1
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Cornet F, Blanchais C, Dusfour-Castan R, Meunier A, Quebre V, Sekkouri Alaoui H, Boudsoq F, Campos M, Crozat E, Guynet C, Pasta F, Rousseau P, Ton Hoang B, Bouet JY. DNA Segregation in Enterobacteria. EcoSal Plus 2023; 11:eesp00382020. [PMID: 37220081 DOI: 10.1128/ecosalplus.esp-0038-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/13/2023] [Indexed: 01/28/2024]
Abstract
DNA segregation ensures that cell offspring receive at least one copy of each DNA molecule, or replicon, after their replication. This important cellular process includes different phases leading to the physical separation of the replicons and their movement toward the future daughter cells. Here, we review these phases and processes in enterobacteria with emphasis on the molecular mechanisms at play and their controls.
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Affiliation(s)
- François Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Corentin Blanchais
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Romane Dusfour-Castan
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Alix Meunier
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Valentin Quebre
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Hicham Sekkouri Alaoui
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - François Boudsoq
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Manuel Campos
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Estelle Crozat
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Catherine Guynet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Franck Pasta
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Bao Ton Hoang
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
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2
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Sarosh A, Kwong SM, Jensen SO, Northern F, Walton WG, Eakes TC, Redinbo MR, Firth N, McLaughlin KJ. pSK41/pGO1-family conjugative plasmids of Staphylococcus aureus encode a cryptic repressor of replication. Plasmid 2023; 128:102708. [PMID: 37967733 DOI: 10.1016/j.plasmid.2023.102708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
The majority of large multiresistance plasmids of Staphylococcus aureus utilise a RepA_N-type replication initiation protein, the expression of which is regulated by a small antisense RNA (RNAI) that overlaps the rep mRNA leader. The pSK41/pGO1-family of conjugative plasmids additionally possess a small (86 codon) divergently transcribed ORF (orf86) located upstream of the rep locus. The product of pSK41 orf86 was predicted to have a helix-turn-helix motif suggestive of a likely function in transcriptional repression. In this study, we investigated the effect of Orf86 on transcription of thirteen pSK41 backbone promoters. We found that Orf86 only repressed transcription from the rep promoter, and hence now redesignate the product as Cop. Over-expression of Cop in trans reduced the copy number of pSK41 mini-replicons, both in the presence and absence of rnaI. in vitro protein-DNA binding experiments with purified 6 × His-Cop demonstrated specific DNA binding, adjacent to, and partially overlapping the -35 hexamer of the rep promoter. The crystal structure of Cop revealed a dimeric structure similar to other known transcriptional regulators. Cop mRNA was found to result from "read-through" transcription from the strong RNAI promoter that escapes the rnaI terminator. Thus, PrnaI is responsible for transcription of two distinct negative regulators of plasmid copy number; the antisense RNAI that primarily represses Rep translation, and Cop protein that can repress rep transcription. Deletion of cop in a native plasmid did not appear to impact copy number, indicating a cryptic auxiliary role.
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Affiliation(s)
- Alvina Sarosh
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales 2751, Australia; Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, New South Wales 2170, Australia
| | - Faith Northern
- Chemistry Department, Vassar College, Poughkeepsie, NY 12604, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Thomas C Eakes
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biochemistry, Microbiology and Genomics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.
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3
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Siguier P, Campos M, Cornet F, Bouet JY, Guynet C. Atypical low-copy number plasmid segregation systems, all in one? Plasmid 2023; 127:102694. [PMID: 37301314 DOI: 10.1016/j.plasmid.2023.102694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Plasmid families harbor different maintenances functions, depending on their size and copy number. Low copy number plasmids rely on active partition systems, organizing a partition complex at specific centromere sites that is actively positioned using NTPase proteins. Some low copy number plasmids lack an active partition system, but carry atypical intracellular positioning systems using a single protein that binds to the centromere site but without an associated NTPase. These systems have been studied in the case of the Escherichia coli R388 and of the Staphylococcus aureus pSK1 plasmids. Here we review these two systems, which appear to be unrelated but share common features, such as their distribution on plasmids of medium size and copy number, certain activities of their centromere-binding proteins, StbA and Par, respectively, as well as their mode of action, which may involve dynamic interactions with the nucleoid-packed chromosome of their hosts.
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Affiliation(s)
- Patricia Siguier
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Manuel Campos
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - François Cornet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Catherine Guynet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France.
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4
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Carman PJ, Rebowski G, Dominguez R, Alqassim SS. Single particle cryo-EM analysis of Rickettsia conorii Sca2 reveals a formin-like core. J Struct Biol 2023; 215:107960. [PMID: 37028467 DOI: 10.1016/j.jsb.2023.107960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/16/2023] [Accepted: 04/01/2023] [Indexed: 04/08/2023]
Abstract
Spotted fever group Rickettsia undergo actin-based motility inside infected eukaryotic cells using Sca2 (surface cell antigen 2): an ∼1800 amino-acid monomeric autotransporter protein that is surface-attached to the bacterium and responsible for the assembly of long unbranched actin tails. Sca2 is the only known functional mimic of eukaryotic formins, yet it shares no sequence similarities to the latter. Using structural and biochemical approaches we have previously shown that Sca2 uses a novel actin assembly mechanism. The first ∼400 amino acids fold into helix-loop-helix repeats that form a crescent shape reminiscent of a formin FH2 monomer. Additionally, the N- and C- terminal halves of Sca2 display intramolecular interaction in an end-to-end manner and cooperate for actin assembly, mimicking a formin FH2 dimer. Towards a better structural understanding of this mechanism, we performed single-particle cryo-electron microscopy analysis of Sca2. While high-resolution structural details remain elusive, our model confirms the presence of a formin-like core: Sca2 indeed forms a doughnut shape, similar in diameter to a formin FH2 dimer and can accommodate two actin subunits. Extra electron density, thought to be contributed by the C-terminal repeat domain (CRD), covering one side is also observed. This structural analysis allows us to propose an updated model where nucleation proceeds by encircling two actin subunits, and elongation proceeds either by a formin-like mechanism that necessitates conformational changes in the observed Sca2 model, or via an insertional mechanism akin to that observed in the ParMRC system.
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Affiliation(s)
- Peter J Carman
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Grzegorz Rebowski
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Saif S Alqassim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
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5
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Molecular Analysis of pSK1 par: A Novel Plasmid Partitioning System Encoded by Staphylococcal Multiresistance Plasmids. J Mol Biol 2022; 434:167770. [PMID: 35907571 DOI: 10.1016/j.jmb.2022.167770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/23/2022]
Abstract
The segregation of prokaryotic plasmids typically requires a centromere-like site and two proteins, a centromere-binding protein (CBP) and an NTPase. By contrast, a single 245 residue Par protein mediates partition of the prototypical staphylococcal multiresistance plasmid pSK1 in the absence of an identifiable NTPase component. To gain insight into centromere binding by pSK1 Par and its segregation function we performed structural, biochemical and in vivo studies. Here we show that pSK1 Par binds a centromere consisting of seven repeat elements. We demonstrate this Par-centromere interaction also mediates Par autoregulation. To elucidate the Par centromere binding mechanism, we obtained a structure of the Par N-terminal DNA-binding domain bound to centromere DNA to 2.25 Å. The pSK1 Par structure, which harbors a winged-helix-turn-helix (wHTH), is distinct from other plasmid CBP structures but shows homology to the B. subtilis chromosome segregation protein, RacA. Biochemical studies suggest the region C-terminal to the Par wHTH forms coiled coils and mediates oligomerization. Fluorescence microscopy analyses show that pSK1 Par enhances the separation of plasmids from clusters, driving effective segregation upon cell division. Combined the data provide insight into the molecular properties of a single protein partition system.
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6
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Characterization of the DNA Binding Domain of StbA, A Key Protein of A New Type of DNA Segregation System. J Mol Biol 2022; 434:167752. [PMID: 35868361 DOI: 10.1016/j.jmb.2022.167752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 11/21/2022]
Abstract
Low-copy-number plasmids require sophisticated genetic devices to achieve efficient segregation of plasmid copies during cell division. Plasmid R388 uses a unique segregation mechanism, based on StbA, a small multifunctional protein. StbA is the key protein in a segregation system not involving a plasmid-encoded NTPase partner, it regulates the expression of several plasmid operons, and it is the main regulator of plasmid conjugation. The mechanisms by which StbA, together with the centromere-like sequence stbS, achieves segregation, is largely uncharacterized. To better understand the molecular basis of R388 segregation, we determined the crystal structure of the conserved N-terminal domain of StbA to 1.9 Å resolution. It folds into an HTH DNA-binding domain, structurally related to that of the PadR subfamily II of transcriptional regulators. StbA is organized in two domains. Its N-terminal domain carries the specific stbS DNA binding activity. A truncated version of StbA, deleted of its C-terminal domain, displays only partial activities in vivo, indicating that the non-conserved C-terminal domain is required for efficient segregation and subcellular plasmid positioning. The structure of StbA DNA-binding domain also provides some insight into how StbA monomers cooperate to repress transcription by binding to the stbDR and to form the segregation complex with stbS.
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7
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The Specificity of ParR Binding Determines the Incompatibility of Conjugative Plasmids in Clostridium perfringens. mBio 2022; 13:e0135622. [PMID: 35726914 PMCID: PMC9426499 DOI: 10.1128/mbio.01356-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Plasmids that encode the same replication machinery are generally unable to coexist in the same bacterial cell. However, Clostridium perfringens strains often carry multiple conjugative toxin or antibiotic resistance plasmids that are closely related and encode similar Rep proteins. In many bacteria, plasmid partitioning upon cell division involves a ParMRC system; in C. perfringens plasmids, there are approximately 10 different ParMRC families, with significant differences in amino acid sequences between each ParM family (15% to 54% identity). Since plasmids carrying genes belonging to the same ParMRC family are not observed in the same strain, these families appear to represent the basis for plasmid compatibility in C. perfringens. To understand this process, we examined the key recognition steps between ParR DNA-binding proteins and their parC binding sites. The ParR proteins bound to sequences within a parC site from the same ParMRC family but could not interact with a parC site from a different ParMRC family. These data provide evidence that compatibility of the conjugative toxin plasmids of C. perfringens is mediated by their parMRC-like partitioning systems. This process provides a selective advantage by enabling the host bacterium to maintain separate plasmids that encode toxins that are specific for different host targets.
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8
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Yen CY, Lin MG, Chen BW, Ng IW, Read N, Kabli AF, Wu CT, Shen YY, Chen CH, Barillà D, Sun YJ, Hsiao CD. Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly. Nucleic Acids Res 2021; 49:13150-13164. [PMID: 34850144 PMCID: PMC8682754 DOI: 10.1093/nar/gkab1155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Genome segregation is a vital process in all organisms. Chromosome partitioning remains obscure in Archaea, the third domain of life. Here, we investigated the SegAB system from Sulfolobus solfataricus. SegA is a ParA Walker-type ATPase and SegB is a site-specific DNA-binding protein. We determined the structures of both proteins and those of SegA–DNA and SegB–DNA complexes. The SegA structure revealed an atypical, novel non-sandwich dimer that binds DNA either in the presence or in the absence of ATP. The SegB structure disclosed a ribbon–helix–helix motif through which the protein binds DNA site specifically. The association of multiple interacting SegB dimers with the DNA results in a higher order chromatin-like structure. The unstructured SegB N-terminus plays an essential catalytic role in stimulating SegA ATPase activity and an architectural regulatory role in segrosome (SegA–SegB–DNA) formation. Electron microscopy results also provide a compact ring-like segrosome structure related to chromosome organization. These findings contribute a novel mechanistic perspective on archaeal chromosome segregation.
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Affiliation(s)
- Cheng-Yi Yen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Bo-Wei Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Irene W Ng
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Nicholas Read
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Azhar F Kabli
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Che-Ting Wu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yo-You Shen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Chen-Hao Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Daniela Barillà
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
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9
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Gogou C, Japaridze A, Dekker C. Mechanisms for Chromosome Segregation in Bacteria. Front Microbiol 2021; 12:685687. [PMID: 34220773 PMCID: PMC8242196 DOI: 10.3389/fmicb.2021.685687] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
The process of DNA segregation, the redistribution of newly replicated genomic material to daughter cells, is a crucial step in the life cycle of all living systems. Here, we review DNA segregation in bacteria which evolved a variety of mechanisms for partitioning newly replicated DNA. Bacterial species such as Caulobacter crescentus and Bacillus subtilis contain pushing and pulling mechanisms that exert forces and directionality to mediate the moving of newly synthesized chromosomes to the bacterial poles. Other bacteria such as Escherichia coli lack such active segregation systems, yet exhibit a spontaneous de-mixing of chromosomes due to entropic forces as DNA is being replicated under the confinement of the cell wall. Furthermore, we present a synopsis of the main players that contribute to prokaryotic genome segregation. We finish with emphasizing the importance of bottom-up approaches for the investigation of the various factors that contribute to genome segregation.
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Affiliation(s)
- Christos Gogou
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
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10
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Abstract
Plasmids are ubiquitous in the microbial world and have been identified in almost all species of bacteria that have been examined. Their localization inside the bacterial cell has been examined for about two decades; typically, they are not randomly distributed, and their positioning depends on copy number and their mode of segregation. Low-copy-number plasmids promote their own stable inheritance in their bacterial hosts by encoding active partition systems, which ensure that copies are positioned in both halves of a dividing cell. High-copy plasmids rely on passive diffusion of some copies, but many remain clustered together in the nucleoid-free regions of the cell. Here we review plasmid localization and partition (Par) systems, with particular emphasis on plasmids from Enterobacteriaceae and on recent results describing the in vivo localization properties and molecular mechanisms of each system. Partition systems also cause plasmid incompatibility such that distinct plasmids (with different replicons) with the same Par system cannot be stably maintained in the same cells. We discuss how partition-mediated incompatibility is a consequence of the partition mechanism.
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11
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Schumacher MA, Henderson M, Zhang H. Structures of maintenance of carboxysome distribution Walker-box McdA and McdB adaptor homologs. Nucleic Acids Res 2019; 47:5950-5962. [PMID: 31106331 PMCID: PMC6582323 DOI: 10.1093/nar/gkz314] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/06/2019] [Accepted: 04/27/2019] [Indexed: 12/31/2022] Open
Abstract
Carboxysomes, protein-coated organelles in cyanobacteria, are important in global carbon fixation. However, these organelles are present at low copy in each cell and hence must be segregated to ensure transmission from one generation to the next. Recent studies revealed that a DNA partition-like ParA–ParB system mediates carboxysome maintenance, called McdA-McdB. Here, we describe the first McdA and McdB homolog structures. McdA is similar to partition ParA Walker-box proteins, but lacks the P-loop signature lysine involved in ATP binding. Strikingly, a McdA-ATP structure shows that a lysine distant from the P-loop and conserved in McdA homologs, enables ATP-dependent nucleotide sandwich dimer formation. Similar to partition ParA proteins this ATP-bound form binds nonspecific-DNA. McdB, which we show directly binds McdA, harbors a unique fold and appears to form higher-order oligomers like partition ParB proteins. Thus, our data reveal a new signature motif that enables McdA dimer formation and indicates that, similar to DNA segregation, carboxysome maintenance systems employ Walker-box proteins as DNA-binding motors while McdB proteins form higher order oligomers, which could function as adaptors to link carboxysomes and provide for stable transport by the McdA proteins.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Max Henderson
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hengshan Zhang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
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12
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The structure of a 15-stranded actin-like filament from Clostridium botulinum. Nat Commun 2019; 10:2856. [PMID: 31253774 PMCID: PMC6599009 DOI: 10.1038/s41467-019-10779-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/20/2019] [Indexed: 02/02/2023] Open
Abstract
Microfilaments (actin) and microtubules represent the extremes in eukaryotic cytoskeleton cross-sectional dimensions, raising the question of whether filament architectures are limited by protein fold. Here, we report the cryoelectron microscopy structure of a complex filament formed from 15 protofilaments of an actin-like protein. This actin-like ParM is encoded on the large pCBH Clostridium botulinum plasmid. In cross-section, the ~26 nm diameter filament comprises a central helical protofilament surrounded by intermediate and outer layers of six and eight twisted protofilaments, respectively. Alternating polarity of the layers allows for similar lateral contacts between each layer. This filament design is stiffer than the actin filament, and has likely been selected for during evolution to move large cargos. The comparable sizes of microtubule and pCBH ParM filaments indicate that larger filament architectures are not limited by the protomer fold. Instead, function appears to have been the evolutionary driving force to produce broad, complex filaments. The plasmid-segregating actin-like protein ParM is encoded on the large, toxin carrying plasmid pCBH from Clostridium botulinum. Here the authors present the cryo-EM structure of the ParM filament that is formed from the association of 15 protofilaments and discuss its architecture.
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13
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Abstract
Strains of Staphylococcus aureus, and to a lesser extent other staphylococcal species, are a significant cause of morbidity and mortality. An important factor in the notoriety of these organisms stems from their frequent resistance to many antimicrobial agents used for chemotherapy. This review catalogues the variety of mobile genetic elements that have been identified in staphylococci, with a primary focus on those associated with the recruitment and spread of antimicrobial resistance genes. These include plasmids, transposable elements such as insertion sequences and transposons, and integrative elements including ICE and SCC elements. In concert, these diverse entities facilitate the intra- and inter-cellular gene mobility that enables horizontal genetic exchange, and have also been found to play additional roles in modulating gene expression and genome rearrangement.
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14
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1101] [Impact Index Per Article: 183.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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15
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Martín-García B, Martín-González A, Carrasco C, Hernández-Arriaga AM, Ruíz-Quero R, Díaz-Orejas R, Aicart-Ramos C, Moreno-Herrero F, Oliva MA. The TubR-centromere complex adopts a double-ring segrosome structure in Type III partition systems. Nucleic Acids Res 2018; 46:5704-5716. [PMID: 29762781 PMCID: PMC6009700 DOI: 10.1093/nar/gky370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/27/2018] [Indexed: 11/26/2022] Open
Abstract
In prokaryotes, the centromere is a specialized segment of DNA that promotes the assembly of the segrosome upon binding of the Centromere Binding Protein (CBP). The segrosome structure exposes a specific surface for the interaction of the CBP with the motor protein that mediates DNA movement during cell division. Additionally, the CBP usually controls the transcriptional regulation of the segregation system as a cell cycle checkpoint. Correct segrosome functioning is therefore indispensable for accurate DNA segregation. Here, we combine biochemical reconstruction and structural and biophysical analysis to bring light to the architecture of the segrosome complex in Type III partition systems. We present the particular features of the centromere site, tubC, of the model system encoded in Clostridium botulinum prophage c-st. We find that the split centromere site contains two different iterons involved in the binding and spreading of the CBP, TubR. The resulting nucleoprotein complex consists of a novel double-ring structure that covers part of the predicted promoter. Single molecule data provides a mechanism for the formation of the segrosome structure based on DNA bending and unwinding upon TubR binding.
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Affiliation(s)
- Bárbara Martín-García
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | | | - Carolina Carrasco
- Department of Macromolecular Structures, CSIC-Centro Nacional de Biotecnología, Madrid 28049, Spain
| | - Ana M Hernández-Arriaga
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | - Rubén Ruíz-Quero
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | - Ramón Díaz-Orejas
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, CSIC-Centro Nacional de Biotecnología, Madrid 28049, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, CSIC-Centro Nacional de Biotecnología, Madrid 28049, Spain
| | - María A Oliva
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
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16
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Szewczak-Harris A, Löwe J. Cryo-EM reconstruction of AlfA from Bacillus subtilis reveals the structure of a simplified actin-like filament at 3.4-Å resolution. Proc Natl Acad Sci U S A 2018; 115:3458-3463. [PMID: 29440489 PMCID: PMC5879667 DOI: 10.1073/pnas.1716424115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Low copy-number plasmid pLS32 of Bacillus subtilis subsp. natto contains a partitioning system that ensures segregation of plasmid copies during cell division. The partitioning locus comprises actin-like protein AlfA, adaptor protein AlfB, and the centromeric sequence parN Similar to the ParMRC partitioning system from Escherichia coli plasmid R1, AlfA filaments form actin-like double helical filaments that arrange into an antiparallel bipolar spindle, which attaches its growing ends to sister plasmids through interactions with AlfB and parN Because, compared with ParM and other actin-like proteins, AlfA is highly diverged in sequence, we determined the atomic structure of nonbundling AlfA filaments to 3.4-Å resolution by cryo-EM. The structure reveals how the deletion of subdomain IIB of the canonical actin fold has been accommodated by unique longitudinal and lateral contacts, while still enabling formation of left-handed, double helical, polar and staggered filaments that are architecturally similar to ParM. Through cryo-EM reconstruction of bundling AlfA filaments, we obtained a pseudoatomic model of AlfA doublets: the assembly of two filaments. The filaments are antiparallel, as required by the segregation mechanism, and exactly antiphasic with near eightfold helical symmetry, to enable efficient doublet formation. The structure of AlfA filaments and doublets shows, in atomic detail, how deletion of an entire domain of the actin fold is compensated by changes to all interfaces so that the required properties of polymerization, nucleotide hydrolysis, and antiparallel doublet formation are retained to fulfill the system's biological raison d'être.
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Affiliation(s)
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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17
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The complex simplicity of the bacterial cytoskeleton. Proc Natl Acad Sci U S A 2018; 115:3205-3206. [PMID: 29549153 DOI: 10.1073/pnas.1801783115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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18
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Wagstaff J, Löwe J. Prokaryotic cytoskeletons: protein filaments organizing small cells. Nat Rev Microbiol 2018; 16:187-201. [PMID: 29355854 DOI: 10.1038/nrmicro.2017.153] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Most, if not all, bacterial and archaeal cells contain at least one protein filament system. Although these filament systems in some cases form structures that are very similar to eukaryotic cytoskeletons, the term 'prokaryotic cytoskeletons' is used to refer to many different kinds of protein filaments. Cytoskeletons achieve their functions through polymerization of protein monomers and the resulting ability to access length scales larger than the size of the monomer. Prokaryotic cytoskeletons are involved in many fundamental aspects of prokaryotic cell biology and have important roles in cell shape determination, cell division and nonchromosomal DNA segregation. Some of the filament-forming proteins have been classified into a small number of conserved protein families, for example, the almost ubiquitous tubulin and actin superfamilies. To understand what makes filaments special and how the cytoskeletons they form enable cells to perform essential functions, the structure and function of cytoskeletal molecules and their filaments have been investigated in diverse bacteria and archaea. In this Review, we bring these data together to highlight the diverse ways that linear protein polymers can be used to organize other molecules and structures in bacteria and archaea.
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Affiliation(s)
- James Wagstaff
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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19
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Forde AJ, Albrecht N, Klingl A, Donovan C, Bramkamp M. Polymerization Dynamics of the Prophage-Encoded Actin-Like Protein AlpC Is Influenced by the DNA-Binding Adapter AlpA. Front Microbiol 2017; 8:1429. [PMID: 28824563 PMCID: PMC5539076 DOI: 10.3389/fmicb.2017.01429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/14/2017] [Indexed: 11/13/2022] Open
Abstract
The Corynebacterium glutamicum ATCC 13032 prophage CGP3 encodes an actin-like protein, AlpC that was shown to be involved in viral DNA transport and efficient viral DNA replication. AlpC binds to an adapter, AlpA that in turn binds to specific DNA sequences, termed alpS sites. Thus, the AlpAC system is similar to the known plasmid segregation system ParMRS. So far it is unclear how the AlpACS system mediates DNA transport and, whether AlpA and AlpC functionally interact. We show here that AlpA modulates AlpC filamentation dynamics in a dual way. Unbound AlpA stimulates AlpC filament disassembly, while AlpA bound to alpS sites allows for AlpC filament formation. Based on these results we propose a simple search and capture model that explains DNA segregation by viral AlpACS DNA segregation system.
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20
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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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21
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Zhang H, Schumacher MA. Structures of partition protein ParA with nonspecific DNA and ParB effector reveal molecular insights into principles governing Walker-box DNA segregation. Genes Dev 2017; 31:481-492. [PMID: 28373206 PMCID: PMC5393062 DOI: 10.1101/gad.296319.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 02/22/2017] [Indexed: 02/02/2023]
Abstract
Walker-box partition systems are ubiquitous in nature and mediate the segregation of bacterial and archaeal DNA. Well-studied plasmid Walker-box partition modules require ParA, centromere-DNA, and a centromere-binding protein, ParB. In these systems, ParA-ATP binds nucleoid DNA and uses it as a substratum to deliver ParB-attached cargo DNA, and ParB drives ParA dynamics, allowing ParA progression along the nucleoid. How ParA-ATP binds nonspecific DNA and is regulated by ParB is unclear. Also under debate is whether ParA polymerizes on DNA to mediate segregation. Here we describe structures of key ParA segregation complexes. The ParA-β,γ-imidoadenosine 5'-triphosphate (AMPPNP)-DNA structure revealed no polymers. Instead, ParA-AMPPNP dimerization creates a multifaceted DNA-binding surface, allowing it to preferentially bind high-density DNA regions (HDRs). DNA-bound ParA-AMPPNP adopts a dimer conformation distinct from the ATP sandwich dimer, optimized for DNA association. Our ParA-AMPPNP-ParB structure reveals that ParB binds at the ParA dimer interface, stabilizing the ATPase-competent ATP sandwich dimer, ultimately driving ParA DNA dissociation. Thus, the data indicate how harnessing a conformationally adaptive dimer can drive large-scale cargo movement without the requirement for polymers and suggest a segregation mechanism by which ParA-ATP dimers equilibrate to HDRs shown to be localized near cell poles of dividing chromosomes, thus mediating equipartition of attached ParB-DNA substrates.
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Affiliation(s)
- Hengshan Zhang
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Maria A Schumacher
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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22
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Gayathri P, Harne S. Structure and Dynamics of Actin-Like Cytomotive Filaments in Plasmid Segregation. Subcell Biochem 2017; 84:299-321. [PMID: 28500530 DOI: 10.1007/978-3-319-53047-5_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
One of the well-known functions of the bacterial cytoskeleton is plasmid segregation. Type II plasmid segregation systems, among the best characterized with respect to the mechanism of action, possess an actin-like cytomotive filament as the motor component. This chapter describes the essential components of the plasmid segregation machinery and their mechanism of action, concentrating on the actin-like protein family of the bacterial cytoskeleton. The structures of the actin-like filaments depend on their nucleotide state and these in turn contribute to the dynamics of the filaments. The components that link the filaments to the plasmid DNA also regulate filament dynamics. The modulation of the dynamics facilitates the cytomotive filament to function as a mitotic spindle with a minimal number of components.
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Affiliation(s)
- Pananghat Gayathri
- Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India.
| | - Shrikant Harne
- Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
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23
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Oliva MA. Segrosome Complex Formation during DNA Trafficking in Bacterial Cell Division. Front Mol Biosci 2016; 3:51. [PMID: 27668216 PMCID: PMC5016525 DOI: 10.3389/fmolb.2016.00051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/24/2016] [Indexed: 12/18/2022] Open
Abstract
Bacterial extrachromosomal DNAs often contribute to virulence in pathogenic organisms or facilitate adaptation to particular environments. The transmission of genetic information from one generation to the next requires sufficient partitioning of DNA molecules to ensure that at least one copy reaches each side of the division plane and is inherited by the daughter cells. Segregation of the bacterial chromosome occurs during or after replication and probably involves a strategy in which several protein complexes participate to modify the folding pattern and distribution first of the origin domain and then of the rest of the chromosome. Low-copy number plasmids rely on specialized partitioning systems, which in some cases use a mechanism that show striking similarity to eukaryotic DNA segregation. Overall, there have been multiple systems implicated in the dynamic transport of DNA cargo to a new cellular position during the cell cycle but most seem to share a common initial DNA partitioning step, involving the formation of a nucleoprotein complex called the segrosome. The particular features and complex topologies of individual segrosomes depend on both the nature of the DNA binding protein involved and on the recognized centromeric DNA sequence, both of which vary across systems. The combination of in vivo and in vitro approaches, with structural biology has significantly furthered our understanding of the mechanisms underlying DNA trafficking in bacteria. Here, I discuss recent advances and the molecular details of the DNA segregation machinery, focusing on the formation of the segrosome complex.
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Affiliation(s)
- María A Oliva
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
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24
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Dynamic Filament Formation by a Divergent Bacterial Actin-Like ParM Protein. PLoS One 2016; 11:e0156944. [PMID: 27310470 PMCID: PMC4911067 DOI: 10.1371/journal.pone.0156944] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 05/23/2016] [Indexed: 01/24/2023] Open
Abstract
Actin-like proteins (Alps) are a diverse family of proteins whose genes are abundant in the chromosomes and mobile genetic elements of many bacteria. The low-copy-number staphylococcal multiresistance plasmid pSK41 encodes ParM, an Alp involved in efficient plasmid partitioning. pSK41 ParM has previously been shown to form filaments in vitro that are structurally dissimilar to those formed by other bacterial Alps. The mechanistic implications of these differences are not known. In order to gain insights into the properties and behavior of the pSK41 ParM Alp in vivo, we reconstituted the parMRC system in the ectopic rod-shaped host, E. coli, which is larger and more genetically amenable than the native host, Staphylococcus aureus. Fluorescence microscopy showed a functional fusion protein, ParM-YFP, formed straight filaments in vivo when expressed in isolation. Strikingly, however, in the presence of ParR and parC, ParM-YFP adopted a dramatically different structure, instead forming axial curved filaments. Time-lapse imaging and selective photobleaching experiments revealed that, in the presence of all components of the parMRC system, ParM-YFP filaments were dynamic in nature. Finally, molecular dissection of the parMRC operon revealed that all components of the system are essential for the generation of dynamic filaments.
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25
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Novel actin filaments from Bacillus thuringiensis form nanotubules for plasmid DNA segregation. Proc Natl Acad Sci U S A 2016; 113:E1200-5. [PMID: 26873105 DOI: 10.1073/pnas.1600129113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Here we report the discovery of a bacterial DNA-segregating actin-like protein (BtParM) from Bacillus thuringiensis, which forms novel antiparallel, two-stranded, supercoiled, nonpolar helical filaments, as determined by electron microscopy. The BtParM filament features of supercoiling and forming antiparallel double-strands are unique within the actin fold superfamily, and entirely different to the straight, double-stranded, polar helical filaments of all other known ParMs and of eukaryotic F-actin. The BtParM polymers show dynamic assembly and subsequent disassembly in the presence of ATP. BtParR, the DNA-BtParM linking protein, stimulated ATP hydrolysis/phosphate release by BtParM and paired two supercoiled BtParM filaments to form a cylinder, comprised of four strands with inner and outer diameters of 57 Å and 145 Å, respectively. Thus, in this prokaryote, the actin fold has evolved to produce a filament system with comparable features to the eukaryotic chromosome-segregating microtubule.
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26
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Abstract
The stable maintenance of low-copy-number plasmids in bacteria is actively driven by partition mechanisms that are responsible for the positioning of plasmids inside the cell. Partition systems are ubiquitous in the microbial world and are encoded by many bacterial chromosomes as well as plasmids. These systems, although different in sequence and mechanism, typically consist of two proteins and a DNA partition site, or prokaryotic centromere, on the plasmid or chromosome. One protein binds site-specifically to the centromere to form a partition complex, and the other protein uses the energy of nucleotide binding and hydrolysis to transport the plasmid, via interactions with this partition complex inside the cell. For plasmids, this minimal cassette is sufficient to direct proper segregation in bacterial cells. There has been significant progress in the last several years in our understanding of partition mechanisms. Two general areas that have developed are (i) the structural biology of partition proteins and their interactions with DNA and (ii) the action and dynamics of the partition ATPases that drive the process. In addition, systems that use tubulin-like GTPases to partition plasmids have recently been identified. In this chapter, we concentrate on these recent developments and the molecular details of plasmid partition mechanisms.
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27
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Sanchez A, Cattoni D, Walter JC, Rech J, Parmeggiani A, Nollmann M, Bouet JY. Stochastic Self-Assembly of ParB Proteins Builds the Bacterial DNA Segregation Apparatus. Cell Syst 2015; 1:163-73. [DOI: 10.1016/j.cels.2015.07.013] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/15/2015] [Accepted: 07/30/2015] [Indexed: 11/25/2022]
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28
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Bharat TA, Murshudov GN, Sachse C, Löwe J. Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles. Nature 2015; 523:106-10. [PMID: 25915019 PMCID: PMC4493928 DOI: 10.1038/nature14356] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/02/2015] [Indexed: 12/03/2022]
Abstract
Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with centromeric parC plasmid DNA, while facilitating the addition of subunits to ParM filaments. Growing ParMRC spindles push sister plasmids to the cell poles. Here, using modern electron cryomicroscopy methods, we investigate the structures and arrangements of ParM filaments in vitro and in cells, revealing at near-atomic resolution how subunits and filaments come together to produce the simplest known mitotic machinery. To understand the mechanism of dynamic instability, we determine structures of ParM filaments in different nucleotide states. The structure of filaments bound to the ATP analogue AMPPNP is determined at 4.3 Å resolution and refined. The ParM filament structure shows strong longitudinal interfaces and weaker lateral interactions. Also using electron cryomicroscopy, we reconstruct ParM doublets forming antiparallel spindles. Finally, with whole-cell electron cryotomography, we show that doublets are abundant in bacterial cells containing low-copy-number plasmids with the ParMRC locus, leading to an asynchronous model of R1 plasmid segregation.
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Affiliation(s)
- Tanmay A.M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Garib N. Murshudov
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Carsten Sachse
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany
| | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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29
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Song N, Xu J, Li Z, Hernalsteens JP. Curing a large endogenous plasmid by single substitution of a partitioning gene. Plasmid 2015; 82:10-6. [PMID: 26123974 DOI: 10.1016/j.plasmid.2015.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 11/30/2022]
Abstract
To investigate whether plasmid-free cells of pathogenic Escherichia coli can be isolated by disrupting a single gene in an endogenous plasmid without further treatment, the effect of the disruption of partitioning genes on the inheritance of the endogenous plasmid pUTI89 of the uropathogenic E. coli strain UTI89 was studied. We found that mutation of parB, which encodes a type Ib partitioning protein, could cause loss of the endogenous plasmid at a ratio of about 1%. Clones derived from parB mutants, identified by antibiotic sensitivity, were all plasmid free. Plasmid instability caused by the parB mutation was found to correlate with a negative effect on host cell growth. Thus, in this pathogenic E. coli, an endogenous plasmid as large as 114 kbp could be cured effectively by targeting a single type Ib partitioning gene followed by passaging, which may facilitate further investigations on the function of endogenous plasmids in their natural hosts.
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Affiliation(s)
- Ningning Song
- State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 150001 Harbin, China; Microbiology Research Group, Faculty of Science and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Jie Xu
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, 200127 Shanghai, China
| | - Zhaoli Li
- State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 150001 Harbin, China; Viral Genetics Research Group, Faculty of Science and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Jean-Pierre Hernalsteens
- Viral Genetics Research Group, Faculty of Science and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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30
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Eun YJ, Kapoor M, Hussain S, Garner EC. Bacterial Filament Systems: Toward Understanding Their Emergent Behavior and Cellular Functions. J Biol Chem 2015; 290:17181-9. [PMID: 25957405 DOI: 10.1074/jbc.r115.637876] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteria use homologs of eukaryotic cytoskeletal filaments to conduct many different tasks, controlling cell shape, division, and DNA segregation. These filaments, combined with factors that regulate their polymerization, create emergent self-organizing machines. Here, we summarize the current understanding of the assembly of these polymers and their spatial regulation by accessory factors, framing them in the context of being dynamical systems. We highlight how comparing the in vivo dynamics of the filaments with those measured in vitro has provided insight into the regulation, emergent behavior, and cellular functions of these polymeric systems.
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Affiliation(s)
- Ye-Jin Eun
- From the Molecular and Cellular Biology Department and Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Mrinal Kapoor
- From the Molecular and Cellular Biology Department and Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Saman Hussain
- From the Molecular and Cellular Biology Department and Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Ethan C Garner
- From the Molecular and Cellular Biology Department and Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138
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31
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Taylor JA, Pastrana CL, Butterer A, Pernstich C, Gwynn EJ, Sobott F, Moreno-Herrero F, Dillingham MS. Specific and non-specific interactions of ParB with DNA: implications for chromosome segregation. Nucleic Acids Res 2015; 43:719-31. [PMID: 25572315 PMCID: PMC4333373 DOI: 10.1093/nar/gku1295] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The segregation of many bacterial chromosomes is dependent on the interactions of ParB proteins with centromere-like DNA sequences called parS that are located close to the origin of replication. In this work, we have investigated the binding of Bacillus subtilis ParB to DNA in vitro using a variety of biochemical and biophysical techniques. We observe tight and specific binding of a ParB homodimer to the parS sequence. Binding of ParB to non-specific DNA is more complex and displays apparent positive co-operativity that is associated with the formation of larger, poorly defined, nucleoprotein complexes. Experiments with magnetic tweezers demonstrate that non-specific binding leads to DNA condensation that is reversible by protein unbinding or force. The condensed DNA structure is not well ordered and we infer that it is formed by many looping interactions between neighbouring DNA segments. Consistent with this view, ParB is also able to stabilize writhe in single supercoiled DNA molecules and to bridge segments from two different DNA molecules in trans. The experiments provide no evidence for the promotion of non-specific DNA binding and/or condensation events by the presence of parS sequences. The implications of these observations for chromosome segregation are discussed.
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Affiliation(s)
- James A Taylor
- DNA:Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Cesar L Pastrana
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Annika Butterer
- Biomolecular & Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Christian Pernstich
- DNA:Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Emma J Gwynn
- DNA:Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium Center for Proteomics (CFP-CeProMa), University of Antwerp, 2020 Antwerpen, Belgium
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Mark S Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
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Yuan Y, Peng Q, Wu D, Kou Z, Wu Y, Liu P, Gao M. Effects of actin-like proteins encoded by two Bacillus pumilus phages on unstable lysogeny, revealed by genomic analysis. Appl Environ Microbiol 2015; 81:339-50. [PMID: 25344242 PMCID: PMC4272706 DOI: 10.1128/aem.02889-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/20/2014] [Indexed: 12/16/2022] Open
Abstract
We characterized two newly isolated myoviruses, Bp8p-C and Bp8p-T, infecting the ginger rhizome rot disease pathogen Bacillus pumilus GR8. The plaque of Bp8p-T exhibited a clear center with a turbid rim, suggesting that Bp8p-T could transform into latent phage. Lysogeny assays showed that both the two phages could form latent states, while Bp8p-T could form latent phage at a higher frequency and stability than Bp8p-C. The genomes of Bp8p-C and Bp8p-T were 151,417 and 151,419 bp, respectively; both encoded 212 putative proteins, and only differed by three nucleotides. Moreover, owing to this difference, Bp8p-C encoded a truncated, putative actin-like plasmid segregation protein Gp27-C. Functional analysis of protein Gp27 showed that Gp27-T encoded by Bp8p-T exhibited higher ATPase activity and assembly ability than Gp27-C. The results indicate that the difference in Gp27 affected the phage lysogenic ability. Structural proteome analysis of Bp8p-C virion resulted in the identification of 14 structural proteins, among which a pectin lyase-like protein, a putative poly-gamma-glutamate hydrolase, and three proteins with unknown function, were firstly identified as components of the phage virion. Both phages exhibited specific lytic ability to the host strain GR8. Bp8p-C showed better control effect on the pathogen in ginger rhizome slices than Bp8p-T, suggesting that Bp8p-C has a potential application in bio-control of ginger rhizome rot disease.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Qin Peng
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Dandan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Zheng Kou
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Yan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Pengming Liu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
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A model for the evolution of biological specificity: a cross-reacting DNA-binding protein causes plasmid incompatibility. J Bacteriol 2014; 196:3002-11. [PMID: 24914185 DOI: 10.1128/jb.01811-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Few biological systems permit rigorous testing of how changes in DNA sequence give rise to adaptive phenotypes. In this study, we sought a simplified experimental system with a detailed understanding of the genotype-to-phenotype relationship that could be altered by environmental perturbations. We focused on plasmid fitness, i.e., the ability of plasmids to be stably maintained in a bacterial population, which is dictated by the plasmid's replication and segregation machinery. Although plasmid replication depends on host proteins, the type II plasmid partitioning (Par) machinery is entirely plasmid encoded and relies solely on three components: parC, a centromere-like DNA sequence, ParR, a DNA-binding protein that interacts with parC, and ParM, which forms actin-like filaments that push two plasmids away from each other at cell division. Interactions between the Par operons of two related plasmids can cause incompatibility and the reduced transmission of one or both plasmids. We have identified segregation-dependent plasmid incompatibility between the highly divergent Par operons of plasmids pB171 and pCP301. Genetic and biochemical studies revealed that the incompatibility is due to the functional promiscuity of the DNA-binding protein ParRpB171, which interacts with both parC DNA sequences to direct plasmid segregation, indicating that the lack of DNA binding specificity is detrimental to plasmid fitness in this environment. This study therefore successfully utilized plasmid segregation to dissect the molecular interactions between genotype, phenotype, and fitness.
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Ozaki S, Matsuda Y, Keyamura K, Kawakami H, Noguchi Y, Kasho K, Nagata K, Masuda T, Sakiyama Y, Katayama T. A replicase clamp-binding dynamin-like protein promotes colocalization of nascent DNA strands and equipartitioning of chromosomes in E. coli. Cell Rep 2013; 4:985-95. [PMID: 23994470 DOI: 10.1016/j.celrep.2013.07.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/02/2013] [Accepted: 07/25/2013] [Indexed: 10/26/2022] Open
Abstract
In Escherichia coli, bidirectional chromosomal replication is accompanied by the colocalization of sister replication forks. However, the biological significance of this mechanism and the key factors involved are still largely unknown. In this study, we found that a protein, termed CrfC, helps sustain the colocalization of nascent DNA regions of sister replisomes and promote chromosome equipartitioning. CrfC formed homomultimers that bound to multiple molecules of the clamp, a replisome subunit that encircles DNA, and colocalized with nascent DNA regions in a clamp-binding-dependent manner in living cells. CrfC is a dynamin homolog; however, it lacks the typical membrane-binding moiety and instead possesses a clamp-binding motif. Given that clamps remain bound to DNA after Okazaki fragment synthesis, we suggest that CrfC sustains the colocalization of sister replication forks in a unique manner by linking together the clamp-loaded nascent DNA strands, thereby laying the basis for subsequent chromosome equipartitioning.
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Affiliation(s)
- Shogo Ozaki
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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35
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Okibe N, Suzuki N, Inui M, Yukawa H. pCGR2 copy number depends on the par
locus that forms a ParC-ParB-DNA partition complex in Corynebacterium glutamicum. J Appl Microbiol 2013; 115:495-508. [DOI: 10.1111/jam.12257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/12/2013] [Accepted: 04/29/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Naoko Okibe
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
| | - Nobuaki Suzuki
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
| | - Hideaki Yukawa
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
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36
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Brzoska AJ, Firth N. Two-plasmid vector system for independently controlled expression of green and red fluorescent fusion proteins in Staphylococcus aureus. Appl Environ Microbiol 2013; 79:3133-6. [PMID: 23455338 PMCID: PMC3623144 DOI: 10.1128/aem.00144-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 02/21/2013] [Indexed: 02/07/2023] Open
Abstract
We have constructed a system for the regulated coexpression of green fluorescent protein (GFP) and red fluorescent protein (RFP) fusions in Staphylococcus aureus. It was validated by simultaneous localization of cell division proteins FtsZ and Noc and used to detect filament formation by an actin-like ParM plasmid partitioning protein in its native coccoid host.
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Affiliation(s)
- Anthony J Brzoska
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
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37
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Gayathri P, Fujii T, Namba K, Löwe J. Structure of the ParM filament at 8.5Å resolution. J Struct Biol 2013; 184:33-42. [PMID: 23462100 PMCID: PMC3794156 DOI: 10.1016/j.jsb.2013.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/08/2013] [Accepted: 02/12/2013] [Indexed: 01/19/2023]
Abstract
The actin-like protein ParM forms the cytomotive filament of the ParMRC system, a type II plasmid segregation system encoded by Escherichia coli R1 plasmid. We report an 8.5 Å resolution reconstruction of the ParM filament, obtained using cryo-electron microscopy. Fitting of the 3D density reconstruction with monomeric crystal structures of ParM provides insights into dynamic instability of ParM filaments. The structural analysis suggests that a ParM conformation, corresponding to a metastable state, is held within the filament by intrafilament contacts. This filament conformation of ParM can be attained only from the ATP-bound state, and induces a change in conformation of the bound nucleotide. The structural analysis also provides a rationale for the observed stimulation of hydrolysis upon polymerisation into the filament.
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Liu MA, Kwong SM, Jensen SO, Brzoska AJ, Firth N. Biology of the staphylococcal conjugative multiresistance plasmid pSK41. Plasmid 2013; 70:42-51. [PMID: 23415796 DOI: 10.1016/j.plasmid.2013.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 02/01/2013] [Accepted: 02/03/2013] [Indexed: 11/27/2022]
Abstract
Plasmid pSK41 is a large, low-copy-number, conjugative plasmid from Staphylococcus aureus that is representative of a family of staphylococcal plasmids that confer multiple resistances to a wide range of antimicrobial agents. The plasmid consists of a conserved plasmid backbone containing the genes for plasmid housekeeping functions, which is punctuated by copies of IS257 that flank a Tn4001-hybrid structure and cointegrated plasmids that harbour resistance genes. This review summarises the current understanding of the biology of pSK41, focussing on the systems responsible for its replication, maintenance and transmission, and their regulation.
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Affiliation(s)
- Michael A Liu
- School of Biological Sciences, University of Sydney, NSW 2006, Australia
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39
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Li S, Zhao H, Li Y, Niu S, Cai B. Complete nucleotide sequence of plasmid pND6-2 from Pseudomonas putida ND6 and characterization of conjugative genes. Gene 2013; 512:148-56. [DOI: 10.1016/j.gene.2012.09.065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/22/2012] [Accepted: 09/12/2012] [Indexed: 11/27/2022]
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40
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Qian S, Dean R, Urban VS, Chaudhuri BN. The internal organization of mycobacterial partition assembly: does the DNA wrap a protein core? PLoS One 2012; 7:e52690. [PMID: 23285150 PMCID: PMC3527565 DOI: 10.1371/journal.pone.0052690] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/20/2012] [Indexed: 11/18/2022] Open
Abstract
Before cell division in many bacteria, the ParBs spread on a large segment of DNA encompassing the origin-proximal parS site(s) to form the partition assembly that participates in chromosome segregation. Little is known about the structural organization of chromosomal partition assembly. We report solution X-ray and neutron scattering data characterizing the size parameters and internal organization of a nucleoprotein assembly formed by the mycobacterial chromosomal ParB and a 120-meric DNA containing a parS-encompassing region from the mycobacterial genome. The cross-sectional radii of gyration and linear mass density describing the rod-like ParB-DNA assembly were determined from solution scattering. A "DNA outside, protein inside" mode of partition assembly organization consistent with the neutron scattering hydrogen/deuterium contrast variation data is discussed. In this organization, the high scattering DNA is positioned towards the outer region of the partition assembly. The new results presented here provide a basis for understanding how ParBs organize the parS-proximal chromosome, thus setting the stage for further interactions with the DNA condensins, the origin tethering factors and the ParA.
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Affiliation(s)
- Shuo Qian
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Rebecca Dean
- Hauptman Woodward Institute, Buffalo, New York, United States of America
| | - Volker S. Urban
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Barnali N. Chaudhuri
- Hauptman Woodward Institute, Buffalo, New York, United States of America
- Department of Structural Biology, State University of New York, Buffalo, New York, United States of America
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41
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Sequence of two plasmids from Clostridium perfringens chicken necrotic enteritis isolates and comparison with C. perfringens conjugative plasmids. PLoS One 2012. [PMID: 23189158 PMCID: PMC3506638 DOI: 10.1371/journal.pone.0049753] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Twenty-six isolates of Clostridium perfringens of different MLST types from chickens with necrotic enteritis (NE) (15 netB-positive) or from healthy chickens (6 netB-positive, 5 netB-negative) were found to contain 1–4 large plasmids, with most netB-positive isolates containing 3 large and variably sized plasmids which were more numerous and larger than plasmids in netB-negative isolates. NetB and cpb2 were found on different plasmids consistent with previous studies. The pathogenicity locus NELoc1, which includes netB, was largely conserved in these plasmids whereas NeLoc3, present in the cpb2 containing plasmids, was less well conserved. A netB-positive and a cpb2-positive plasmid were likely to be conjugative, and the plasmids were completely sequenced. Both plasmids possessed the intact tcp conjugative region characteristic of C. perfringens conjugative plasmids. Comparative genomic analysis of nine CpCPs, including the two plasmids described here, showed extensive gene rearrangements including pathogenicity locus and accessory gene insertions around rather than within the backbone region. The pattern that emerges from this analysis is that the major toxin-containing regions of the variety of virulence-associated CpCPs are organized as complex pathogenicity loci. How these different but related CpCPs can co-exist in the same host has been an unanswered question. Analysis of the replication-partition region of these plasmids suggests that this region controls plasmid incompatibility, and that CpCPs can be grouped into at least four incompatibility groups.
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42
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Gayathri P, Fujii T, Møller-Jensen J, van den Ent F, Namba K, Löwe J. A bipolar spindle of antiparallel ParM filaments drives bacterial plasmid segregation. Science 2012; 338:1334-7. [PMID: 23112295 DOI: 10.1126/science.1229091] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
To ensure their stable inheritance by daughter cells during cell division, bacterial low-copy-number plasmids make simple DNA segregating machines that use an elongating protein filament between sister plasmids. In the ParMRC system of the Escherichia coli R1 plasmid, ParM, an actinlike protein, forms the spindle between ParRC complexes on sister plasmids. By using a combination of structural work and total internal reflection fluorescence microscopy, we show that ParRC bound and could accelerate growth at only one end of polar ParM filaments, mechanistically resembling eukaryotic formins. The architecture of ParM filaments enabled two ParRC-bound filaments to associate in an antiparallel orientation, forming a bipolar spindle. The spindle elongated as a bundle of at least two antiparallel filaments, thereby pushing two plasmid clusters toward the poles.
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Affiliation(s)
- P Gayathri
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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43
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Superstructure of the centromeric complex of TubZRC plasmid partitioning systems. Proc Natl Acad Sci U S A 2012; 109:16522-7. [PMID: 23010931 DOI: 10.1073/pnas.1210899109] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial plasmid partitioning systems segregate plasmids into each daughter cell. In the well-understood ParMRC plasmid partitioning system, adapter protein ParR binds to centromere parC, forming a helix around which the DNA is externally wrapped. This complex stabilizes the growth of a filament of actin-like ParM protein, which pushes the plasmids to the poles. The TubZRC plasmid partitioning system consists of two proteins, tubulin-like TubZ and TubR, and a DNA centromere, tubC, which perform analogous roles to those in ParMRC, despite being unrelated in sequence and structure. We have dissected in detail the binding sites that comprise Bacillus thuringiensis tubC, visualized the TubRC complex by electron microscopy, and determined a crystal structure of TubR bound to the tubC repeat. We show that the TubRC complex takes the form of a flexible DNA-protein filament, formed by lateral coating along the plasmid from tubC, the full length of which is required for the successful in vitro stabilization of TubZ filaments. We also show that TubR from Bacillus megaterium forms a helical superstructure resembling that of ParR. We suggest that the TubRC DNA-protein filament may bind to, and stabilize, the TubZ filament by forming such a ring-like structure around it. The helical superstructure of this TubRC may indicate convergent evolution between the actin-containing ParMRC and tubulin-containing TubZRC systems.
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44
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Malhotra S, Sowdhamini R. Re-visiting protein-centric two-tier classification of existing DNA-protein complexes. BMC Bioinformatics 2012; 13:165. [PMID: 22800292 PMCID: PMC3472317 DOI: 10.1186/1471-2105-13-165] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 03/26/2012] [Indexed: 01/28/2023] Open
Abstract
Background Precise DNA-protein interactions play most important and vital role in maintaining the normal physiological functioning of the cell, as it controls many high fidelity cellular processes. Detailed study of the nature of these interactions has paved the way for understanding the mechanisms behind the biological processes in which they are involved. Earlier in 2000, a systematic classification of DNA-protein complexes based on the structural analysis of the proteins was proposed at two tiers, namely groups and families. With the advancement in the number and resolution of structures of DNA-protein complexes deposited in the Protein Data Bank, it is important to revisit the existing classification. Results On the basis of the sequence analysis of DNA binding proteins, we have built upon the protein centric, two-tier classification of DNA-protein complexes by adding new members to existing families and making new families and groups. While classifying the new complexes, we also realised the emergence of new groups and families. The new group observed was where β-propeller was seen to interact with DNA. There were 34 SCOP folds which were observed to be present in the complexes of both old and new classifications, whereas 28 folds are present exclusively in the new complexes. Some new families noticed were NarL transcription factor, Z-α DNA binding proteins, Forkhead transcription factor, AP2 protein, Methyl CpG binding protein etc. Conclusions Our results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold. The folds present exclusively in newly classified complexes is suggestive of inclusion of proteins with new function in new classification, the most populated of which are the folds responsible for DNA damage repair. The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins. Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.
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Affiliation(s)
- Sony Malhotra
- National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560 065, India
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45
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Schumacher MA, Ye Q, Barge MT, Zampini M, Barillà D, Hayes F. Structural mechanism of ATP-induced polymerization of the partition factor ParF: implications for DNA segregation. J Biol Chem 2012; 287:26146-54. [PMID: 22674577 DOI: 10.1074/jbc.m112.373696] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Segregation of the bacterial multidrug resistance plasmid TP228 requires the centromere-binding protein ParG, the parH centromere, and the Walker box ATPase ParF. The cycling of ParF between ADP- and ATP-bound states drives TP228 partition; ATP binding stimulates ParF polymerization, which is essential for segregation, whereas ADP binding antagonizes polymerization and inhibits DNA partition. The molecular mechanism involved in this adenine nucleotide switch is unclear. Moreover, it is unknown how any Walker box protein polymerizes in an ATP-dependent manner. Here, we describe multiple ParF structures in ADP- and phosphomethylphosphonic acid adenylate ester (AMPPCP)-bound states. ParF-ADP is monomeric but dimerizes when complexed with AMPPCP. Strikingly, in ParF-AMPPCP structures, the dimers interact to create dimer-of-dimer "units" that generate a specific linear filament. Mutation of interface residues prevents both polymerization and DNA segregation in vivo. Thus, these data provide insight into a unique mechanism by which a Walker box protein forms polymers that involves the generation of ATP-induced dimer-of-dimer building blocks.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA.
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46
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Bacterial actin homolog ParM: arguments for an apolar, antiparallel double helix. J Mol Biol 2012; 422:461-3. [PMID: 22651984 DOI: 10.1016/j.jmb.2012.05.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 04/18/2012] [Accepted: 05/15/2012] [Indexed: 11/21/2022]
Abstract
The bacterial actin homolog ParM has always been modeled as a polar filament, comprising two parallel helical strands, like actin itself. I present arguments here that ParM may be an apolar filament, in which the two helical strands are antiparallel.
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47
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Alp7R regulates expression of the actin-like protein Alp7A in Bacillus subtilis. J Bacteriol 2012; 194:2715-24. [PMID: 22427628 DOI: 10.1128/jb.06550-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alp7A is a bacterial actin from Bacillus subtilis plasmid pLS20 that functions in plasmid segregation. Alp7A's function requires that it assemble into filaments that treadmill and exhibit dynamic instability. These dynamic properties require the two other components of the alp7A operon, the downstream alp7R gene and the upstream alp7C sequence, as does the ability of Alp7A to form filaments at its physiological concentration in the cell. Here, we show that these two other components of the operon also determine the amount of Alp7A that is produced in the cell. The deletion of alp7R leads to overproduction of Alp7A, which assembles into large, amorphous, static filaments that disrupt chromosome segregation and cell division. The product of the alp7R gene is a DNA-binding protein that represses transcription of the alp7A operon. Purified Alp7R protein binds specifically to alp7C, which contains two σ(A) promoters embedded within a series of near-repeats of a 10-mer. Alp7R also shows the typical nonspecific binding activity of a DNA-binding protein: Alp7R-GFP (green fluorescent protein) associates with the chromosomes of cells that lack alp7C. When Alp7A-GFP is produced in B. subtilis along with untagged Alp7R, Alp7A-GFP also colocalizes with the chromosome, indicating that Alp7R associates with Alp7A. Hence Alp7R, determines both the activity and the cellular concentration of Alp7A, and it can associate with Alp7A even if it is not bound to alp7C.
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48
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Schumacher MA. Bacterial plasmid partition machinery: a minimalist approach to survival. Curr Opin Struct Biol 2011; 22:72-9. [PMID: 22153351 DOI: 10.1016/j.sbi.2011.11.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/05/2011] [Accepted: 11/09/2011] [Indexed: 10/25/2022]
Abstract
The accurate segregation or partition of replicated DNA is essential for ensuring stable genome transmission. Partition of bacterial plasmids requires only three elements: a centromere-like DNA site and two proteins, a partition NTPase, and a centromere-binding protein (CBP). Because of this simplicity, partition systems have served as tractable model systems to study the fundamental molecular mechanisms required for DNA segregation at an atomic level. In the last few years, great progress has been made in this endeavor. Surprisingly, these studies have revealed that although the basic partition components are functionally conserved between three types of plasmid partition systems, these systems employ distinct mechanisms of DNA segregation. This review summarizes the molecular insights into plasmid segregation that have been achieved through these recent structural studies.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.
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49
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ParA ATPases can move and position DNA and subcellular structures. Curr Opin Microbiol 2011; 14:712-8. [PMID: 21963112 DOI: 10.1016/j.mib.2011.09.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/06/2011] [Accepted: 09/08/2011] [Indexed: 11/24/2022]
Abstract
Prokaryotic chromosomes and plasmids can be actively segregated by partitioning (par) loci. The common ParA-encoding par loci segregate plasmids by arranging them in regular arrays over the nucleoid by an unknown mechanism. Recent observations indicate that ParA moves plasmids and chromosomes by a pulling mechanism. Even though ParAs form filaments in vitro it is not known whether similar structures are present in vivo. ParA of P1 forms filaments in vitro at very high concentrations only and filament-like structures have not been observed in vivo. Consequently, a 'diffusion-ratchet' mechanism was suggested to explain plasmid movement by ParA of P1. We compare this mechanism with our previously proposed filament model for plasmid movement by ParA. Remarkably, ParA homologues have been discovered to arrange subcellular structures such as carboxysomes and chemotaxis sensory receptors in a regular manner very similar to those of the plasmid arrays.
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50
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Pillet F, Sanchez A, Lane D, Anton Leberre V, Bouet JY. Centromere binding specificity in assembly of the F plasmid partition complex. Nucleic Acids Res 2011; 39:7477-86. [PMID: 21653553 PMCID: PMC3177203 DOI: 10.1093/nar/gkr457] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The segregation of plasmid F of Escherichia coli is highly reliable. The Sop partition locus, responsible for this stable maintenance, is composed of two genes, sopA and sopB and a centromere, sopC, consisting of 12 direct repeats of 43 bp. Each repeat carries a 16-bp inverted repeat motif to which SopB binds to form a nucleoprotein assembly called the partition complex. A database search for sequences closely related to sopC revealed unexpected features that appeared highly conserved. We have investigated the requirements for specific SopB-sopC interactions using a surface plasmon resonance imaging technique. We show that (i) only 10 repeats interact specifically with SopB, (ii) no base outside the 16-bp sopC sites is involved in binding specificity, whereas five bases present in each arm are required for interactions, and (iii) the A-C central bases contribute to binding efficiency by conforming to a need for a purine-pyrimidine dinucleotide. We have refined the SopB-sopC binding pattern by electro-mobility shift assay and found that all 16 bp are necessary for optimal SopB binding. These data and the model we propose, define the basis of the high binding specificity of F partition complex assembly, without which, dispersal of SopB over DNA would result in defective segregation.
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Affiliation(s)
- Flavien Pillet
- Université de Toulouse, INSA, UPS, INP, LISBP, Toulouse, France
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