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Gudeta DD, Zhao S, Aljahdali N, Foley SL. Coupling antitoxins and blue/white screening with parAB/resolvase mutation as a strategy for Salmonella spp. plasmid curing. Microbiol Spectr 2024:e0122024. [PMID: 39315784 DOI: 10.1128/spectrum.01220-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/21/2024] [Indexed: 09/25/2024] Open
Abstract
Despite the dissemination of multidrug resistance plasmids, including those carrying virulence genes in Salmonella spp., efficient plasmid curing tools are lacking. Plasmid partitioning and multimer resolution systems are attractive targets for plasmid cure. However, plasmid curing strategies targeting these systems are often hindered by the host addiction system through a process known as post-segregation killing. Here, we developed vector tools that can mutate the above systems while replenishing short-lived antitoxins. Cloning was performed using Gibson assembly. parAB or resolvase (res) genes on Incompatibility Group (Inc)FIB, IncA/C, IncX4, and plasmids carried by Salmonella species were deleted by first knocking in the N-terminal ß-galactosidase encoding gene (bgaB), followed by in-frame insertion of its C-terminal region using pDG1 and pDG2 vectors, respectively. pDG1 was used as a backbone to develop a vector, designated as pDG-At, expressing 13 antitoxins driven by strong promoters. Plasmid curing was achieved by transforming pDG-At to parAB or res mutants followed by blue-white screening and PCR; however, parAB mutant isolation with this method was low and often non-reproducible. To elucidate whether the prior presence of pDG-At in cells improves viable mutant isolation, we re-constructed pDG-At, designated as pDG-Atπ, using a vector with the R6Kϒ origin of replication with its π-factor required for replication under araBAD promoter. Results showed that pDG-Atπ can replicate in the absence of arabinose but can be cured by growing cells in glucose-rich media. Next, we repeated IncFIB's parAB deletion using pDG1 but in cells carrying pDG-Atπ. Many white colonies were detected on X-Gal-supplemented media but none of them carried the target parA mutation; however, ~80% of the white colonies lost IncFIB plasmid, while the others retained the wild-type plasmid. Similar results were obtained for IncX4 plasmid curing but also found that this method was not reproducible as the white colonies obtained after allelic replacement did not always result in plasmid curing or mutant isolation. This is the first report describing a simple blue/white screening method for plasmid curing that can avoid laborious screening procedures. IMPORTANCE Plasmids play an important role in bacterial physiology, adaptation, evolution, virulence, and antibiotic resistance. An in-depth study of these roles partly depends on the generation of plasmid-free cells. This study shows that vector tools that target genes required for plasmid stability in the presence of an antitoxin-expressing helper plasmid are a viable approach to cure specific plasmids. Expression of bgaB from target plasmids can greatly facilitate visual detection of plasmid cured colonies avoiding time-consuming screening procedures. This approach can be refined for the development of a universal plasmid curing system that can be used to generate plasmid-free cells in other human bacterial pathogens including Gram positives and Gram negatives.
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Affiliation(s)
- Dereje D Gudeta
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Shaohua Zhao
- Office of Applied Science, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Nesreen Aljahdali
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Steven L Foley
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
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2
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Amoros J, Fattar N, Buysse M, Louni M, Bertaux J, Bouchon D, Duron O. Reassessment of the genetic basis of natural rifampin resistance in the genus Rickettsia. Microbiologyopen 2024; 13:e1431. [PMID: 39082505 PMCID: PMC11289727 DOI: 10.1002/mbo3.1431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/12/2024] [Accepted: 07/20/2024] [Indexed: 08/03/2024] Open
Abstract
Rickettsia, a genus of obligate intracellular bacteria, includes species that cause significant human diseases. This study challenges previous claims that the Leucine-973 residue in the RNA polymerase beta subunit is the primary determinant of rifampin resistance in Rickettsia. We investigated a previously untested Rickettsia species, R. lusitaniae, from the Transitional group and found it susceptible to rifampin, despite possessing the Leu-973 residue. Interestingly, we observed the conservation of this residue in several rifampin-susceptible species across most Rickettsia phylogenetic groups. Comparative genomics revealed potential alternative resistance mechanisms, including additional amino acid variants that could hinder rifampin binding and genes that could facilitate rifampin detoxification through efflux pumps. Importantly, the evolutionary history of Rickettsia genomes indicates that the emergence of natural rifampin resistance is phylogenetically constrained within the genus, originating from ancient genetic features shared among a unique set of closely related Rickettsia species. Phylogenetic patterns appear to be the most reliable predictors of natural rifampin resistance, which is confined to a distinct monophyletic subclade known as Massiliae. The distinctive features of the RNA polymerase beta subunit in certain untested Rickettsia species suggest that R. raoultii, R. amblyommatis, R. gravesii, and R. kotlanii may also be naturally rifampin-resistant species.
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Affiliation(s)
- Julien Amoros
- MIVEGEC, CNRS, IRDUniversity of MontpellierMontpellierFrance
| | - Noor Fattar
- MIVEGEC, CNRS, IRDUniversity of MontpellierMontpellierFrance
| | - Marie Buysse
- MIVEGEC, CNRS, IRDUniversity of MontpellierMontpellierFrance
| | | | | | | | - Olivier Duron
- MIVEGEC, CNRS, IRDUniversity of MontpellierMontpellierFrance
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3
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Beamud B, Benz F, Bikard D. Going viral: The role of mobile genetic elements in bacterial immunity. Cell Host Microbe 2024; 32:804-819. [PMID: 38870898 DOI: 10.1016/j.chom.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
Bacteriophages and other mobile genetic elements (MGEs) pose a significant threat to bacteria, subjecting them to constant attacks. In response, bacteria have evolved a sophisticated immune system that employs diverse defensive strategies and mechanisms. Remarkably, a growing body of evidence suggests that most of these defenses are encoded by MGEs themselves. This realization challenges our traditional understanding of bacterial immunity and raises intriguing questions about the evolutionary forces at play. Our review provides a comprehensive overview of the latest findings on the main families of MGEs and the defense systems they encode. We also highlight how a vast diversity of defense systems remains to be discovered and their mechanism of mobility understood. Altogether, the composition and distribution of defense systems in bacterial genomes only makes sense in the light of the ecological and evolutionary interactions of a complex network of MGEs.
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Affiliation(s)
- Beatriz Beamud
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
| | - Fabienne Benz
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - David Bikard
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
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4
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Quiñonero-Coronel MDM, Devos DP, Garcillán-Barcia MP. Specificities and commonalities of the Planctomycetes plasmidome. Environ Microbiol 2024; 26:e16638. [PMID: 38733104 DOI: 10.1111/1462-2920.16638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.
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Affiliation(s)
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD, CSIC-Universidad Pablo de Olavide), Sevilla, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, CSIC-Universidad de Cantabria), Cantabria, Spain
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5
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Gutschmann B, Högl TH, Huang B, Maldonado Simões M, Junne S, Neubauer P, Grimm T, Riedel SL. Polyhydroxyalkanoate production from animal by-products: Development of a pneumatic feeding system for solid fat/protein-emulsions. Microb Biotechnol 2022; 16:286-294. [PMID: 36168730 PMCID: PMC9871516 DOI: 10.1111/1751-7915.14150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/02/2022] [Accepted: 09/10/2022] [Indexed: 01/27/2023] Open
Abstract
Fat-containing animal by-product streams are locally available in large quantities. Depending on their quality, they can be inexpensive substrates for biotechnological processes. To accelerate industrial polyhydroxyalkanoate (PHA) bioplastic production, the development of efficient bioprocesses that are based on animal by-product streams is a promising approach to reduce overall production costs. However, the solid nature of animal by-product streams requires a tailor-made process development. In this study, a fat/protein-emulsion (FPE), which is a by-product stream from industrial-scale pharmaceutical heparin production and of which several hundred tons are available annually, was evaluated for PHA production with Ralstonia eutropha. The FPE was used as the sole source of carbon and nitrogen in shake flask and bioreactor cultivations. A tailored pneumatic feeding system was built for laboratory bioreactors to facilitate fed-batch cultivations with the solid FPE. The process yielded up to 51 g L-1 cell dry weight containing 71 wt% PHA with a space-time yield of 0.6 gPHA L-1 h-1 without using any carbon or nitrogen sources other than FPE. The presented approach highlights the potential of animal by-product stream valorization into PHA and contributes to a transition towards a circular bioeconomy.
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Affiliation(s)
- Björn Gutschmann
- Technische Universität Berlin, Chair of Bioprocess EngineeringBerlinGermany
| | - Thomas H. Högl
- Technische Universität Berlin, Chair of Bioprocess EngineeringBerlinGermany
| | - Boyang Huang
- Technische Universität Berlin, Chair of Bioprocess EngineeringBerlinGermany
| | | | - Stefan Junne
- Technische Universität Berlin, Chair of Bioprocess EngineeringBerlinGermany
| | - Peter Neubauer
- Technische Universität Berlin, Chair of Bioprocess EngineeringBerlinGermany
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6
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Bell PJL. Eukaryogenesis: The Rise of an Emergent Superorganism. Front Microbiol 2022; 13:858064. [PMID: 35633668 PMCID: PMC9130767 DOI: 10.3389/fmicb.2022.858064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/15/2022] [Indexed: 12/11/2022] Open
Abstract
Although it is widely taught that all modern life descended via modification from a last universal common ancestor (LUCA), this dominant paradigm is yet to provide a generally accepted explanation for the chasm in design between prokaryotic and eukaryotic cells. Counter to this dominant paradigm, the viral eukaryogenesis (VE) hypothesis proposes that the eukaryotes originated as an emergent superorganism and thus did not evolve from LUCA via descent with incremental modification. According to the VE hypothesis, the eukaryotic nucleus descends from a viral factory, the mitochondrion descends from an enslaved alpha-proteobacteria and the cytoplasm and plasma membrane descend from an archaeal host. A virus initiated the eukaryogenesis process by colonising an archaeal host to create a virocell that had its metabolism reprogrammed to support the viral factory. Subsequently, viral processes facilitated the entry of a bacterium into the archaeal cytoplasm which was also eventually reprogrammed to support the viral factory. As the viral factory increased control of the consortium, the archaeal genome was lost, the bacterial genome was greatly reduced and the viral factory eventually evolved into the nucleus. It is proposed that the interaction between these three simple components generated a superorganism whose emergent properties allowed the evolution of eukaryotic complexity. If the radical tenets of the VE hypothesis are ultimately accepted, current biological paradigms regarding viruses, cell theory, LUCA and the universal Tree of Life (ToL) should be fundamentally altered or completely abandoned.
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Mishra D, Srinivasan R. Catching a Walker in the Act-DNA Partitioning by ParA Family of Proteins. Front Microbiol 2022; 13:856547. [PMID: 35694299 PMCID: PMC9178275 DOI: 10.3389/fmicb.2022.856547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/28/2022] [Indexed: 12/01/2022] Open
Abstract
Partitioning the replicated genetic material is a crucial process in the cell cycle program of any life form. In bacteria, many plasmids utilize cytoskeletal proteins that include ParM and TubZ, the ancestors of the eukaryotic actin and tubulin, respectively, to segregate the plasmids into the daughter cells. Another distinct class of cytoskeletal proteins, known as the Walker A type Cytoskeletal ATPases (WACA), is unique to Bacteria and Archaea. ParA, a WACA family protein, is involved in DNA partitioning and is more widespread. A centromere-like sequence parS, in the DNA is bound by ParB, an adaptor protein with CTPase activity to form the segregation complex. The ParA ATPase, interacts with the segregation complex and partitions the DNA into the daughter cells. Furthermore, the Walker A motif-containing ParA superfamily of proteins is associated with a diverse set of functions ranging from DNA segregation to cell division, cell polarity, chemotaxis cluster assembly, cellulose biosynthesis and carboxysome maintenance. Unifying principles underlying the varied range of cellular roles in which the ParA superfamily of proteins function are outlined. Here, we provide an overview of the recent findings on the structure and function of the ParB adaptor protein and review the current models and mechanisms by which the ParA family of proteins function in the partitioning of the replicated DNA into the newly born daughter cells.
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Affiliation(s)
- Dipika Mishra
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
- Homi Bhabha National Institutes, Mumbai, India
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
- Homi Bhabha National Institutes, Mumbai, India
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8
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Immethun CM, Kathol M, Changa T, Saha R. Synthetic Biology Tool Development Advances Predictable Gene Expression in the Metabolically Versatile Soil Bacterium Rhodopseudomonas palustris. Front Bioeng Biotechnol 2022; 10:800734. [PMID: 35372317 PMCID: PMC8966681 DOI: 10.3389/fbioe.2022.800734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
Harnessing the unique biochemical capabilities of non-model microorganisms would expand the array of biomanufacturing substrates, process conditions, and products. There are non-model microorganisms that fix nitrogen and carbon dioxide, derive energy from light, catabolize methane and lignin-derived aromatics, are tolerant to physiochemical stresses and harsh environmental conditions, store lipids in large quantities, and produce hydrogen. Model microorganisms often only break down simple sugars and require low stress conditions, but they have been engineered for the sustainable manufacture of numerous products, such as fragrances, pharmaceuticals, cosmetics, surfactants, and specialty chemicals, often by using tools from synthetic biology. Transferring complex pathways has proven to be exceedingly difficult, as the cofactors, cellular conditions, and energy sources necessary for this pathway to function may not be present in the host organism. Utilization of unique biochemical capabilities could also be achieved by engineering the host; although, synthetic biology tools developed for model microbes often do not perform as designed in other microorganisms. The metabolically versatile Rhodopseudomonas palustris CGA009, a purple non-sulfur bacterium, catabolizes aromatic compounds derived from lignin in both aerobic and anaerobic conditions and can use light, inorganic, and organic compounds for its source of energy. R. palustris utilizes three nitrogenase isozymes to fulfill its nitrogen requirements while also generating hydrogen. Furthermore, the bacterium produces two forms of RuBisCo in response to carbon dioxide/bicarbonate availability. While this potential chassis harbors many beneficial traits, stable heterologous gene expression has been problematic due to its intrinsic resistance to many antibiotics and the lack of synthetic biology parts investigated in this microbe. To address these problems, we have characterized gene expression and plasmid maintenance for different selection markers, started a synthetic biology toolbox specifically for the photosynthetic R. palustris, including origins of replication, fluorescent reporters, terminators, and 5′ untranslated regions, and employed the microbe’s endogenous plasmid for exogenous protein production. This work provides essential synthetic biology tools for engineering R. palustris’ many unique biochemical processes and has helped define the principles for expressing heterologous genes in this promising microbe through a methodology that could be applied to other non-model microorganisms.
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9
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Xia TY, Chen XA, Liu YQ, Scharf DH, Zhao QW, Li YQ. Redirection of acyl donor metabolic flux for lipopeptide A40926B0 biosynthesis. Microb Biotechnol 2022; 15:1852-1866. [PMID: 35213090 PMCID: PMC9151331 DOI: 10.1111/1751-7915.14021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/13/2022] [Accepted: 02/13/2022] [Indexed: 11/30/2022] Open
Abstract
The metabolic flux of fatty acyl‐CoAs determines lipopeptide biosynthesis efficiency, because acyl donor competition often occurs from polyketide biosynthesis and homologous pathways. We used A40926B0 as a model to investigate this mechanism. The lipopeptide A40926B0 with a fatty acyl group is the active precursor of dalbavancin, which is considered as a new lipoglycopeptide antibiotic. The biosynthetic pathway of fatty acyl‐CoAs in the A40926B0 producer Nonomuraea gerenzanensis L70 was efficiently engineered using endogenous replicon CRISPR (erCRISPR). A polyketide pathway and straight‐chain fatty acid biosynthesis were identified as major competitors in the malonyl‐CoA pool. Therefore, we modified both pathways to concentrate acyl donors for the production of the desired compound. Combined with multiple engineering approaches, including blockage of an acetylation side reaction, overexpression of acetyl‐CoA carboxylase, duplication of the dbv gene cluster and optimization of the fermentation parameters, the final strain produced 702.4 mg l‐1 of A40926B0, a 2.66‐fold increase, and the ratio was increased from 36.2% to 81.5%. Additionally, an efficient erCRISPR‐Cas9 editing system based on an endogenous replicon was specifically developed for L70, which increased conjugation efficiency by 660% and gene‐editing efficiency was up to 90%. Our strategy of redirecting acyl donor metabolic flux can be widely adopted for the metabolic engineering of lipopeptide biosynthesis.
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Affiliation(s)
- Tian-Yu Xia
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Xin-Ai Chen
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Yan-Qiu Liu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Daniel H Scharf
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
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10
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Abstract
Naturally occurring plasmids come in different sizes. The smallest are less than a kilobase of DNA, while the largest can be over three orders of magnitude larger. Historically, research has tended to focus on smaller plasmids that are usually easier to isolate, manipulate and sequence, but with improved genome assemblies made possible by long-read sequencing, there is increased appreciation that very large plasmids—known as megaplasmids—are widespread, diverse, complex, and often encode key traits in the biology of their host microorganisms. Why are megaplasmids so big? What other features come with large plasmid size that could affect bacterial ecology and evolution? Are megaplasmids 'just' big plasmids, or do they have distinct characteristics? In this perspective, we reflect on the distribution, diversity, biology, and gene content of megaplasmids, providing an overview to these large, yet often overlooked, mobile genetic elements. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
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Affiliation(s)
- James P J Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - João Botelho
- Antibiotic Resistance Evolution Group, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian Albrechts University, Kiel, Germany
| | - Adrian Cazares
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
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11
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Abstract
The molecular mechanisms that help to place the division septum in bacteria is of fundamental importance to ensure cell proliferation and maintenance of cell shape and size. The Min protein system, found in many rod-shaped bacteria, is thought to play a major role in division site selection. Division site selection is a vital process to ensure generation of viable offspring. In many rod-shaped bacteria, a dynamic protein system, termed the Min system, acts as a central regulator of division site placement. The Min system is best studied in Escherichia coli, where it shows a remarkable oscillation from pole to pole with a time-averaged density minimum at midcell. Several components of the Min system are conserved in the Gram-positive model organism Bacillus subtilis. However, in B. subtilis, it is commonly believed that the system forms a stationary bipolar gradient from the cell poles to midcell. Here, we show that the Min system of B. subtilis localizes dynamically to active sites of division, often organized in clusters. We provide physical modeling using measured diffusion constants that describe the observed enrichment of the Min system at the septum. Mathematical modeling suggests that the observed localization pattern of Min proteins corresponds to a dynamic equilibrium state. Our data provide evidence for the importance of ongoing septation for the Min dynamics, consistent with a major role of the Min system in controlling active division sites but not cell pole areas.
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12
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Sheng D, Chen X, Li Y, Wang J, Zhuo L, Li Y. ParC, a New Partitioning Protein, Is Necessary for the Active Form of ParA From Myxococcus pMF1 Plasmid. Front Microbiol 2021; 11:623699. [PMID: 33519784 PMCID: PMC7843461 DOI: 10.3389/fmicb.2020.623699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/16/2020] [Indexed: 11/13/2022] Open
Abstract
The ParABS partitioning system, a main driver of DNA segregation in bacteria, employs two proteins, ParA and ParB, for plasmid partition. The pMF1 plasmid from Myxococcus fulvus 124B02 has a par operon encoding a small acidic protein, ParC, in addition to type I ParA and ParB homologs. Here, we show that expression of parC upstream of parA (as in the natural case), but not ectopic expression, is essential for the plasmid inheritance in Myxococcus cells. Co-expression of parC upstream of parA was determined to form a soluble ParC-ParA heterodimer at a 1:1 ratio, while individual expression of parA or co-expression of parA with ectopic parC formed insoluble ParA proteins. Purified ParA proteins alone had no ATPase activity and was easily dimerized, while mixing ParA with ParC formed the ParC-ParA heterodimer with the ATPase and polymerization activities. Fusing ParC and ParA also produced soluble proteins and some chimeras restored the ATPase activity and plasmid inheritance. The results highlight that proximal location of parC before parA is critical to realize the functions of ParA in the partition of Myxococcus plasmid pMF1 and shed light on a new mechanism to realize a protein function by two separate proteins.
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Affiliation(s)
- Duohong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaojing Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yajie Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jingjing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Li Zhuo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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13
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Saleski TE, Chung MT, Carruthers DN, Khasbaatar A, Kurabayashi K, Lin XN. Optimized gene expression from bacterial chromosome by high-throughput integration and screening. SCIENCE ADVANCES 2021; 7:7/7/eabe1767. [PMID: 33579713 PMCID: PMC7880599 DOI: 10.1126/sciadv.abe1767] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/30/2020] [Indexed: 06/01/2023]
Abstract
Chromosomal integration of recombinant genes is desirable compared with expression from plasmids due to increased stability, reduced cell-to-cell variability, and elimination of the need for antibiotics for plasmid maintenance. Here, we present a new approach for tuning pathway gene expression levels via random integration and high-throughput screening. We demonstrate multiplexed gene integration and expression-level optimization for isobutanol production in Escherichia coli The integrated strains could, with far lower expression levels than plasmid-based expression, produce high titers (10.0 ± 0.9 g/liter isobutanol in 48 hours) and yields (69% of the theoretical maximum). Close examination of pathway expression in the top-performing, as well as other isolates, reveals the complexity of cellular metabolism and regulation, underscoring the need for precise optimization while integrating pathway genes into the chromosome. We expect this method for pathway integration and optimization can be readily extended to a wide range of pathways and chassis to create robust and efficient production strains.
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Affiliation(s)
- Tatyana E Saleski
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Meng Ting Chung
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - David N Carruthers
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Azzaya Khasbaatar
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katsuo Kurabayashi
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoxia Nina Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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Adamczyk M, Lewicka E, Szatkowska R, Nieznanska H, Ludwiczak J, Jasiński M, Dunin-Horkawicz S, Sitkiewicz E, Swiderska B, Goch G, Jagura-Burdzy G. Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins. BMC Microbiol 2021; 21:32. [PMID: 33482722 PMCID: PMC7821693 DOI: 10.1186/s12866-020-02079-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/20/2020] [Indexed: 01/22/2023] Open
Abstract
Background DNA binding KfrA-type proteins of broad-host-range bacterial plasmids belonging to IncP-1 and IncU incompatibility groups are characterized by globular N-terminal head domains and long alpha-helical coiled-coil tails. They have been shown to act as transcriptional auto-regulators. Results This study was focused on two members of the growing family of KfrA-type proteins encoded by the broad-host-range plasmids, R751 of IncP-1β and RA3 of IncU groups. Comparative in vitro and in silico studies on KfrAR751 and KfrARA3 confirmed their similar biophysical properties despite low conservation of the amino acid sequences. They form a wide range of oligomeric forms in vitro and, in the presence of their cognate DNA binding sites, they polymerize into the higher order filaments visualized as “threads” by negative staining electron microscopy. The studies revealed also temperature-dependent changes in the coiled-coil segment of KfrA proteins that is involved in the stabilization of dimers required for DNA interactions. Conclusion KfrAR751 and KfrARA3 are structural homologues. We postulate that KfrA type proteins have moonlighting activity. They not only act as transcriptional auto-regulators but form cytoskeletal structures, which might facilitate plasmid DNA delivery and positioning in the cells before cell division, involving thermal energy. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02079-w.
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Affiliation(s)
- M Adamczyk
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Noakowskiego 3, 00-664, Warsaw, Poland.
| | - E Lewicka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - R Szatkowska
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - H Nieznanska
- Nencki Institute of Experimental Biology PAS, Laboratory of Electron Microscopy, Pasteura 3, 02-093, Warsaw, Poland
| | - J Ludwiczak
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland.,Nencki Institute of Experimental Biology, Laboratory of Bioinformatics, Pasteura 3, 02-093, Warsaw, Poland
| | - M Jasiński
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland
| | - S Dunin-Horkawicz
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland
| | - E Sitkiewicz
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - B Swiderska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - G Goch
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - G Jagura-Burdzy
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
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15
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Mishra D, Pahujani S, Mitra N, Srivastava A, Srinivasan R. Identification of a Potential Membrane-Targeting Sequence in the C-Terminus of the F Plasmid Segregation Protein SopA. J Membr Biol 2021; 254:243-257. [PMID: 33427942 DOI: 10.1007/s00232-020-00157-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
Stable maintenance and partitioning of the 'Fertility' plasmid or the F plasmid in its host Escherichia coli require the function of a ParA superfamily of proteins known as SopA. The mechanism by which SopA mediates plasmid segregation is well studied. SopA is a nucleoid-binding protein and binds DNA in an ATP-dependent but sequence non-specific manner. ATP hydrolysis stimulated by the binding of the SopBC complex mediates the release of SopA from the nucleoid. Cycles of ATP-binding and hydrolysis generate an ATPase gradient that moves the plasmid through a chemophoresis force. Nucleoid binding of SopA thus assumes a central role in its plasmid-partitioning function. However, earlier work also suggests that the F plasmid can be partitioned into anucleate cells, thus implicating nucleoid independent partitioning. Interestingly, SopA is also reported to be associated with the inner membrane of the bacteria. Here, we report the identification of a possible membrane-targeting sequence, a predicted amphipathic helix, at the C-terminus of SopA. Molecular dynamics simulations indicate that the predicted amphipathic helical motif of SopA has weak affinity for membranes. Moreover, we experimentally show that SopA can associate with bacterial membranes, is detectable in the membrane fractions of bacterial lysates, and is sensitive to the membrane potential. Further, unlike the wild-type SopA, a deletion of the C-terminal 29 amino acids results in the loss of F plasmids from bacterial cells.
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Affiliation(s)
- Dipika Mishra
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institutes, Bhubaneswar, Odisha, 752050, India
| | - Sakshi Pahujani
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institutes, Bhubaneswar, Odisha, 752050, India.,Molecular Biophysics Unit, Indian Institute of Science-Bangalore, C. V. Raman Road, Bangalore, Karnataka, 560012, India
| | - Nivedita Mitra
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institutes, Bhubaneswar, Odisha, 752050, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science-Bangalore, C. V. Raman Road, Bangalore, Karnataka, 560012, India.
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institutes, Bhubaneswar, Odisha, 752050, India.
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16
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Hayashi I. The C-terminal region of the plasmid partitioning protein TubY is a tetramer that can bind membranes and DNA. J Biol Chem 2020; 295:17770-17780. [PMID: 33454013 PMCID: PMC7762940 DOI: 10.1074/jbc.ra120.014705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/13/2020] [Indexed: 01/07/2023] Open
Abstract
Bacterial low-copy-number plasmids require partition (par) systems to ensure their stable inheritance by daughter cells. In general, these systems consist of three components: a centromeric DNA sequence, a centromere-binding protein and a nucleotide hydrolase that polymerizes and functions as a motor. Type III systems, however, segregate plasmids using three proteins: the FtsZ/tubulin-like GTPase TubZ, the centromere-binding protein TubR and the MerR-like transcriptional regulator TubY. Although the TubZ filament is sufficient to transport the TubR-centromere complex in vitro, TubY is still necessary for the stable maintenance of the plasmid. TubY contains an N-terminal DNA-binding helix-turn-helix motif and a C-terminal coiled-coil followed by a cluster of lysine residues. This study determined the crystal structure of the C-terminal domain of TubY from the Bacillus cereus pXO1-like plasmid and showed that it forms a tetrameric parallel four-helix bundle that differs from the typical MerR family proteins with a dimeric anti-parallel coiled-coil. Biochemical analyses revealed that the C-terminal tail with the conserved lysine cluster helps TubY to stably associate with the TubR-centromere complex as well as to nonspecifically bind DNA. Furthermore, this C-terminal tail forms an amphipathic helix in the presence of lipids but must oligomerize to localize the protein to the membrane in vivo. Taken together, these data suggest that TubY is a component of the nucleoprotein complex within the partitioning machinery, and that lipid membranes act as mediators of type III systems.
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Affiliation(s)
- Ikuko Hayashi
- Department of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Kanagawa, Japan
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17
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Virolle C, Goldlust K, Djermoun S, Bigot S, Lesterlin C. Plasmid Transfer by Conjugation in Gram-Negative Bacteria: From the Cellular to the Community Level. Genes (Basel) 2020; 11:genes11111239. [PMID: 33105635 PMCID: PMC7690428 DOI: 10.3390/genes11111239] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms, and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic lifestyle, virulence, biofilm formation, resistance to heavy metals, and, most importantly, resistance to antibiotics. These properties make conjugation a fundamentally important process, and it is thus the focus of extensive study. Here, we review the key steps of plasmid transfer by conjugation in Gram-negative bacteria, by following the life cycle of the F factor during its transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms.
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18
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Barajas C, Del Vecchio D. Effects of spatial heterogeneity on bacterial genetic circuits. PLoS Comput Biol 2020; 16:e1008159. [PMID: 32925923 PMCID: PMC7515207 DOI: 10.1371/journal.pcbi.1008159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 09/24/2020] [Accepted: 07/17/2020] [Indexed: 12/17/2022] Open
Abstract
Intracellular spatial heterogeneity is frequently observed in bacteria, where the chromosome occupies part of the cell's volume and a circuit's DNA often localizes within the cell. How this heterogeneity affects core processes and genetic circuits is still poorly understood. In fact, commonly used ordinary differential equation (ODE) models of genetic circuits assume a well-mixed ensemble of molecules and, as such, do not capture spatial aspects. Reaction-diffusion partial differential equation (PDE) models have been only occasionally used since they are difficult to integrate and do not provide mechanistic understanding of the effects of spatial heterogeneity. In this paper, we derive a reduced ODE model that captures spatial effects, yet has the same dimension as commonly used well-mixed models. In particular, the only difference with respect to a well-mixed ODE model is that the association rate constant of binding reactions is multiplied by a coefficient, which we refer to as the binding correction factor (BCF). The BCF depends on the size of interacting molecules and on their location when fixed in space and it is equal to unity in a well-mixed ODE model. The BCF can be used to investigate how spatial heterogeneity affects the behavior of core processes and genetic circuits. Specifically, our reduced model indicates that transcription and its regulation are more effective for genes located at the cell poles than for genes located on the chromosome. The extent of these effects depends on the value of the BCF, which we found to be close to unity. For translation, the value of the BCF is always greater than unity, it increases with mRNA size, and, with biologically relevant parameters, is substantially larger than unity. Our model has broad validity, has the same dimension as a well-mixed model, yet it incorporates spatial heterogeneity. This simple-to-use model can be used to both analyze and design genetic circuits while accounting for spatial intracellular effects.
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Affiliation(s)
- Carlos Barajas
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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19
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Lewicka E, Dolowy P, Godziszewska J, Litwin E, Ludwiczak M, Jagura-Burdzy G. Transcriptional Organization of the Stability Module of Broad-Host-Range Plasmid RA3, from the IncU Group. Appl Environ Microbiol 2020; 86:e00847-20. [PMID: 32532870 PMCID: PMC7414963 DOI: 10.1128/aem.00847-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/06/2020] [Indexed: 02/06/2023] Open
Abstract
The broad-host-range (BHR) conjugative plasmids have developed diverse adaptive mechanisms defining the range of their promiscuity. The BHR conjugative RA3 plasmid, the archetype of the IncU group, can transfer between, replicate in, and be maintained in representatives of Alpha-, Beta-, and Gammaproteobacteria Its stability module encompasses ten open reading frames (ORFs) apparently organized into five operons, all transcribed in the same direction from several strong promoters that are tightly regulated either by autorepressors or by global plasmid-encoded regulators. In this paper, we demonstrate that owing to an efficient RNA polymerase (RNAP) read-through, the transcription from the first promoter, orf02p, may continue through the whole module. Moreover, an analysis of mRNA produced from the wild-type (WT) stability module and its deletion variants deprived of particular internal transcription initiation sites reveals that in fact each operon may be transcribed from any upstream promoter, giving rise to multicistronic transcripts of variable length and creating an additional level of gene expression control by transcript dosage adjustment. The gene expression patterns differ among various hosts, indicating that promoter recognition, regulation, and the RNAP read-through mechanisms are modulated in a species-specific manner.IMPORTANCE The efficiently disseminating conjugative or mobilizable BHR plasmids play key roles in the horizontal spread of genetic information between closely related and phylogenetically distant species, which can be harmful from the medical, veterinary, or industrial point of view. Understanding the mechanisms determining the plasmid's ability to function in diverse hosts is essential to help limit the spread of undesirable plasmid-encoded traits, e.g., antibiotic resistance. The range of a plasmid's promiscuity depends on the adaptations of its transfer, replication, and stability functions to the various hosts. IncU plasmids, with the archetype plasmid RA3, are considered to constitute a reservoir of antibiotic resistance genes in aquatic environments; however, the molecular mechanisms determining their adaptability to a broad range of hosts are rather poorly characterized. Here, we present the transcriptional organization of the stability module and show that the gene transcript dosage effect is an important determinant of the stable maintenance of RA3 in different hosts.
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Affiliation(s)
- Ewa Lewicka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Patrycja Dolowy
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jolanta Godziszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Emilia Litwin
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Ludwiczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Grazyna Jagura-Burdzy
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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20
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Duprey A, Groisman EA. FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo. mBio 2020; 11:e01053-20. [PMID: 32723920 PMCID: PMC7387798 DOI: 10.1128/mbio.01053-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/24/2020] [Indexed: 11/20/2022] Open
Abstract
DNA supercoiling (DS) is essential for life because it controls critical processes, including transcription, replication, and recombination. Current methods to measure DNA supercoiling in vivo are laborious and unable to examine single cells. Here, we report a method for high-throughput measurement of bacterial DNA supercoiling in vivoFluorescent evaluation of DNA supercoiling (FEDS) utilizes a plasmid harboring the gene for a green fluorescent protein transcribed by a discovered promoter that responds exclusively to DNA supercoiling and the gene for a red fluorescent protein transcribed by a constitutive promoter as the internal standard. Using FEDS, we uncovered single-cell heterogeneity in DNA supercoiling and established that, surprisingly, population-level decreases in DNA supercoiling result from a low-mean/high-variance DNA supercoiling subpopulation rather than from a homogeneous shift in supercoiling of the whole population. In addition, we identified a regulatory loop in which a gene that decreases DNA supercoiling is transcriptionally repressed when DNA supercoiling increases.IMPORTANCE DNA represents the chemical support of genetic information in all forms of life. In addition to its linear sequence of nucleotides, it bears critical information in its structure. This information, called DNA supercoiling, is central to all fundamental DNA processes, such as transcription and replication, and defines cellular physiology. Unlike reading of a nucleotide sequence, DNA supercoiling determinations have been laborious. We have now developed a method for rapid measurement of DNA supercoiling and established its utility by identifying a novel regulator of DNA supercoiling in the bacterium Salmonella enterica as well as behaviors that could not have been discovered with current methods.
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Affiliation(s)
- Alexandre Duprey
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
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21
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Cury J, Oliveira PH, de la Cruz F, Rocha EPC. Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements. Mol Biol Evol 2020; 35:2230-2239. [PMID: 29905872 PMCID: PMC6107060 DOI: 10.1093/molbev/msy123] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Self-transmissible mobile genetic elements drive horizontal gene transfer between prokaryotes. Some of these elements integrate in the chromosome, whereas others replicate autonomously as plasmids. Recent works showed the existence of few differences, and occasional interconversion, between the two types of elements. Here, we enquired on why evolutionary processes have maintained the two types of mobile genetic elements by comparing integrative and conjugative elements (ICE) with extrachromosomal ones (conjugative plasmids) of the highly abundant MPFT conjugative type. We observed that plasmids encode more replicases, partition systems, and antibiotic resistance genes, whereas ICEs encode more integrases and metabolism-associated genes. ICEs and plasmids have similar average sizes, but plasmids are much more variable, have more DNA repeats, and exchange genes more frequently. On the other hand, we found that ICEs are more frequently transferred between distant taxa. We propose a model where the different genetic plasticity and amplitude of host range between elements explain the co-occurrence of integrative and extrachromosomal elements in microbial populations. In particular, the conversion from ICE to plasmid allows ICE to be more plastic, while the conversion from plasmid to ICE allows the expansion of the element's host range.
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Affiliation(s)
- Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.,CNRS, UMR3525, Paris, France
| | - Pedro H Oliveira
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.,CNRS, UMR3525, Paris, France
| | - Fernando de la Cruz
- Departamento de Biologia Molecular e Instituto de Biomedicina y Biotecnologia de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.,CNRS, UMR3525, Paris, France
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22
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Physical Views on ParABS-Mediated DNA Segregation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1267:45-58. [PMID: 32894476 DOI: 10.1007/978-3-030-46886-6_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this chapter, we will focus on ParABS: an apparently simple, three-component system, required for the segregation of bacterial chromosomes and plasmids. We will specifically describe how biophysical measurements combined with physical modeling advanced our understanding of the mechanism of ParABS-mediated complex assembly, segregation and positioning.
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23
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New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies. Sci Rep 2019; 9:16444. [PMID: 31712730 PMCID: PMC6848147 DOI: 10.1038/s41598-019-52832-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Pseudoalteromonas haloplanktis TAC125 is among the most commonly studied bacteria adapted to cold environments. Aside from its ecological relevance, P. haloplanktis has a potential use for biotechnological applications. Due to its importance, we decided to take advantage of next generation sequencing (Illumina) and third generation sequencing (PacBio and Oxford Nanopore) technologies to resequence its genome. The availability of a reference genome, obtained using whole genome shotgun sequencing, allowed us to study and compare the results obtained by the different technologies and draw useful conclusions for future de novo genome assembly projects. We found that assembly polishing using Illumina reads is needed to achieve a consensus accuracy over 99.9% when using Oxford Nanopore sequencing, but not in PacBio sequencing. However, the dependency of consensus accuracy on coverage is lower in Oxford Nanopore than in PacBio, suggesting that a cost-effective solution might be the use of low coverage Oxford Nanopore sequencing together with Illumina reads. Despite the differences in consensus accuracy, all sequencing technologies revealed the presence of a large plasmid, pMEGA, which was undiscovered until now. Among the most interesting features of pMEGA is the presence of a putative error-prone polymerase regulated through the SOS response. Aside from the characterization of the newly discovered plasmid, we confirmed the sequence of the small plasmid pMtBL and uncovered the presence of a potential partitioning system. Crucially, this study shows that the combination of next and third generation sequencing technologies give us an unprecedented opportunity to characterize our bacterial model organisms at a very detailed level.
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Abstract
Plasmids have a major role in the development of disease caused by enteric bacterial pathogens. Virulence plasmids are usually large (>40 kb) low copy elements and encode genes that promote host-pathogen interactions. Although virulence plasmids provide advantages to bacteria in specific conditions, they often impose fitness costs on their host. In this Review, we discuss virulence plasmids in Enterobacteriaceae that are important causes of diarrhoea in humans, Shigella spp., Salmonella spp., Yersinia spp and pathovars of Escherichia coli. We contrast these plasmids with those that are routinely used in the laboratory and outline the mechanisms by which virulence plasmids are maintained in bacterial populations. We highlight examples of virulence plasmids that encode multiple mechanisms for their maintenance (for example, toxin-antitoxin and partitioning systems) and speculate on how these might contribute to their propagation and success.
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25
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Random Chromosome Partitioning in the Polyploid Bacterium Thermus thermophilus HB27. G3-GENES GENOMES GENETICS 2019; 9:1249-1261. [PMID: 30792193 PMCID: PMC6469415 DOI: 10.1534/g3.119.400086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Little is known about chromosome segregation in polyploid prokaryotes. In this study, whether stringent or variable chromosome segregation occurs in polyploid thermophilic bacterium Thermus thermophilus was analyzed. A stable heterozygous strain (HL01) containing two antibiotic resistance markers at one gene locus was generated. The inheritance of the two alleles in the progeny of the heterozygous strain was then followed. During incubation without selection pressure, the fraction of heterozygous cells decreased and that of homozygous cells increased, while the relative abundance of each allele in the whole population remained constant, suggesting chromosome segregation had experienced random event. Consistently, in comparison with Bacillus subtilis in which the sister chromosomes were segregated equally, the ratios of DNA content in two daughter cells of T. thermophilus had a broader distribution and a larger standard deviation, indicating that the DNA content in the two daughter cells was not always identical. Further, the protein homologs (i.e., ParA and MreB) which have been suggested to be involved in bacterial chromosome partitioning did not actively participate in the chromosome segregation in T. thermophilus. Therefore, it seems that protein-based chromosome segregation machineries are less critical for the polyploid T. thermophilus, and chromosome segregation in this bacterium are not stringently controlled but tend to be variable, and random segregation can occur.
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26
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Ferreira C, Bogas D, Bikarolla SK, Varela AR, Frykholm K, Linheiro R, Nunes OC, Westerlund F, Manaia CM. Genetic variation in the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain. CHEMOSPHERE 2019; 220:748-759. [PMID: 30611073 DOI: 10.1016/j.chemosphere.2018.12.130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/23/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Bacteria harboring conjugative plasmids have the potential for spreading antibiotic resistance through horizontal gene transfer. It is described that the selection and dissemination of antibiotic resistance is enhanced by stressors, like metals or antibiotics, which can occur as environmental contaminants. This study aimed at unveiling the composition of the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain (H1FC54) under different mating conditions. To meet this objective, plasmid pulsed field gel electrophoresis, optical mapping analyses and DNA sequencing were used in combination with phenotype analysis. Strain H1FC54 was observed to harbor five plasmids, three of which were conjugative and two of these, pH1FC54_330 and pH1FC54_140, contained metal and antibiotic resistance genes. Transconjugants obtained in the absence or presence of tellurite (0.5 μM or 5 μM), arsenite (0.5 μM, 5 μM or 15 μM) or ceftazidime (10 mg/L) and selected in the presence of sodium azide (100 mg/L) and tetracycline (16 mg/L) presented distinct phenotypes, associated with the acquisition of different plasmid combinations, including two co-integrate plasmids, of 310 kbp and 517 kbp. The variable composition of the conjugative plasmidome, the formation of co-integrates during conjugation, as well as the transfer of non-transferable plasmids via co-integration, and the possible association between antibiotic, arsenite and tellurite tolerance was demonstrated. These evidences bring interesting insights into the comprehension of the molecular and physiological mechanisms that underlie antibiotic resistance propagation in the environment.
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Affiliation(s)
- Catarina Ferreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal
| | - Diana Bogas
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal
| | - Santosh K Bikarolla
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE-412 96, Gothenburg, Sweden
| | - Ana Rita Varela
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Karolin Frykholm
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE-412 96, Gothenburg, Sweden
| | - Raquel Linheiro
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal
| | - Olga C Nunes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE-412 96, Gothenburg, Sweden
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal.
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McVicker G, Hollingshead S, Pilla G, Tang CM. Maintenance of the virulence plasmid in Shigella flexneri is influenced by Lon and two functional partitioning systems. Mol Microbiol 2019; 111:1355-1366. [PMID: 30767313 PMCID: PMC6519299 DOI: 10.1111/mmi.14225] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2019] [Indexed: 11/30/2022]
Abstract
Members of the genus Shigella carry a large plasmid, pINV, which is essential for virulence. In Shigella flexneri, pINV harbours three toxin‐antitoxin (TA) systems, CcdAB, GmvAT and VapBC that promote vertical transmission of the plasmid. Type II TA systems, such as those on pINV, consist of a toxic protein and protein antitoxin. Selective degradation of the antitoxin by proteases leads to the unopposed action of the toxin once genes encoding a TA system have been lost, such as following failure to inherit a plasmid harbouring a TA system. Here, we investigate the role of proteases in the function of the pINV TA systems and demonstrate that Lon, but not ClpP, is required for their activity during plasmid stability. This provides the first evidence that acetyltransferase family TA systems, such as GmvAT, can be regulated by Lon. Interestingly, S. flexneri pINV also harbours two putative partitioning systems, ParAB and StbAB. We show that both systems are functional for plasmid maintenance although their activity is masked by other systems on pINV. Using a model vector based on the pINV replicon, we observe temperature‐dependent differences between the two partitioning systems that contribute to our understanding of the maintenance of virulence in Shigella species.
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Affiliation(s)
- Gareth McVicker
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sarah Hollingshead
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Giulia Pilla
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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Hürtgen D, Murray SM, Mascarenhas J, Sourjik V. DNA Segregation in Natural and Synthetic Minimal Systems. ACTA ACUST UNITED AC 2019; 3:e1800316. [DOI: 10.1002/adbi.201800316] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/18/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Daniel Hürtgen
- MPI for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (Synmikro) Marburg 35043 Germany
| | - Seán M. Murray
- MPI for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (Synmikro) Marburg 35043 Germany
| | - Judita Mascarenhas
- MPI for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (Synmikro) Marburg 35043 Germany
| | - Victor Sourjik
- MPI for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (Synmikro) Marburg 35043 Germany
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29
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Ravi A, Valdés-Varela L, Gueimonde M, Rudi K. Transmission and persistence of IncF conjugative plasmids in the gut microbiota of full-term infants. FEMS Microbiol Ecol 2019; 94:4638523. [PMID: 29161377 DOI: 10.1093/femsec/fix158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 11/16/2017] [Indexed: 11/12/2022] Open
Abstract
Conjugative plasmids represent major reservoirs for horizontal transmission of antibiotic resistance and virulence genes. Our knowledge about the ecology and persistence of these plasmids in the gut microbiota remains limited. The IncF plasmids are the most widespread in clinical samples and in healthy humans and the main aim of this work was to study their ecology and association with the developing gut microbiota. Using a longitudinal (2, 10, 30 and 90 days) cohort of full-term infants, we investigated the transmission and persistence of IncFIA and IncFIB plasmids. The prevalence of IncFIB plasmids was higher than IncFIA in the cohort, while IncFIA always co-occurred with IncFIB. However, the relative gene abundance of IncFIA was significantly higher than IncFIB for all time points, indicating that IncFIA may be a higher copy-number plasmid. Through linear discriminant analysis effect size and operational taxonomic unit-level associations, we observed major differences in the abundance of Enterobacteriaceae in samples positive and negative for IncFIB. This association was significant at 2, 10 and 30 days and showed an association with vaginal delivery. From shot-gun analyses, we assembled de novo multi-replicon shared (IncFIA/IncFIB) and integrated (IncFIA/IB) plasmids that were persistent through the dataset. Overall, the study demonstrates the nature of IncF plasmids in complex microbial communities.
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Affiliation(s)
- Anuradha Ravi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science Department (KBM), Campus Ås, Ås, Norway
| | - Lorena Valdés-Varela
- Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Knut Rudi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science Department (KBM), Campus Ås, Ås, Norway
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Sau S, Ghosh SK, Liu YT, Ma CH, Jayaram M. Hitchhiking on chromosomes: A persistence strategy shared by diverse selfish DNA elements. Plasmid 2019; 102:19-28. [PMID: 30726706 DOI: 10.1016/j.plasmid.2019.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/12/2022]
Abstract
An underlying theme in the segregation of low-copy bacterial plasmids is the assembly of a 'segrosome' by DNA-protein and protein-protein interactions, followed by energy-driven directed movement. Analogous partitioning mechanisms drive the segregation of host chromosomes as well. Eukaryotic extra-chromosomal elements, exemplified by budding yeast plasmids and episomes of certain mammalian viruses, harbor partitioning systems that promote their physical association with chromosomes. In doing so, they indirectly take advantage of the spindle force that directs chromosome movement to opposite cell poles. Molecular-genetic, biochemical and cell biological studies have revealed several unsuspected aspects of 'chromosome hitchhiking' by the yeast 2-micron plasmid, including the ability of plasmid sisters to associate symmetrically with sister chromatids. As a result, the plasmid overcomes the 'mother bias' experienced by plasmids lacking a partitioning system, and elevates itself to near chromosome status in equal segregation. Chromosome association for stable propagation, without direct energy expenditure, may also be utilized by a small minority of bacterial plasmids-at least one case has been reported. Given the near perfect accuracy of chromosome segregation, it is not surprising that elements residing in evolutionarily distant host organisms have converged upon the common strategy of gaining passage to daughter cells as passengers on chromosomes.
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Affiliation(s)
- Soumitra Sau
- Amity Institute of Biotechnology, Amity University Kolkata, Kolkata 700135, India
| | - Santanu Kumar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Yen-Ting Liu
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA
| | - Chien-Hui Ma
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA.
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31
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Hayashi I, Oda T, Sato M, Fuchigami S. Cooperative DNA Binding of the Plasmid Partitioning Protein TubR from the Bacillus cereus pXO1 Plasmid. J Mol Biol 2018; 430:5015-5028. [PMID: 30414406 DOI: 10.1016/j.jmb.2018.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 11/19/2022]
Abstract
Tubulin/FtsZ-like GTPase TubZ is responsible for maintaining the stability of pXO1-like plasmids in virulent Bacilli. TubZ forms a filament in a GTP-dependent manner, and like other partitioning systems of low-copy-number plasmids, it requires the centromere-binding protein TubR that connects the plasmid to the TubZ filament. Systems regulating TubZ partitioning have been identified in Clostridium prophages as well as virulent Bacillus species, in which TubZ facilitates partitioning by binding and towing the segrosome: the nucleoprotein complex composed of TubR and the centromere. However, the molecular mechanisms of segrosome assembly and the transient on-off interactions between the segrosome and the TubZ filament remain poorly understood. Here, we determined the crystal structure of TubR from Bacillus cereus at 2.0-Å resolution and investigated the DNA-binding ability of TubR using hydroxyl radical footprinting and electrophoretic mobility shift assays. The TubR dimer possesses 2-fold symmetry and binds to a 15-bp palindromic consensus sequence in the tubRZ promoter region. Continuous TubR-binding sites overlap each other, which enables efficient binding of TubR in a cooperative manner. Interestingly, the segrosome adopts an extended DNA-protein filament structure and likely gains conformational flexibility by introducing non-consensus residues into the palindromes in an asymmetric manner. Together, our experimental results and structural model indicate that the unique centromere recognition mechanism of TubR allows transient complex formation between the segrosome and the dynamic polymer of TubZ.
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Affiliation(s)
- Ikuko Hayashi
- Department of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
| | - Takashi Oda
- Department of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mamoru Sato
- Department of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Sotaro Fuchigami
- Department of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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Li YJ, Liu Y, Zhang Z, Chen XJ, Gong Y, Li YZ. A Post-segregational Killing Mechanism for Maintaining Plasmid PMF1 in Its Myxococcus fulvus Host. Front Cell Infect Microbiol 2018; 8:274. [PMID: 30131946 PMCID: PMC6091211 DOI: 10.3389/fcimb.2018.00274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/23/2018] [Indexed: 01/04/2023] Open
Abstract
Although plasmids provide additional functions for cellular adaptation to the environment, they also create a metabolic burden, which causes the host cells to be less competitive with their siblings. Low-copy-number plasmids have thus evolved several mechanisms for their long-term maintenance in host cells. pMF1, discovered in Myxococcus fulvus 124B02, is the only endogenous autonomously replicated plasmid yet found in myxobacteria. Here we report that a post-segregational killing system, encoded by a co-transcriptional gene pair of pMF1.19 and pMF1.20, is involved in maintaining the pMF1 plasmid in its host cells. We demonstrate that the protein encoded by pMF1.20 is a new kind of nuclease, which is able to cleave DNA in vitro. The nuclease activity can be neutralized by the protein encoded by pMF1.19 through protein–protein interaction, suggesting that the protein is an immune protein for nuclease cleavage. We propose that the post-segregational killing mechanism of the nuclease toxin and immune protein pair encoded by pMF1.20 and pMF1.19 is helpful for the stable maintenance of pMF1 in M. fulvus cells.
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Affiliation(s)
- Ya-Jie Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xiao-Jing Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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33
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Misra HS, Maurya GK, Kota S, Charaka VK. Maintenance of multipartite genome system and its functional significance in bacteria. J Genet 2018. [DOI: 10.1007/s12041-018-0969-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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34
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Kiu R, Hall LJ. An update on the human and animal enteric pathogen Clostridium perfringens. Emerg Microbes Infect 2018; 7:141. [PMID: 30082713 PMCID: PMC6079034 DOI: 10.1038/s41426-018-0144-8] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 12/18/2022]
Abstract
Clostridium perfringens, a rapid-growing pathogen known to secrete an arsenal of >20 virulent toxins, has been associated with intestinal diseases in both animals and humans throughout the past century. Recent advances in genomic analysis and experimental systems make it timely to re-visit this clinically and veterinary important pathogen. This Review will summarise our understanding of the genomics and virulence-linked factors, including antimicrobial potentials and secreted toxins of this gut pathogen, and then its up-to-date clinical epidemiology and biological role in the pathogenesis of several important human and animal-associated intestinal diseases, including pre-term necrotising enterocolitis. Finally, we highlight some of the important unresolved questions in relation to C. perfringens-mediated infections, and implications for future research directions.
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Affiliation(s)
- Raymond Kiu
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Lindsay J Hall
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
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A toxin-antitoxin system is essential for the stability of mosquitocidal plasmid pBsph of Lysinibacillus sphaericus. Microbiol Res 2018; 214:114-122. [PMID: 30031473 DOI: 10.1016/j.micres.2018.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 06/13/2018] [Accepted: 06/23/2018] [Indexed: 11/22/2022]
Abstract
Lysinibacillus sphaericus C3-41 carries a large low-copy-number plasmid pBsph, which encodes binary toxin proteins. Our previous study found that the transcriptional activator TubX plays an important role in the newly identified type Ⅲ TubRZC replication/partition system in pBsph, and that a vector consisting of tubRZC and tubX is not as stable as pBsph, indicating the presence of other maintenance module(s). In this study, we identified that orf9 and orf10 are necessary for the stability of pBsph by a series of deletion and complementation experiments. Bioinformatics analysis showed that ORF9 contains a PIN domain of VapBC toxin-antitoxin (TA) system, whereas ORF10 share no significant sequence similarity to any of the characterized antitoxins in the database. Further studies revealed that orf9 and orf10 are transcribed as an operon. The overexpression of ORF9 repressed the growth of both Escherichia coli and L. sphaericus, which can be alleviated by overexpression of ORF10. The deletion of orf10 individually or orf9-10 together resulted a decrease on plasmid stability which was restored by the complementation of corresponding gene(s), suggesting that ORF10 plays an important role in plasmid stability. In addition, it was found the plasmid stability is related with the transcription level of tubRZ, and overexpression of TubRZ could neutralize the negative effect on plasmid stability caused by the deletion of orf9-orf10. Moreover, the recombinant vector containing tubRZC, tubX and orf9-10 was more stable than the ones containing only tubRZC and either tubX or orf9-10. The data indicate that the plasmid maintenance system on pBsph includes orf9-orf10 TA system.
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36
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Misra HS, Maurya GK, Chaudhary R, Misra CS. Interdependence of bacterial cell division and genome segregation and its potential in drug development. Microbiol Res 2018; 208:12-24. [DOI: 10.1016/j.micres.2017.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 12/05/2017] [Accepted: 12/31/2017] [Indexed: 11/28/2022]
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37
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Afroj S, Aldahami K, Reddy G, Guard J, Adesiyun A, Samuel T, Abdela W. Simultaneous Detection of Multiple Salmonella Serovars from Milk and Chicken Meat by Real-Time PCR Using Unique Genomic Target Regions. J Food Prot 2017; 80:1944-1957. [PMID: 29058479 DOI: 10.4315/0362-028x.jfp-17-133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/19/2017] [Indexed: 12/29/2022]
Abstract
A novel genomic and plasmid target-based PCR platform was developed for the detection of Salmonella serovars Heidelberg, Dublin, Hadar, Kentucky, and Enteritidis. Unique genome loci were obtained through extensive genome mining of protein databases and comparative genomic analysis of these serovars. Assays targeting Salmonella serovars Hadar, Heidelberg, Kentucky, and Dublin had 100% specificity and sensitivity, whereas those for Salmonella Enteritidis had 97% specificity and 88% sensitivity. The limits of detection for Salmonella serovars Heidelberg, Kentucky, Hadar, Enteritidis, and Dublin were 12, 9, 40, 13, and 5,280 CFU, respectively. A sensitivity assay was also performed by using milk artificially inoculated with pooled Salmonella serovars, yielding a detection limit of 1 to10 CFU/25 mL of milk samples after enrichment. The minimum DNA detected using the multiplexed TaqMan assay was 75.8 fg (1.53 × 101 genomic equivalents [GE]) for Salmonella Heidelberg, 140.8 fg (2.8 × 101 GE) for Salmonella Enteritidis, and 3.48 pg (6.96 × 102 GE) for Salmonella Dublin. PCR efficiencies were 89.8% for Salmonella Heidelberg, 94.5% for Salmonella Enteritidis, and 75.5% for Salmonella Dublin. Four types of 30 pasteurized milk samples were tested negative by culture techniques and with a genus-specific Salmonella invA gene PCR assay. Among 30 chicken samples similarly tested, 12 (40%) were positive by both culture and the invA PCR. Testing of these 12 samples with the serovar-specific PCR assay detected single and mixed contamination with Salmonella Kentucky, Salmonella Enteritidis, and Salmonella Heidelberg. Five unique primers were designed and tested by multiplex conventional PCR in conjunction with the use of the multiplex TaqMan assay with three of the primers. The diagnostic assays developed in this study could be used as tools for routine detection of these five Salmonella serovars and for epidemiological investigations of foodborne disease outbreaks.
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Affiliation(s)
- Sayma Afroj
- Department of Biology and.,Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.]).,Cellular and Molecular Biosciences Program, Auburn University, Auburn, Alabama 36849, USA
| | - Khaled Aldahami
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Gopal Reddy
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Jean Guard
- U.S. Department of Agriculture, Agricultural Research Service, Athens, Georgia 30602, USA
| | - Abiodun Adesiyun
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Temesgen Samuel
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Woubit Abdela
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
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Compensatory mutations improve general permissiveness to antibiotic resistance plasmids. Nat Ecol Evol 2017; 1:1354-1363. [PMID: 29046540 PMCID: PMC5649373 DOI: 10.1038/s41559-017-0243-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/16/2017] [Indexed: 11/08/2022]
Abstract
Horizontal gene transfer mediated by broad-host-range plasmids is an important mechanism of antibiotic resistance spread. While not all bacteria maintain plasmids equally well, plasmid persistence can improve over time, yet no general evolutionary mechanisms have emerged. Our goal was to identify these mechanisms and to assess if adaptation to one plasmid affects the permissiveness to others. We experimentally evolved Pseudomonas sp. H2 containing multidrug resistance plasmid RP4, determined plasmid persistence and cost using a joint experimental-modelling approach, resequenced evolved clones, and reconstructed key mutations. Plasmid persistence improved in fewer than 600 generations because the fitness cost turned into a benefit. Improved retention of naive plasmids indicated that the host evolved towards increased plasmid permissiveness. Key chromosomal mutations affected two accessory helicases and the RNA polymerase β-subunit. Our and other findings suggest that poor plasmid persistence can be caused by a high cost involving helicase-plasmid interactions that can be rapidly ameliorated.
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39
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Direct and convenient measurement of plasmid stability in lab and clinical isolates of E. coli. Sci Rep 2017; 7:4788. [PMID: 28684862 PMCID: PMC5500522 DOI: 10.1038/s41598-017-05219-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/25/2017] [Indexed: 01/01/2023] Open
Abstract
Plasmids are important mobile elements in bacteria, contributing to evolution, virulence, and antibiotic resistance. Natural plasmids are generally large and maintained at low copy number and thus prone to be lost. Therefore, dedicated plasmid maintenance systems have evolved, leading to plasmid loss rates as low as 1 per 107 divisions. These low rates complicate studies of plasmid loss, as traditional techniques for measuring plasmid loss are laborious and not quantitative. To overcome these limitations, we leveraged a stringent negative selection system to develop a method for performing direct, quantitative measurements of plasmid loss in E. coli. We applied our method to gain mechanistic insights into a heterologously reconstituted segregation system in lab strains and clinical isolates of E. coli. We also performed direct stability studies of a currently circulating resistance plasmid in a clinical isolate, strain EC958, which is a member of the rapidly expanding global ST131 E. coli clone. Our results establish the foundational assays required to screen for small molecules targeting plasmid stability, which could complement current strategies for reducing the spread of antibiotic resistance, complementing other strategies for treating antibiotic resistant bacteria.
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40
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Hu L, Vecchiarelli AG, Mizuuchi K, Neuman KC, Liu J. Brownian Ratchet Mechanism for Faithful Segregation of Low-Copy-Number Plasmids. Biophys J 2017; 112:1489-1502. [PMID: 28402891 PMCID: PMC5390091 DOI: 10.1016/j.bpj.2017.02.039] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/19/2017] [Accepted: 02/28/2017] [Indexed: 11/16/2022] Open
Abstract
Bacterial plasmids are extrachromosomal DNA that provides selective advantages for bacterial survival. Plasmid partitioning can be remarkably robust. For high-copy-number plasmids, diffusion ensures that both daughter cells inherit plasmids after cell division. In contrast, most low-copy-number plasmids need to be actively partitioned by a conserved tripartite ParA-type system. ParA is an ATPase that binds to chromosomal DNA; ParB is the stimulator of the ParA ATPase and specifically binds to the plasmid at a centromere-like site, parS. ParB stimulation of the ParA ATPase releases ParA from the bacterial chromosome, after which it takes a long time to reset its DNA-binding affinity. We previously demonstrated in vitro that the ParA system can exploit this biochemical asymmetry for directed cargo transport. Multiple ParA-ParB bonds can bridge a parS-coated cargo to a DNA carpet, and they can work collectively as a Brownian ratchet that directs persistent cargo movement with a ParA-depletion zone trailing behind. By extending this model, we suggest that a similar Brownian ratchet mechanism recapitulates the full range of actively segregated plasmid motilities observed in vivo. We demonstrate that plasmid motility is tuned as the replenishment rate of the ParA-depletion zone progressively increases relative to the cargo speed, evolving from diffusion to pole-to-pole oscillation, local excursions, and, finally, immobility. When the plasmid replicates, the daughters largely display motilities similar to that of their mother, except that when the single-focus progenitor is locally excursive, the daughter foci undergo directed segregation. We show that directed segregation maximizes the fidelity of plasmid partition. Given that local excursion and directed segregation are the most commonly observed modes of plasmid motility in vivo, we suggest that the operation of the ParA-type partition system has been shaped by evolution for high fidelity of plasmid segregation.
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Affiliation(s)
- Longhua Hu
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology (MCDB), University of Michigan, Ann Arbor, Michigan
| | - Kiyoshi Mizuuchi
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Keir C Neuman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Jian Liu
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland.
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41
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Cox KEL, Schildbach JF. Sequence of the R1 plasmid and comparison to F and R100. Plasmid 2017; 91:53-60. [PMID: 28359666 DOI: 10.1016/j.plasmid.2017.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/13/2017] [Accepted: 03/26/2017] [Indexed: 12/29/2022]
Abstract
The R1 antibiotic resistance plasmid, originally discovered in a clinical Salmonella isolate in London, 1963, has served for decades as a key model for understanding conjugative plasmids. Despite its scientific importance, a complete sequence of this plasmid has never been reported. We present the complete genome sequence of R1 along with a brief review of the current knowledge concerning its various genetic systems and a comparison to the F and R100 plasmids. R1 is 97,566 nucleotides long and contains 120 genes. The plasmid consists of a backbone largely similar to that of F and R100, a Tn21-like transposon that is nearly identical to that of R100, and a unique 9-kb sequence that bears some resemblance to sequences found in certain Klebsiella oxytoca strains. These three regions of R1 are separated by copies of the insertion sequence IS1. Overall, the structure of R1 and comparison to F and R100 suggest a fairly stable shared conjugative plasmid backbone into which a variety of mobile elements have inserted to form an "accessory" genome, containing multiple antibiotic resistance genes, transposons, remnants of phage genes, and genes whose functions remain unknown.
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Affiliation(s)
- Katherine E L Cox
- Department of Biology, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218, USA.
| | - Joel F Schildbach
- Department of Biology, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218, USA.
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Lobato-Márquez D, Molina-García L, Moreno-Córdoba I, García-Del Portillo F, Díaz-Orejas R. Stabilization of the Virulence Plasmid pSLT of Salmonella Typhimurium by Three Maintenance Systems and Its Evaluation by Using a New Stability Test. Front Mol Biosci 2016; 3:66. [PMID: 27800482 PMCID: PMC5065971 DOI: 10.3389/fmolb.2016.00066] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 09/27/2016] [Indexed: 12/27/2022] Open
Abstract
Certain Salmonella enterica serovars belonging to subspecies I carry low-copy-number virulence plasmids of variable size (50–90 kb). All of these plasmids share the spv operon, which is important for systemic infection. Virulence plasmids are present at low copy numbers. Few copies reduce metabolic burden but suppose a risk of plasmid loss during bacterial division. This drawback is counterbalanced by maintenance modules that ensure plasmid stability, including partition systems and toxin-antitoxin (TA) loci. The low-copy number virulence pSLT plasmid of Salmonella enterica serovar Typhimurium encodes three auxiliary maintenance systems: one partition system (parAB) and two TA systems (ccdABST and vapBC2ST). The TA module ccdABST has previously been shown to contribute to pSLT plasmid stability and vapBC2ST to bacterial virulence. Here we describe a novel assay to measure plasmid stability based on the selection of plasmid-free cells following elimination of plasmid-containing cells by ParE toxin, a DNA gyrase inhibitor. Using this new maintenance assay we confirmed a crucial role of parAB in pSLT maintenance. We also showed that vapBC2ST, in addition to contribute to bacterial virulence, is important for plasmid stability. We have previously shown that ccdABST encodes an inactive CcdBST toxin. Using our new stability assay we monitored the contribution to plasmid stability of a ccdABST variant containing a single mutation (R99W) that restores the toxicity of CcdBST. The “activation” of CcdBST (R99W) did not increase pSLT stability by ccdABST. In contrast, ccdABST behaves as a canonical type II TA system in terms of transcriptional regulation. Of interest, ccdABST was shown to control the expression of a polycistronic operon in the pSLT plasmid. Collectively, these results show that the contribution of the CcdBST toxin to pSLT plasmid stability may depend on its role as a co-repressor in coordination with CcdAST antitoxin more than on its toxic activity.
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Affiliation(s)
- Damián Lobato-Márquez
- Section of Microbiology, Department of Medicine, Centre for Molecular Bacteriology and Infection, Imperial College London London, UK
| | - Laura Molina-García
- Department of Cell and Developmental Biology, University College London London, UK
| | - Inma Moreno-Córdoba
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas-Spanish National Research Council Madrid, Spain
| | - Francisco García-Del Portillo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Spanish National Research Council Madrid, Spain
| | - Ramón Díaz-Orejas
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas-Spanish National Research Council Madrid, Spain
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Toro-Nahuelpan M, Müller FD, Klumpp S, Plitzko JM, Bramkamp M, Schüler D. Segregation of prokaryotic magnetosomes organelles is driven by treadmilling of a dynamic actin-like MamK filament. BMC Biol 2016; 14:88. [PMID: 27733152 PMCID: PMC5059902 DOI: 10.1186/s12915-016-0290-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The navigation of magnetotactic bacteria relies on specific intracellular organelles, the magnetosomes, which are membrane-enclosed crystals of magnetite aligned into a linear chain. The magnetosome chain acts as a cellular compass, aligning the cells in the geomagnetic field in order to search for suitable environmental conditions in chemically stratified water columns and sediments. During cytokinesis, magnetosome chains have to be properly positioned, cleaved and separated in order to be evenly passed into daughter cells. In Magnetospirillum gryphiswaldense, the assembly of the magnetosome chain is controlled by the actin-like MamK, which polymerizes into cytoskeletal filaments that are connected to magnetosomes through the acidic MamJ protein. MamK filaments were speculated to recruit the magnetosome chain to cellular division sites, thus ensuring equal organelle inheritance. However, the underlying mechanism of magnetic organelle segregation has remained largely unknown. RESULTS Here, we performed in vivo time-lapse fluorescence imaging to directly track the intracellular movement and dynamics of magnetosome chains as well as photokinetic and ultrastructural analyses of the actin-like cytoskeletal MamK filament. We show that magnetosome chains undergo rapid intracellular repositioning from the new poles towards midcell into the newborn daughter cells, and the driving force for magnetosomes movement is likely provided by the pole-to-midcell treadmilling growth of MamK filaments. We further discovered that splitting and equipartitioning of magnetosome chains occurs with unexpectedly high accuracy, which depends directly on the dynamics of MamK filaments. CONCLUSION We propose a novel mechanism for prokaryotic organelle segregation that, similar to the type-II bacterial partitioning system of plasmids, relies on the action of cytomotive actin-like filaments together with specific connectors, which transport the magnetosome cargo in a fashion reminiscent of eukaryotic actin-organelle transport and segregation mechanisms.
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Affiliation(s)
- Mauricio Toro-Nahuelpan
- Department of Microbiology, University of Bayreuth, 95447, Bayreuth, Germany.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Planegg-Martinsried, Germany
| | - Frank D Müller
- Department of Microbiology, University of Bayreuth, 95447, Bayreuth, Germany
| | - Stefan Klumpp
- Department Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.,Institute for Nonlinear Dynamics, Georg August University Göttingen, Göttingen, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Planegg-Martinsried, Germany
| | - Marc Bramkamp
- Department of Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, 95447, Bayreuth, Germany.
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Munro JE, Liew EF, Ly MA, Coleman NV. A New Catabolic Plasmid in Xanthobacter and Starkeya spp. from a 1,2-Dichloroethane-Contaminated Site. Appl Environ Microbiol 2016; 82:5298-308. [PMID: 27342553 PMCID: PMC4988179 DOI: 10.1128/aem.01373-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 06/13/2016] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED 1,2-Dichloroethane (DCA) is a problematic xenobiotic groundwater pollutant. Bacteria are capable of biodegrading DCA, but the evolution of such bacteria is not well understood. In particular, the mechanisms by which bacteria acquire the key dehalogenase genes dhlA and dhlB have not been well defined. In this study, the genomic context of dhlA and dhlB was determined in three aerobic DCA-degrading bacteria (Starkeya novella strain EL1, Xanthobacter autotrophicus strain EL4, and Xanthobacter flavus strain EL8) isolated from a groundwater treatment plant (GTP). A haloalkane dehalogenase gene (dhlA) identical to the canonical dhlA gene from Xanthobacter sp. strain GJ10 was present in all three isolates, and, in each case, the dhlA gene was carried on a variant of a 37-kb circular plasmid, which was named pDCA. Sequence analysis of the repA replication initiator gene indicated that pDCA was a member of the pTAR plasmid family, related to catabolic plasmids from the Alphaproteobacteria, which enable growth on aromatics, dimethylformamide, and tartrate. Genes for plasmid replication, mobilization, and stabilization were identified, along with two insertion sequences (ISXa1 and ISPme1) which were likely to have mobilized dhlA and dhlB and played a role in the evolution of aerobic DCA-degrading bacteria. Two haloacid dehalogenase genes (dhlB1 and dhlB2) were detected in the GTP isolates; dhlB1 was most likely chromosomal and was similar to the canonical dhlB gene from strain GJ10, while dhlB2 was carried on pDCA and was not closely related to dhlB1 Heterologous expression of the DhlB2 protein confirmed that this plasmid-borne dehalogenase was capable of chloroacetate dechlorination. IMPORTANCE Earlier studies on the DCA-degrading Xanthobacter sp. strain GJ10 indicated that the key dehalogenases dhlA and dhlB were carried on a 225-kb linear plasmid and on the chromosome, respectively. The present study has found a dramatically different gene organization in more recently isolated DCA-degrading Xanthobacter strains from Australia, in which a relatively small circular plasmid (pDCA) carries both dhlA and dhlB homologs. pDCA represents a true organochlorine-catabolic plasmid, first because its only obvious metabolic phenotype is dehalogenation of organochlorines, and second because acquisition of this plasmid provides both key enzymes required for carbon-chlorine bond cleavage. The discovery of the alternative haloacid dehalogenase dhlB2 in pDCA increases the known genetic diversity of bacterial chloroacetate-hydrolyzing enzymes.
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Affiliation(s)
- Jacob E Munro
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Elissa F Liew
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Mai-Anh Ly
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Nicholas V Coleman
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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Bacterial partition complexes segregate within the volume of the nucleoid. Nat Commun 2016; 7:12107. [PMID: 27377966 PMCID: PMC4935973 DOI: 10.1038/ncomms12107] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/31/2016] [Indexed: 11/08/2022] Open
Abstract
Precise and rapid DNA segregation is required for proper inheritance of genetic material. In most bacteria and archaea, this process is assured by a broadly conserved mitotic-like apparatus in which a NTPase (ParA) displaces the partition complex. Competing observations and models imply starkly different 3D localization patterns of the components of the partition machinery during segregation. Here we use super-resolution microscopies to localize in 3D each component of the segregation apparatus with respect to the bacterial chromosome. We show that Par proteins locate within the nucleoid volume and reveal that proper volumetric localization and segregation of partition complexes requires ATPase and DNA-binding activities of ParA. Finally, we find that the localization patterns of the different components of the partition system highly correlate with dense chromosomal regions. We propose a new mechanism in which the nucleoid provides a scaffold to guide the proper segregation of partition complexes. In most bacteria and archaea, a broadly conserved mitotic-like apparatus assures the inheritance of duplicated genetic material before cell division. Here, the authors use super-resolution microscopies to dissect the activities required for proper DNA segregation through the nucleoid interior.
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Dedrick RM, Mavrich TN, Ng WL, Cervantes Reyes JC, Olm MR, Rush RE, Jacobs-Sera D, Russell DA, Hatfull GF. Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems. Mol Microbiol 2016; 101:625-44. [PMID: 27146086 DOI: 10.1111/mmi.13414] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2016] [Indexed: 11/27/2022]
Abstract
More than 180 individual phages infecting hosts in the phylum Actinobacteria have been sequenced and grouped into Cluster A because of their similar overall nucleotide sequences and genome architectures. These Cluster A phages are either temperate or derivatives of temperate parents, and most have an integration cassette near the centre of the genome containing an integrase gene and attP. However, about 20% of the phages lack an integration cassette, which is replaced by a 1.4 kbp segment with predicted partitioning functions, including plasmid-like parA and parB genes. Phage RedRock forms stable lysogens in Mycobacterium smegmatis in which the prophage replicates at 2.4 copies/chromosome and the partitioning system confers prophage maintenance. The parAB genes are expressed upon RedRock infection of M. smegmatis, but are downregulated once lysogeny is established by binding of RedRock ParB to parS-L, one of two centromere-like sites flanking the parAB genes. The RedRock parS-L and parS-R sites are composed of eight directly repeated copies of an 8 bp motif that is recognized by ParB. The actinobacteriophage parABS cassettes span considerable sequence diversity and specificity, providing a suite of tools for use in mycobacterial genetics.
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Affiliation(s)
- Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Travis N Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Wei L Ng
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | | | - Matthew R Olm
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Rachael E Rush
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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Loftie-Eaton W, Yano H, Burleigh S, Simmons RS, Hughes JM, Rogers LM, Hunter SS, Settles ML, Forney LJ, Ponciano JM, Top EM. Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance. Mol Biol Evol 2016; 33:885-97. [PMID: 26668183 PMCID: PMC4840908 DOI: 10.1093/molbev/msv339] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The World Health Organization has declared the emergence of antibiotic resistance to be a global threat to human health. Broad-host-range plasmids have a key role in causing this health crisis because they transfer multiple resistance genes to a wide range of bacteria. To limit the spread of antibiotic resistance, we need to gain insight into the mechanisms by which the host range of plasmids evolves. Although initially unstable plasmids have been shown to improve their persistence through evolution of the plasmid, the host, or both, the means by which this occurs are poorly understood. Here, we sought to identify the underlying genetic basis of expanded plasmid host-range and increased persistence of an antibiotic resistance plasmid using a combined experimental-modeling approach that included whole-genome resequencing, molecular genetics and a plasmid population dynamics model. In nine of the ten previously evolved clones, changes in host and plasmid each slightly improved plasmid persistence, but their combination resulted in a much larger improvement, which indicated positive epistasis. The only genetic change in the plasmid was the acquisition of a transposable element from a plasmid native to the Pseudomonas host used in these studies. The analysis of genetic deletions showed that the critical genes on this transposon encode a putative toxin-antitoxin (TA) and a cointegrate resolution system. As evolved plasmids were able to persist longer in multiple naïve hosts, acquisition of this transposon also expanded the plasmid's host range, which has important implications for the spread of antibiotic resistance.
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Affiliation(s)
- Wesley Loftie-Eaton
- Department of Biological Sciences, University of Idaho Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
| | - Hirokazu Yano
- Department of Biological Sciences, University of Idaho Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
| | | | | | - Julie M Hughes
- Department of Biological Sciences, University of Idaho Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
| | - Linda M Rogers
- Department of Biological Sciences, University of Idaho Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
| | - Matthew L Settles
- Department of Biological Sciences, University of Idaho Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
| | - Larry J Forney
- Department of Biological Sciences, University of Idaho Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
| | | | - Eva M Top
- Department of Biological Sciences, University of Idaho Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
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The Interplay between Different Stability Systems Contributes to Faithful Segregation: Streptococcus pyogenes pSM19035 as a Model. Microbiol Spectr 2016; 2:PLAS-0007-2013. [PMID: 26104212 DOI: 10.1128/microbiolspec.plas-0007-2013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The Streptococcus pyogenes pSM19035 low-copy-number θ-replicating plasmid encodes five segregation (seg) loci that contribute to plasmid maintenance. These loci map outside of the minimal replicon. The segA locus comprises β2 recombinase and two six sites, and segC includes segA and also the γ topoisomerase and two ssiA sites. Recombinase β2 plays a role both in maximizing random segregation by resolving plasmid dimers (segA) and in catalyzing inversion between two inversely oriented six sites. segA, in concert with segC, facilitates replication fork pausing at ssiA sites and overcomes the accumulation of "toxic" replication intermediates. The segB1 locus encodes ω, ε, and ζ genes. The short-lived ε2 antitoxin and the long-lived ζ toxin form an inactive ζε2ζ complex. Free ζ toxin halts cell proliferation upon decay of the ε2 antitoxin and enhances survival. If ε2 expression is not recovered, by loss of the plasmid, the toxin raises lethality. The segB2 locus comprises δ and ω genes and six parS sites. Proteins δ2 and ω2, by forming complexes with parS and chromosomal DNA, pair the plasmid copies at the nucleoid, leading to the formation of a dynamic δ2 gradient that separates the plasmids to ensure roughly equal distribution to daughter cells at cell division. The segD locus, which comprises ω2 (or ω2 plus ω22) and parS sites, coordinates expression of genes that control copy number, better-than-random segregation, faithful partition, and antibiotic resistance. The interplay of the seg loci and with the rep locus facilitates almost absolute plasmid stability.
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Versatile plasmid-based expression systems for Gram-negative bacteria—General essentials exemplified with the bacterium Ralstonia eutropha H16. N Biotechnol 2015; 32:552-8. [DOI: 10.1016/j.nbt.2015.03.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 03/12/2015] [Accepted: 03/20/2015] [Indexed: 12/13/2022]
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Abstract
Traditionally eukaryotes exclusive cytoskeleton has been found in bacteria and other prokaryotes. FtsZ, MreB and CreS are bacterial counterpart of eukaryotic tubulin, actin filaments and intermediate filaments, respectively. FtsZ can assemble to a Z-ring at the cell division site, regulate bacterial cell division; MreB can form helical structure, and involve in maintaining cell shape, regulating chromosome segregation; CreS, found in Caulobacter crescentus (C. crescentus), can form curve or helical filaments in intracellular membrane. CreS is crucial for cell morphology maintenance. There are also some prokaryotic unique cytoskeleton components playing crucial roles in cell division, chromosome segregation and cell morphology. The cytoskeleton components of Mycobacterium tuberculosis (M. tuberculosis), together with their dynamics during exposure to antibiotics are summarized in this article to provide insights into the unique organization of this formidable pathogen and druggable targets for new antibiotics.
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Affiliation(s)
- Huan Wang
- a Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University , Chongqing , China
| | - Longxiang Xie
- a Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University , Chongqing , China
| | - Hongping Luo
- a Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University , Chongqing , China
| | - Jianping Xie
- a Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University , Chongqing , China
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