in an almost linear manner throughout the cell cycle. Segregation was slowed down, but not arrested, by treatment of cells that led to transient blocks in DNA replication, showing that segregation is highly robust against cell cycle perturbation. Computer simulations based on entropy-driven separation of newly synthesized DNA polymers can recapitulate sudden bursts of movement and segregation patterns compatible with the observed in vivo patterns, indicating that for Bacillus, segregation patterns may include entropic forces helping to separate chromosomes during the cell cycle.
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Zhang X, Liu X, Li L, Wei G, Zhang D, Liang Y, Miao B. Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations. BMC Genomics 2019; 20:438. [PMID: 31146680 PMCID: PMC6543593 DOI: 10.1186/s12864-019-5827-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/23/2019] [Indexed: 01/18/2023] Open
Abstract
Background Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. Results Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case study, taxonomic reclassifications of many isolates provides novel insights into their phylogenetic lineage. Whole-genome-based comparisons were attempted to investigate the intra- and inter-species divergence. Recent studies clarified that functional and structural specificities of bacterial strains might provide opportunities for adaptive evolution responding to local environmental conditions. Acidophilic microorganisms play a key role in the acidification of natural waters and thus the formation of extremely acidic environments, and the feedbacks of the latter might confer the distinct evolutionary patterns of Acidithiobacillus spp. Varied horizontal gene transfer events occurred in different bacterial strains, probably resulting in the expansion of Acidithiobacillus genomes. Gene loss as another evolutionary force might cause the adaptive phenotypic diversity. A conceptual model for potential community-dependent evolutionary adaptation was thus proposed to illustrate the observed genome differentiation. Conclusions Collectively, the findings shed light on the phylogeny and divergent evolution of Acidithiobacillus strains, and provided a useful reference for evolutionary studies of other extremophiles. Electronic supplementary material The online version of this article (10.1186/s12864-019-5827-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanyun Wei
- School of Life Sciences, Nantong University, Nantong, China
| | - Danli Zhang
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Abstract
Spatial organization is a hallmark of all living systems. Even bacteria, the smallest forms of cellular life, display defined shapes and complex internal organization, showcasing a highly structured genome, cytoskeletal filaments, localized scaffolding structures, dynamic spatial patterns, active transport, and occasionally, intracellular organelles. Spatial order is required for faithful and efficient cellular replication and offers a powerful means for the development of unique biological properties. Here, we discuss organizational features of bacterial cells and highlight how bacteria have evolved diverse spatial mechanisms to overcome challenges cells face as self-replicating entities.
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Kohler V, Vaishampayan A, Grohmann E. Broad-host-range Inc18 plasmids: Occurrence, spread and transfer mechanisms. Plasmid 2018; 99:11-21. [PMID: 29932966 DOI: 10.1016/j.plasmid.2018.06.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 11/18/2022]
Abstract
Conjugative plasmid transfer is one of the major mechanisms responsible for the spread of antibiotic resistance and virulence genes. The incompatibility (Inc) 18 group of plasmids is a family of plasmids replicating by the theta-mechanism, whose members have been detected frequently in enterococci and streptococci. Inc18 plasmids encode a variety of antibiotic resistances, including resistance to vancomycin, chloramphenicol and the macrolide-lincosamide-streptogramine (MLS) group of antibiotics. These plasmids comprising insertions of Tn1546 were demonstrated to be responsible for the transfer of vancomycin resistance encoded by the vanA gene from vancomycin resistant enterococci (VRE) to methicillin resistant Staphylococcus aureus (MRSA). Thereby vancomycin resistant S. aureus (VRSA) were generated, which are serious multi-resistant pathogens challenging the health care system. Inc18 plasmids are widespread in the clinic and frequently have been detected in the environment, especially in domestic animals and wastewater. pIP501 is one of the best-characterized conjugative Inc18 plasmids. It was originally isolated from a clinical Streptococcus agalactiae strain and is, due to its small size and simplicity, a model to study conjugative plasmid transfer in Gram-positive bacteria. Here, we report on the occurrence and spread of Inc18-type plasmids in the clinic and in different environments as well as on the exchange of the plasmids among them. In addition, we discuss molecular details on the transfer mechanism of Inc18 plasmids and its regulation, as exemplified by the model plasmid pIP501. We finish with an outlook on promising approaches on how to reduce the emerging spread of antibiotic resistances.
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Affiliation(s)
- Verena Kohler
- Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria
| | - Ankita Vaishampayan
- Life Sciences and Technology, Beuth University of Applied Sciences Berlin, D-13347 Berlin, Germany
| | - Elisabeth Grohmann
- Life Sciences and Technology, Beuth University of Applied Sciences Berlin, D-13347 Berlin, Germany.
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Hu L, Vecchiarelli AG, Mizuuchi K, Neuman KC, Liu J. Brownian ratchet mechanisms of ParA-mediated partitioning. Plasmid 2017; 92:12-16. [PMID: 28529035 PMCID: PMC5568458 DOI: 10.1016/j.plasmid.2017.05.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Longhua Hu
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, United States
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology (MCDB), University of Michigan, Ann Arbor, MI, United States
| | - Kiyoshi Mizuuchi
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, United States
| | - Keir C Neuman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, United States
| | - Jian Liu
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, United States.
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Ullrich SR, González C, Poehlein A, Tischler JS, Daniel R, Schlömann M, Holmes DS, Mühling M. Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum". Front Microbiol 2016; 7:797. [PMID: 27303384 PMCID: PMC4886054 DOI: 10.3389/fmicb.2016.00797] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/11/2016] [Indexed: 01/07/2023] Open
Abstract
Acid mine drainage (AMD), associated with active and abandoned mining sites, is a habitat for acidophilic microorganisms that gain energy from the oxidation of reduced sulfur compounds and ferrous iron and that thrive at pH below 4. Members of the recently proposed genus “Ferrovum” are the first acidophilic iron oxidizers to be described within the Betaproteobacteria. Although they have been detected as typical community members in AMD habitats worldwide, knowledge of their phylogenetic and metabolic diversity is scarce. Genomics approaches appear to be most promising in addressing this lacuna since isolation and cultivation of “Ferrovum” has proven to be extremely difficult and has so far only been successful for the designated type strain “Ferrovum myxofaciens” P3G. In this study, the genomes of two novel strains of “Ferrovum” (PN-J185 and Z-31) derived from water samples of a mine water treatment plant were sequenced. These genomes were compared with those of “Ferrovum” sp. JA12 that also originated from the mine water treatment plant, and of the type strain (P3G). Phylogenomic scrutiny suggests that the four strains represent three “Ferrovum” species that cluster in two groups (1 and 2). Comprehensive analysis of their predicted metabolic pathways revealed that these groups harbor characteristic metabolic profiles, notably with respect to motility, chemotaxis, nitrogen metabolism, biofilm formation and their potential strategies to cope with the acidic environment. For example, while the “F. myxofaciens” strains (group 1) appear to be motile and diazotrophic, the non-motile group 2 strains have the predicted potential to use a greater variety of fixed nitrogen sources. Furthermore, analysis of their genome synteny provides first insights into their genome evolution, suggesting that horizontal gene transfer and genome reduction in the group 2 strains by loss of genes encoding complete metabolic pathways or physiological features contributed to the observed diversification.
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Affiliation(s)
- Sophie R Ullrich
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres BelloSantiago, Chile; Bio-Computing and Applied Genetics Division, Fraunhofer Chile Research Foundation, Center for Systems BiotechnologySantiago, Chile
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Georg-August Universität Göttingen Göttingen, Germany
| | - Judith S Tischler
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Georg-August Universität Göttingen Göttingen, Germany
| | - Michael Schlömann
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello Santiago, Chile
| | - Martin Mühling
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
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Volante A, Carrasco B, Tabone M, Alonso JC. The interaction of ω2 with the RNA polymerase β' subunit functions as an activation to repression switch. Nucleic Acids Res 2015; 43:9249-61. [PMID: 26243774 PMCID: PMC4627068 DOI: 10.1093/nar/gkv788] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/23/2015] [Indexed: 12/03/2022] Open
Abstract
The ω gene is encoded in broad-host range and low-copy plasmids. It is genetically linked to antibiotic resistance genes of the major human pathogens of phylum Firmicutes. The homodimeric forms of ω (ω2) coordinate the plasmid copy number control, faithful partition (ω2 and δ2) and better-than-random segregation (ζϵ2ζ) systems. The promoter (P) of the ωϵζ operon (Pω) transiently interacts with ω2. Adding δ2 facilitates the formation of stable ω2·Pω complexes. Here we show that limiting ω2 interacts with the N-terminal domain of the β’ subunit of the Bacillus subtilis RNA polymerase (RNAP-σA) vegetative holoenzyme. In this way ω2 recruits RNAP-σA onto Pω DNA. Partial Pω occupancy by ω2 increases the rate at which RNAP-σA complex shifts from its closed (RPC) to open (RPO) form. This shift increases transcription activation. Adding δ2 further increases the rate of Pω transcription initiation, perhaps by stabilizing the ω2·Pω complex. In contrast, full operator occupancy by ω2 facilitates RPC formation, but it blocks RPO isomerization and represses Pω utilization. The stimulation and inhibition of RPO formation is the mechanism whereby ω2 mediates copy number fluctuation and stable plasmid segregation. By this mechanism, ω2 also indirectly influences the acquisition of antibiotic resistance genes.
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Affiliation(s)
- Andrea Volante
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3, Darwin Street, 28049 Madrid, Spain
| | - Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3, Darwin Street, 28049 Madrid, Spain
| | - Mariangela Tabone
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3, Darwin Street, 28049 Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3, Darwin Street, 28049 Madrid, Spain
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