1
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Li B, Ni S, Liu Y, Lin J, Wang X. The histone-like nucleoid-structuring protein encoded by the plasmid pMBL6842 regulates both plasmid stability and host physiology of Pseudoalteromonas rubra SCSIO 6842. Microbiol Res 2024; 286:127817. [PMID: 38941922 DOI: 10.1016/j.micres.2024.127817] [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: 02/28/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Plasmids orchestrate bacterial adaptation across diverse environments and facilitate lateral gene transfer within bacterial communities. Their presence can perturb host metabolism, creating a competitive advantage for plasmid-free cells. Plasmid stability hinges on efficient replication and partition mechanisms. While plasmids commonly encode histone-like nucleoid-structuring (H-NS) family proteins, the precise influence of plasmid-encoded H-NS proteins on stability remains elusive. In this study, we examined the conjugative plasmid pMBL6842, harboring the hns gene, and observed its positive regulation of parAB transcription, critical for plasmid segregation. Deletion of hns led to rapid plasmid loss, which was remedied by hns complementation. Further investigations unveiled adverse effects of hns overexpression on the bacterial host. Transcriptome analysis revealed hns's role in regulating numerous bacterial genes, impacting both host growth and swimming motility in the presence of the hns gene. Therefore, our study unveils the multifaceted roles of H-NS in both plasmid stability and host physiology, underscoring its biological significance and paving the way for future inquiries into the involvement of H-NS in horizontal gene transfer events.
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Affiliation(s)
- Baiyuan Li
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Songwei Ni
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yabo Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianzhong Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Patro M, Sivabalasarma S, Gfrerer S, Rodriguez-Franco M, Nußbaum P, Ithurbide S, Albers SV. MinD2 modulates cell shape and motility in the archaeon Haloferax volcanii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.01.606218. [PMID: 39131313 PMCID: PMC11312570 DOI: 10.1101/2024.08.01.606218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
In bacteria and archaea, proteins of the ParA/MinD family of ATPases regulate the spatiotemporal organization of various cellular cargoes, including cell division proteins, motility structures, chemotaxis systems, and chromosomes. In bacteria, such as Escherichia coli, MinD proteins are crucial for the correct placement of the Z-ring at mid-cell during cell division. However, previous studies have shown that none of the 4 MinD homologs present in the archaeon Haloferax volcanii have a role in cell division, suggesting that these proteins regulate different cellular processes in haloarchaea. Here, we show that while deletion of MinD2 in H. volcanii (ΔminD2) does not affect cell growth or division, it impacts cell shape and motility by mispositioning the chemotaxis arrays and archaellum motors. Finally, we explore the links between MinD2 and MinD4, which has been previously shown to modulate the localization of chemosensory arrays and archaella in H. volcanii, finding that the two MinD homologues have synergistic effects in regulating the positioning of the motility machinery. Collectively, our findings identify MinD2 as an important link between cell shape and motility in H. volcanii and further our understanding of the mechanisms by which multiple MinD proteins regulate cellular functions in haloarchaea.
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Affiliation(s)
- Megha Patro
- Molecular Biology of Archaea, Institute of Biology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Shamphavi Sivabalasarma
- Molecular Biology of Archaea, Institute of Biology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Sabrina Gfrerer
- Molecular Biology of Archaea, Institute of Biology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Marta Rodriguez-Franco
- Cell Biology, Institute of Biology, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Phillip Nußbaum
- Molecular Biology of Archaea, Institute of Biology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Solenne Ithurbide
- Molecular Biology of Archaea, Institute of Biology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
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3
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Lin MG, Yen CY, Shen YY, Huang YS, Ng IW, Barillà D, Sun YJ, Hsiao CD. Unraveling the structure and function of a novel SegC protein interacting with the SegAB chromosome segregation complex in Archaea. Nucleic Acids Res 2024:gkae660. [PMID: 39077943 DOI: 10.1093/nar/gkae660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 07/10/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024] Open
Abstract
Genome segregation is a fundamental process that preserves the genetic integrity of all organisms, but the mechanisms driving genome segregation in archaea remain enigmatic. This study delved into the unknown function of SegC (SSO0033), a novel protein thought to be involved in chromosome segregation in archaea. Using fluorescence polarization DNA binding assays, we discovered the ability of SegC to bind DNA without any sequence preference. Furthermore, we determined the crystal structure of SegC at 2.8 Å resolution, revealing the multimeric configuration and forming a large positively charged surface that can bind DNA. SegC has a tertiary structure folding similar to those of the ThDP-binding fold superfamily, but SegC shares only 5-15% sequence identity with those proteins. Unexpectedly, we found that SegC has nucleotide triphosphatase (NTPase) activity. We also determined the SegC-ADP complex structure, identifying the NTP binding pocket and relative SegC residues involved in the interaction. Interestingly, images from negative-stain electron microscopy revealed that SegC forms filamentous structures in the presence of DNA and NTPs. Further, more uniform and larger SegC-filaments are observed, when SegA-ATP was added. Notably, the introduction of SegB disrupts these oligomers, with ATP being essential for regulating filament formation. These findings provide insights into the functional and structural role of SegC in archaeal chromosome segregation.
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Affiliation(s)
- Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Cheng-Yi Yen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yo-You Shen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Sung Huang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Irene W Ng
- Department of Biology, University of York, Wentworth Way, YorkYO10 5DD, UK
| | - Daniela Barillà
- Department of Biology, University of York, Wentworth Way, YorkYO10 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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4
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Chu CH, Wu CT, Lin MG, Yen CY, Wu YZ, Hsiao CD, Sun YJ. Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and HpParB. Nucleic Acids Res 2024; 52:7321-7336. [PMID: 38842933 PMCID: PMC11229316 DOI: 10.1093/nar/gkae450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 07/09/2024] Open
Abstract
The ParABS system, composed of ParA (an ATPase), ParB (a DNA binding protein), and parS (a centromere-like DNA), regulates bacterial chromosome partition. The ParB-parS partition complex interacts with the nucleoid-bound ParA to form the nucleoid-adaptor complex (NAC). In Helicobacter pylori, ParA and ParB homologs are encoded as HpSoj and HpSpo0J (HpParA and HpParB), respectively. We determined the crystal structures of the ATP hydrolysis deficient mutant, HpParAD41A, and the HpParAD41A-DNA complex. We assayed the CTPase activity of HpParB and identified two potential DNA binding modes of HpParB regulated by CTP, one is the specific DNA binding by the DNA binding domain and the other is the non-specific DNA binding through the C-terminal domain under the regulation of CTP. We observed an interaction between HpParAD41A and the N-terminus fragment of HpParB (residue 1-10, HpParBN10) and determined the crystal structure of the ternary complex, HpParAD41A-DNA-HpParBN10 complex which mimics the NAC formation. HpParBN10 binds near the HpParAD41A dimer interface and is clamped by flexible loops, L23 and L34, through a specific cation-π interaction between Arg9 of HpParBN10 and Phe52 of HpParAD41A. We propose a molecular mechanism model of the ParABS system providing insight into chromosome partition in bacteria.
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Affiliation(s)
- Chen-Hsi Chu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Che-Ting Wu
- 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
| | - Cheng-Yi Yen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Zhan Wu
- 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
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
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5
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Pulianmackal LT, Vecchiarelli AG. Positioning of cellular components by the ParA/MinD family of ATPases. Curr Opin Microbiol 2024; 79:102485. [PMID: 38723344 DOI: 10.1016/j.mib.2024.102485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 06/11/2024]
Abstract
The ParA/MinD (A/D) family of ATPases spatially organize an array of genetic- and protein-based cellular cargos across the bacterial and archaeal domains of life. By far, the two best-studied members, and family namesake, are ParA and MinD, involved in bacterial DNA segregation and divisome positioning, respectively. ParA and MinD make protein waves on the nucleoid or membrane to segregate chromosomes and position the divisome. Less studied is the growing list of A/D ATPases widespread across bacteria and implicated in the subcellular organization of diverse protein-based complexes and organelles involved in myriad biological processes, from metabolism to pathogenesis. Here we describe mechanistic commonality, variation, and coordination among the most widespread family of positioning ATPases used in the subcellular organization of disparate cargos across bacteria and archaea.
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Affiliation(s)
- Lisa T Pulianmackal
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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6
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Quiñonero-Coronel MDM, Devos DP, Garcillán-Barcia MP. Specificities and commonalities of the Planctomycetes plasmidome. Environ Microbiol 2024; 26:e16638. [PMID: 38733104 DOI: 10.1111/1462-2920.16638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.
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Affiliation(s)
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD, CSIC-Universidad Pablo de Olavide), Sevilla, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, CSIC-Universidad de Cantabria), Cantabria, Spain
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7
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Bedore AM, Waters CM. Plasmid-free cheater cells commonly evolve during laboratory growth. Appl Environ Microbiol 2024; 90:e0231123. [PMID: 38446071 PMCID: PMC11022567 DOI: 10.1128/aem.02311-23] [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: 12/20/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
It has been nearly a century since the isolation and use of penicillin, heralding the discovery of a wide range of different antibiotics. In addition to clinical applications, such antibiotics have been essential laboratory tools, allowing for selection and maintenance of laboratory plasmids that encode cognate resistance genes. However, antibiotic resistance mechanisms can additionally function as public goods. For example, extracellular beta-lactamases produced by resistant cells that subsequently degrade penicillin and related antibiotics allow neighboring plasmid-free susceptible bacteria to survive antibiotic treatment. How such cooperative mechanisms impact selection of plasmids during experiments in laboratory conditions is poorly understood. Here, we show in multiple bacterial species that the use of plasmid-encoded beta-lactamases leads to significant curing of plasmids in surface-grown bacteria. Furthermore, such curing was also evident for aminoglycoside phosphotransferase and tetracycline antiporter resistance mechanisms. Alternatively, antibiotic selection in liquid growth led to more robust plasmid maintenance, although plasmid loss was still observed. The net outcome of such plasmid loss is the generation of a heterogenous population of plasmid-containing and plasmid-free cells, leading to experimental confounds that are not widely appreciated.IMPORTANCEPlasmids are routinely used in microbiology as readouts of cell biology or tools to manipulate cell function. Central to these studies is the assumption that all cells in an experiment contain the plasmid. Plasmid maintenance in a host cell typically depends on a plasmid-encoded antibiotic resistance marker, which provides a selective advantage when the plasmid-containing cell is grown in the presence of antibiotic. Here, we find that growth of plasmid-containing bacteria on a surface and to a lesser extent in liquid culture in the presence of three distinct antibiotic families leads to the evolution of a significant number of plasmid-free cells, which rely on the resistance mechanisms of the plasmid-containing cells. This process generates a heterogenous population of plasmid-free and plasmid-containing bacteria, an outcome which could confound further experimentation.
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Affiliation(s)
- Amber M. Bedore
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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8
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Murányi G, Szabó M, Acsai K, Kiss J. Two birds with one stone: SGI1 can stabilize itself and expel the IncC helper by hijacking the plasmid parABS system. Nucleic Acids Res 2024; 52:2498-2518. [PMID: 38300764 PMCID: PMC10954446 DOI: 10.1093/nar/gkae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
The SGI1 family integrative mobilizable elements, which are efficient agents in distribution of multidrug resistance in Gammaproteobacteria, have a complex, parasitic relationship with their IncC conjugative helper plasmids. Besides exploiting the transfer apparatus, SGI1 also hijacks IncC plasmid control mechanisms to time its own excision, replication and expression of self-encoded T4SS components, which provides advantages for SGI1 over its helpers in conjugal transfer and stable maintenance. Furthermore, SGI1 destabilizes its helpers in an unknown, replication-dependent way when they are concomitantly present in the same host. Here we report how SGI1 exploits the helper plasmid partitioning system to displace the plasmid and simultaneously increase its own stability. We show that SGI1 carries two copies of sequences mimicking the parS sites of IncC plasmids. These parS-like elements bind the ParB protein encoded by the plasmid and increase SGI1 stability by utilizing the parABS system of the plasmid for its own partitioning, through which SGI1 also destabilizes the helper plasmid. Furthermore, SGI1 expresses a small protein, Sci, which significantly strengthens this plasmid-destabilizing effect, as well as SGI1 maintenance. The plasmid-induced replication of SGI1 results in an increased copy-number of parS-like sequences and Sci expression leading to strong incompatibility with the helper plasmid.
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Affiliation(s)
- Gábor Murányi
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, H2100 Hungary
| | - Mónika Szabó
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, H2100 Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Gödöllő, H2100 Hungary
| | - Károly Acsai
- Ceva Animal Health, Ceva-Phylaxia, Budapest, H1107 Hungary
| | - János Kiss
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, H2100 Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Gödöllő, H2100 Hungary
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9
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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 PMCID: PMC10729935 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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10
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Jager K, Orozco-Hidalgo MT, Springstein BL, Joly-Smith E, Papazotos F, McDonough E, Fleming E, McCallum G, Yuan AH, Hilfinger A, Hochschild A, Potvin-Trottier L. Measuring prion propagation in single bacteria elucidates a mechanism of loss. Proc Natl Acad Sci U S A 2023; 120:e2221539120. [PMID: 37738299 PMCID: PMC10523482 DOI: 10.1073/pnas.2221539120] [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: 01/13/2023] [Accepted: 07/26/2023] [Indexed: 09/24/2023] Open
Abstract
Prions are self-propagating protein aggregates formed by specific proteins that can adopt alternative folds. Prions were discovered as the cause of the fatal transmissible spongiform encephalopathies in mammals, but prions can also constitute nontoxic protein-based elements of inheritance in fungi and other species. Prion propagation has recently been shown to occur in bacteria for more than a hundred cell divisions, yet a fraction of cells in these lineages lost the prion through an unknown mechanism. Here, we investigate prion propagation in single bacterial cells as they divide using microfluidics and fluorescence microscopy. We show that the propagation occurs in two distinct modes. In a fraction of the population, cells had multiple small visible aggregates and lost the prion through random partitioning of aggregates to one of the two daughter cells at division. In the other subpopulation, cells had a stable large aggregate localized to the pole; upon division the mother cell retained this polar aggregate and a daughter cell was generated that contained small aggregates. Extending our findings to prion domains from two orthologous proteins, we observe similar propagation and loss properties. Our findings also provide support for the suggestion that bacterial prions can form more than one self-propagating state. We implement a stochastic version of the molecular model of prion propagation from yeast and mammals that recapitulates all the observed single-cell properties. This model highlights challenges for prion propagation that are unique to prokaryotes and illustrates the conservation of fundamental characteristics of prion propagation.
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Affiliation(s)
- Krista Jager
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | | | | | - Euan Joly-Smith
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
| | - Fotini Papazotos
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | | | - Eleanor Fleming
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Giselle McCallum
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | - Andy H. Yuan
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Andreas Hilfinger
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
- Department of Mathematics, University of Toronto, Toronto, ONM5S 2E4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ONM5S 3G5, Canada
| | - Ann Hochschild
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Laurent Potvin-Trottier
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
- Department of Physics, Concordia University, Montréal, QCH4B 1R6, Canada
- Center for Applied Synthetic Biology, Concordia University, Montréal, QCH4B 1R6, Canada
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11
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Connolley L, Schnabel L, Thanbichler M, Murray SM. Partition complex structure can arise from sliding and bridging of ParB dimers. Nat Commun 2023; 14:4567. [PMID: 37516778 PMCID: PMC10387095 DOI: 10.1038/s41467-023-40320-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/20/2023] [Indexed: 07/31/2023] Open
Abstract
In many bacteria, chromosome segregation requires the association of ParB to the parS-containing centromeric region to form the partition complex. However, the structure and formation of this complex have been unclear. Recently, studies have revealed that CTP binding enables ParB dimers to slide along DNA and condense the centromeric region through the formation of DNA bridges. Using semi-flexible polymer simulations, we demonstrate that these properties can explain partition complex formation. Transient ParB bridges organize DNA into globular states or hairpins and helical structures, depending on bridge lifetime, while separate simulations show that ParB sliding reproduces the multi-peaked binding profile observed in Caulobacter crescentus. Combining sliding and bridging into a unified model, we find that short-lived ParB bridges do not impede sliding and can reproduce both the binding profile and condensation of the nucleoprotein complex. Overall, our model elucidates the mechanism of partition complex formation and predicts its fine structure.
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Affiliation(s)
- Lara Connolley
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043, Marburg, Germany
| | - Lucas Schnabel
- Department of Biology, University of Marburg, 35043, Marburg, Germany
| | - Martin Thanbichler
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043, Marburg, Germany
- Department of Biology, University of Marburg, 35043, Marburg, Germany
| | - Seán M Murray
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043, Marburg, Germany.
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12
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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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13
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Ren Z, Takacs CN, Brandão HB, Jacobs-Wagner C, Wang X. Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi. PLoS Genet 2023; 19:e1010857. [PMID: 37494383 PMCID: PMC10406323 DOI: 10.1371/journal.pgen.1010857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/07/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023] Open
Abstract
Borrelia burgdorferi, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that B. burgdorferi is polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA/ParZ and ParB/Smc. Here, using chromosome conformation capture (Hi-C), we characterized the organization of the B. burgdorferi genome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosome oriC region, and a subset of plasmids interact with each other more than with others. We found that Smc and the Smc-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosome oriC. Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.
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Affiliation(s)
- Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Constantin N. Takacs
- Department of Biology, Stanford University, Stanford, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Hugo B. Brandão
- Illumina Inc., 5200 Illumina Way, San Diego, California, United States of America
| | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Stanford, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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14
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Chodha SS, Brooks AC, Davis PJ, Ramachandran R, Chattoraj D, Hwang L. Kinetic principles of ParA2-ATP cycling guide dynamic subcellular localizations in Vibrio cholerae. Nucleic Acids Res 2023; 51:5603-5620. [PMID: 37140034 PMCID: PMC10287910 DOI: 10.1093/nar/gkad321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
Dynamic protein gradients are exploited for the spatial organization and segregation of replicated chromosomes. However, mechanisms of protein gradient formation and how that spatially organizes chromosomes remain poorly understood. Here, we have determined the kinetic principles of subcellular localizations of ParA2 ATPase, an essential spatial regulator of chromosome 2 segregation in the multichromosome bacterium, Vibrio cholerae. We found that ParA2 gradients self-organize in V. cholerae cells into dynamic pole-to-pole oscillations. We examined the ParA2 ATPase cycle and ParA2 interactions with ParB2 and DNA. In vitro, ParA2-ATP dimers undergo a rate-limiting conformational switch, catalysed by DNA to achieve DNA-binding competence. This active ParA2 state loads onto DNA cooperatively as higher order oligomers. Our results indicate that the midcell localization of ParB2-parS2 complexes stimulate ATP hydrolysis and ParA2 release from the nucleoid, generating an asymmetric ParA2 gradient with maximal concentration toward the poles. This rapid dissociation coupled with slow nucleotide exchange and conformational switch provides for a temporal lag that allows the redistribution of ParA2 to the opposite pole for nucleoid reattachment. Based on our data, we propose a 'Tug-of-war' model that uses dynamic oscillations of ParA2 to spatially regulate symmetric segregation and positioning of bacterial chromosomes.
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Affiliation(s)
- Satpal S Chodha
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Adam C Brooks
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Peter J Davis
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Revathy Ramachandran
- Basic Research Laboratory, Centre for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4260, USA
| | - Dhruba K Chattoraj
- Basic Research Laboratory, Centre for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4260, USA
| | - Ling Chin Hwang
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Medical Technology Research Centre, School of Medicine, Faculty of Health, Education, Medicine & Social Care, Anglia Ruskin University, Chelmsford, UK
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15
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Loyola Irizarry HG, Brito IL. Characterizing conjugative plasmids from an antibiotic-resistant dataset for use as broad-host delivery vectors. Front Microbiol 2023; 14:1199640. [PMID: 37389338 PMCID: PMC10301749 DOI: 10.3389/fmicb.2023.1199640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023] Open
Abstract
Human microbiome engineering is increasingly proposed as a way to modulate health outcomes. However, one of the current limitations to engineering microbial communities in situ is delivery of a genetic payload for introducing or modifying genes. Indeed, there is a need to identify novel broad-host delivery vectors for microbiome engineering. Therefore, in this study, we characterized conjugative plasmids from a publicly available dataset of antibiotic-resistant isolate genomes in order to identify potential broad-host vectors for further applications. From the 199 closed genomes available in the CDC & FDA AR Isolate Bank, we identified 439 plasmids, of which 126 were predicted to be mobilizable and 206 conjugative. Various characteristics of the conjugative plasmids, such as size, replication origin, conjugation machinery, host defense mechanisms, and plasmid stability proteins, were analyzed to determine these plasmids' potential host-range. Following this analysis, we clustered plasmid sequences and chose 22 unique, broad-host range plasmids that would be suitable for use as delivery vectors. This novel set of plasmids will provide a valuable resource for engineering microbial communities.
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16
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Pulianmackal LT, Limcaoco JMI, Ravi K, Yang S, Zhang J, Tran MK, Ghalmi M, O'Meara MJ, Vecchiarelli AG. Multiple ParA/MinD ATPases coordinate the positioning of disparate cargos in a bacterial cell. Nat Commun 2023; 14:3255. [PMID: 37277398 DOI: 10.1038/s41467-023-39019-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
In eukaryotes, linear motor proteins govern intracellular transport and organization. In bacteria, where linear motors involved in spatial regulation are absent, the ParA/MinD family of ATPases organize an array of genetic- and protein-based cellular cargos. The positioning of these cargos has been independently investigated to varying degrees in several bacterial species. However, it remains unclear how multiple ParA/MinD ATPases can coordinate the positioning of diverse cargos in the same cell. Here, we find that over a third of sequenced bacterial genomes encode multiple ParA/MinD ATPases. We identify an organism (Halothiobacillus neapolitanus) with seven ParA/MinD ATPases, demonstrate that five of these are each dedicated to the spatial regulation of a single cellular cargo, and define potential specificity determinants for each system. Furthermore, we show how these positioning reactions can influence each other, stressing the importance of understanding how organelle trafficking, chromosome segregation, and cell division are coordinated in bacterial cells. Together, our data show how multiple ParA/MinD ATPases coexist and function to position a diverse set of fundamental cargos in the same bacterial cell.
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Affiliation(s)
- Lisa T Pulianmackal
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jose Miguel I Limcaoco
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Keerthikka Ravi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sinyu Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffrey Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mimi K Tran
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maria Ghalmi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matthew J O'Meara
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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17
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Bedore AM, Waters CM. Plasmid-free cheater cells commonly evolve during laboratory growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541508. [PMID: 37292590 PMCID: PMC10245762 DOI: 10.1101/2023.05.19.541508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
It has been nearly a century since the isolation and use of penicillin, heralding the discovery of a wide range of different antibiotics. In addition to clinical applications, such antibiotics have been essential laboratory tools, allowing for selection and maintenance of laboratory plasmids that encode cognate resistance genes. However, antibiotic resistance mechanisms can additionally function as public goods. For example, secretion of beta-lactamase from resistant cells, and subsequent degradation of nearby penicillin and related antibiotics, allows neighboring plasmid-free susceptible bacteria to survive antibiotic treatment. How such cooperative mechanisms impact selection of plasmids during experiments in laboratory conditions is poorly understood. Here, we show that the use of plasmid-encoded beta-lactamases leads to significant curing of plasmids in surface grown bacteria. Furthermore, such curing was also evident for aminoglycoside phosphotransferase and tetracycline antiporter resistance mechanisms. Alternatively, antibiotic selection in liquid growth led to more robust plasmid maintenance, although plasmid loss still occurred. The net outcome of such plasmid loss is the generation of a heterogenous population of plasmid-containing and plasmid-free cells, leading to experimental confounds that are not widely appreciated.
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Affiliation(s)
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA, 48824
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18
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Botts RT, Page DM, Bravo JA, Brown ML, Castilleja CC, Guzman VL, Hall S, Henderson JD, Kenney SM, Lensink ME, Paternoster MV, Pyle SL, Ustick L, Walters-Laird CJ, Top EM, Cummings DE. Polluted wetlands contain multidrug-resistance plasmids encoding CTX-M-type extended-spectrum β-lactamases. Plasmid 2023; 126:102682. [PMID: 37023995 PMCID: PMC10213127 DOI: 10.1016/j.plasmid.2023.102682] [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: 12/16/2022] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023]
Abstract
While most detailed analyses of antibiotic resistance plasmids focus on those found in clinical isolates, less is known about the vast environmental reservoir of mobile genetic elements and the resistance and virulence factors they encode. We selectively isolated three strains of cefotaxime-resistant Escherichia coli from a wastewater-impacted coastal wetland. The cefotaxime-resistant phenotype was transmissible to a lab strain of E. coli after one hour, with frequencies as high as 10-3 transconjugants per recipient. Two of the plasmids also transferred cefotaxime resistance to Pseudomonas putida, but these were unable to back-transfer this resistance from P. putida to E. coli. In addition to the cephalosporins, E. coli transconjugants inherited resistance to at least seven distinct classes of antibiotics. Complete nucleotide sequences revealed large IncF-type plasmids with globally distributed replicon sequence types F31:A4:B1 and F18:B1:C4 carrying diverse antibiotic resistance and virulence genes. The plasmids encoded extended-spectrum β-lactamases blaCTX-M-15 or blaCTX-M-55, each associated with the insertion sequence ISEc9, although in different local arrangements. Despite similar resistance profiles, the plasmids shared only one resistance gene in common, the aminoglycoside acetyltransferase aac(3)-IIe. Plasmid accessory cargo also included virulence factors involved in iron acquisition and defense against host immunity. Despite their sequence similarities, several large-scale recombination events were detected, including rearrangements and inversions. In conclusion, selection with a single antibiotic, cefotaxime, yielded conjugative plasmids conferring multiple resistance and virulence factors. Clearly, efforts to limit the spread of antibiotic resistance and virulence among bacteria must include a greater understanding of mobile elements in the natural and human-impacted environments.
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Affiliation(s)
- Ryan T Botts
- Department of Mathematics, Information, and Computer Sciences, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Dawne M Page
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Joseph A Bravo
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Madelaine L Brown
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Claudia C Castilleja
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Victoria L Guzman
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Samantha Hall
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Jacob D Henderson
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Shelby M Kenney
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Mariele E Lensink
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Megan V Paternoster
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Sarah L Pyle
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Lucas Ustick
- Department of Mathematics, Information, and Computer Sciences, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America; Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Chara J Walters-Laird
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Eva M Top
- Department of Biological Sciences, Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, 875 Perimeter Dr., Moscow, ID 83844, United States of America
| | - David E Cummings
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America.
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19
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Ren Z, Takacs CN, Brandão HB, Jacobs-Wagner C, Wang X. Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.19.532819. [PMID: 37066390 PMCID: PMC10103936 DOI: 10.1101/2023.03.19.532819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Borrelia burgdorferi , a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that B. burgdorferi is polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA/ParZ and ParB/SMC. Here, using chromosome conformation capture (Hi-C), we characterized the organization of the B. burgdorferi genome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosome oriC region, and a subset of plasmids interact with each other more than with others. We found that SMC and the SMC-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosome oriC . Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.
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Affiliation(s)
- Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Constantin N. Takacs
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | | | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford, CA 94305, USA
- Corresponding authors: ;
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Corresponding authors: ;
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20
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Roberts DM. A new role for monomeric ParA/Soj in chromosome dynamics in Bacillus subtilis. Microbiologyopen 2023; 12:e1344. [PMID: 36825885 PMCID: PMC9841721 DOI: 10.1002/mbo3.1344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
ParABS (Soj-Spo0J) systems were initially implicated in plasmid and chromosome segregation in bacteria. However, it is now increasingly understood that they play multiple roles in cell cycle events in Bacillus subtilis, and possibly other bacteria. In a recent study, monomeric forms of ParA/Soj have been implicated in regulating aspects of chromosome dynamics during B. subtilis sporulation. In this commentary, I will discuss the known roles of ParABS systems, explore why sporulation is a valuable model for studying these proteins, and the new insights into the role of monomeric ParA/Soj. Finally, I will touch upon some of the future work that remains.
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21
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Takacs CN, Nakajima Y, Haber JE, Jacobs-Wagner C. Cas9-mediated endogenous plasmid loss in Borrelia burgdorferi. PLoS One 2022; 17:e0278151. [PMID: 36441794 PMCID: PMC9704580 DOI: 10.1371/journal.pone.0278151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022] Open
Abstract
The spirochete Borrelia burgdorferi, which causes Lyme disease, has the most segmented genome among known bacteria. In addition to a linear chromosome, the B. burgdorferi genome contains over 20 linear and circular endogenous plasmids. While many of these plasmids are dispensable under in vitro culture conditions, they are maintained during the natural life cycle of the pathogen. Plasmid-encoded functions are required for colonization of the tick vector, transmission to the vertebrate host, and evasion of host immune defenses. Different Borrelia strains can vary substantially in the type of plasmids they carry. The gene composition within the same type of plasmid can also differ from strain to strain, impeding the inference of plasmid function from one strain to another. To facilitate the investigation of the role of specific B. burgdorferi plasmids, we developed a Cas9-based approach that targets a plasmid for removal. As a proof-of-principle, we showed that targeting wild-type Cas9 to several loci on the endogenous plasmids lp25 or lp28-1 of the B. burgdorferi type strain B31 results in sgRNA-specific plasmid loss even when homologous sequences (i.e., potential sequence donors for DNA recombination) are present nearby. Cas9 nickase versions, Cas9D10A or Cas9H840A, also cause plasmid loss, though not as robustly. Thus, sgRNA-directed Cas9 DNA cleavage provides a highly efficient way to eliminate B. burgdorferi endogenous plasmids that are non-essential in axenic culture.
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Affiliation(s)
- Constantin N. Takacs
- Department of Biology, Stanford University, Palo Alto, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Palo Alto, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Palo Alto, California, United States of America
| | - Yuko Nakajima
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - James E. Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Palo Alto, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Palo Alto, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Palo Alto, California, United States of America
- * E-mail:
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22
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Roberts DM, Anchimiuk A, Kloosterman TG, Murray H, Wu LJ, Gruber S, Errington J. Chromosome remodelling by SMC/Condensin in B. subtilis is regulated by monomeric Soj/ParA during growth and sporulation. Proc Natl Acad Sci U S A 2022; 119:e2204042119. [PMID: 36206370 PMCID: PMC9564211 DOI: 10.1073/pnas.2204042119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022] Open
Abstract
SMC complexes, loaded at ParB-parS sites, are key mediators of chromosome organization in bacteria. ParA/Soj proteins interact with ParB/Spo0J in a pathway involving adenosine triphosphate (ATP)-dependent dimerization and DNA binding, facilitating chromosome segregation in bacteria. In Bacillus subtilis, ParA/Soj also regulates DNA replication initiation and along with ParB/Spo0J is involved in cell cycle changes during endospore formation. The first morphological stage in sporulation is the formation of an elongated chromosome structure called an axial filament. Here, we show that a major redistribution of SMC complexes drives axial filament formation in a process regulated by ParA/Soj. Furthermore, and unexpectedly, this regulation is dependent on monomeric forms of ParA/Soj that cannot bind DNA or hydrolyze ATP. These results reveal additional roles for ParA/Soj proteins in the regulation of SMC dynamics in bacteria and yet further complexity in the web of interactions involving chromosome replication, segregation and organization, controlled by ParAB and SMC.
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Affiliation(s)
- David M. Roberts
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Anna Anchimiuk
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 015 Lausanne, Switzerland
| | - Tomas G. Kloosterman
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Heath Murray
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Stephan Gruber
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 015 Lausanne, Switzerland
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
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23
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Martinez J, Ant TH, Murdochy SM, Tong L, da Silva Filipe A, Sinkins SP. Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common. PLoS Genet 2022; 18:e1010406. [PMID: 36121852 PMCID: PMC9560607 DOI: 10.1371/journal.pgen.1010406] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/13/2022] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
Wolbachia are widespread maternally-transmitted bacteria of arthropods that often spread by manipulating their host's reproduction through cytoplasmic incompatibility (CI). Their invasive potential is currently being harnessed in field trials aiming to control mosquito-borne diseases. Wolbachia genomes commonly harbour prophage regions encoding the cif genes which confer their ability to induce CI. Recently, a plasmid-like element was discovered in wPip, a Wolbachia strain infecting Culex mosquitoes; however, it is unclear how common such extra-chromosomal elements are in Wolbachia. Here we sequenced the complete genome of wAlbA, a strain of the symbiont found in Aedes albopictus, after eliminating the co-infecting and higher density wAlbB strain that previously made sequencing of wAlbA challenging. We show that wAlbA is associated with two new plasmids and identified additional Wolbachia plasmids and related chromosomal islands in over 20% of publicly available Wolbachia genome datasets. These plasmids encode a variety of accessory genes, including several phage-like DNA packaging genes as well as genes potentially contributing to host-symbiont interactions. In particular, we recovered divergent homologues of the cif genes in both Wolbachia- and Rickettsia-associated plasmids. Our results indicate that plasmids are common in Wolbachia and raise fundamental questions around their role in symbiosis. In addition, our comparative analysis provides useful information for the future development of genetic tools to manipulate and study Wolbachia symbionts.
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Affiliation(s)
- Julien Martinez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Thomas H. Ant
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Shivan M. Murdochy
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Steven P. Sinkins
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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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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Beyond the ABCs—Discovery of Three New Plasmid Types in Rhodobacterales (RepQ, RepY, RepW). Microorganisms 2022; 10:microorganisms10040738. [PMID: 35456790 PMCID: PMC9025767 DOI: 10.3390/microorganisms10040738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
Copiotrophic marine bacteria of the Roseobacter group (Rhodobacterales, Alphaproteobacteria) are characterized by a multipartite genome organization. We sequenced the genomes of Sulfitobacter indolifex DSM 14862T and four related plasmid-rich isolates in order to investigate the composition, distribution, and evolution of their extrachromosomal replicons (ECRs). A combination of long-read PacBio and short-read Illumina sequencing was required to establish complete closed genomes that comprised up to twelve ECRs. The ECRs were differentiated in stably evolving chromids and genuine plasmids. Among the chromids, a diagnostic RepABC-8 replicon was detected in four Sulfitobacter species that likely reflects an evolutionary innovation that originated in their common ancestor. Classification of the ECRs showed that the most abundant plasmid system is RepABC, followed by RepA, DnaA-like, and RepB. However, the strains also contained three novel plasmid types that were designated RepQ, RepY, and RepW. We confirmed the functionality of their replicases, investigated the genetic inventory of the mostly cryptic plasmids, and retraced their evolutionary origin. Remarkably, the RepY plasmid of S. pontiacus DSM 110277 is the first high copy-number plasmid discovered in Rhodobacterales.
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26
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Mishra D, Jakhmola A, Srinivasan R. A role for the last C-terminal helix of the F plasmid segregating protein SopA in nucleoid binding and plasmid maintenance. Plasmid 2022; 119-120:102617. [PMID: 35041919 DOI: 10.1016/j.plasmid.2022.102617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/10/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022]
Abstract
The rapid emergence and spread of antibiotic resistance is a growing global burden. Antibiotic resistance is often associated with large single or low copy number plasmids, which rely upon cytoskeletal proteins for their stable maintenance. While the mechanism of plasmid partitioning has been well established for the R plasmids, the molecular details by which the F plasmid is maintained is only beginning to emerge. The partitioning function of the F plasmid depends upon a ParA/ MinD family of proteins known as SopA. SopA, by virtue of its ATP-dependent non-specific DNA binding activity and association with the bacterial nucleoid, drives the segregation of the F plasmid into the daughter cells. This function further depends upon the stimulation of the ATPase activity of SopA by the SopBC complex. Here, we report that several residues in the last C-terminal helix in SopA play a crucial but distinct role in SopA function and plasmid maintenance. While the deletion of the last five residues in SopA does not affect its ability to bind the nucleoid or SopB, they severely affect the plasmid partitioning function. Further, we show that while mutations in certain polar residues in the C-terminal helix only mildly affect its localisation to the nucleoid, others cause defects in nsDNA binding and disrupt plasmid maintenance functions.
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Affiliation(s)
- Dipika Mishra
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institutes, Bhubaneswar, Odisha 752050, India
| | - Anirudh Jakhmola
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institutes, Bhubaneswar, Odisha 752050, India
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institutes, Bhubaneswar, Odisha 752050, India.
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27
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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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28
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Smits WK, Roseboom AM, Corver J. Plasmids of Clostridioides difficile. Curr Opin Microbiol 2021; 65:87-94. [PMID: 34775173 DOI: 10.1016/j.mib.2021.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 12/16/2022]
Abstract
Plasmids are ubiquitous in the bacterial world. In many microorganisms, plasmids have been implicated in important aspects of bacterial physiology and contribute to horizontal gene transfer. In contrast, knowledge on plasmids of the enteropathogen Clostridioides difficile is limited, and there appears to be no phenotypic consequence to carriage of many of the identified plasmids. Emerging evidence suggests, however, that plasmids are common in C. difficile and may encode functions relevant to pathogenesis, such as antimicrobial resistance and toxin production. Here, we review our current knowledge about the abundance, functions and clinical relevance of plasmids in C. difficile.
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Affiliation(s)
- Wiep Klaas Smits
- Experimental Bacteriology Group, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands; Centre for Microbial Cell Biology, Leiden, The Netherlands; Leiden University Center for Infectious Diseases (LU-CID), Leiden, The Netherlands.
| | - Anna Maria Roseboom
- Experimental Bacteriology Group, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen Corver
- Experimental Bacteriology Group, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands; Centre for Microbial Cell Biology, Leiden, The Netherlands; Leiden University Center for Infectious Diseases (LU-CID), Leiden, The Netherlands
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29
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Hall JPJ, Wright RCT, Harrison E, Muddiman KJ, Wood AJ, Paterson S, Brockhurst MA. Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. PLoS Biol 2021; 19:e3001225. [PMID: 34644303 PMCID: PMC8544851 DOI: 10.1371/journal.pbio.3001225] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/25/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid carriage are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or gene expression level. By combining the results of experimental evolution with genetics and transcriptomics, we show here that fitness costs of 2 divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid carriage. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by up-regulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained up-regulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer (HGT) due to their propensity for amelioration by single compensatory mutations, helping to explain why plasmids are so common in bacterial genomes.
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Affiliation(s)
- James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Rosanna C. T. Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Katie J. Muddiman
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - A. Jamie Wood
- Department of Biology, University of York, York, United Kingdom
- Department of Mathematics, University of York, York, United Kingdom
| | - Steve Paterson
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Michael A. Brockhurst
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
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30
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Hakim P, Hoang Y, Vecchiarelli AG. Dissection of the ATPase active site of McdA reveals the sequential steps essential for carboxysome distribution. Mol Biol Cell 2021; 32:ar11. [PMID: 34406783 PMCID: PMC8684754 DOI: 10.1091/mbc.e21-03-0151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Carboxysomes, the most prevalent and well-studied anabolic bacterial microcompartment, play a central role in efficient carbon fixation by cyanobacteria and proteobacteria. In previous studies, we identified the two-component system called McdAB that spatially distributes carboxysomes across the bacterial nucleoid. Maintenance of carboxysome distribution protein A (McdA), a partition protein A (ParA)-like ATPase, forms a dynamic oscillating gradient on the nucleoid in response to the carboxysome-localized Maintenance of carboxysome distribution protein B (McdB). As McdB stimulates McdA ATPase activity, McdA is removed from the nucleoid in the vicinity of carboxysomes, propelling these proteinaceous cargos toward regions of highest McdA concentration via a Brownian-ratchet mechanism. How the ATPase cycle of McdA governs its in vivo dynamics and carboxysome positioning remains unresolved. Here, by strategically introducing amino acid substitutions in the ATP-binding region of McdA, we sequentially trap McdA at specific steps in its ATP cycle. We map out critical events in the ATPase cycle of McdA that allows the protein to bind ATP, dimerize, change its conformation into a DNA-binding state, interact with McdB-bound carboxysomes, hydrolyze ATP, and release from the nucleoid. We also find that McdA is a member of a previously unstudied subset of ParA family ATPases, harboring unique interactions with ATP and the nucleoid for trafficking their cognate intracellular cargos.
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Affiliation(s)
- Pusparanee Hakim
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Y Hoang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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31
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Mori K, Verrone V, Amatsu R, Fukui K, Meijer WJJ, Ishikawa S, Wipat A, Yoshida KI. Assessment of Bacillus subtilis Plasmid pLS20 Conjugation in the Absence of Quorum Sensing Repression. Microorganisms 2021; 9:microorganisms9091931. [PMID: 34576826 PMCID: PMC8470214 DOI: 10.3390/microorganisms9091931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 12/21/2022] Open
Abstract
Bacillus subtilis conjugative plasmid pLS20 uses a quorum-sensing mechanism to control expression levels of its conjugation genes, involving the repressor RcopLS20, the anti-repressor RappLS20, and the signaling peptide Phr*pLS20. In previous studies, artificial overexpression of rappLS20 in the donor cells was shown to enhance conjugation efficiency. However, we found that the overexpression of rappLS20 led to various phenotypic traits, including cell aggregation and death, which might have affected the correct determination of the conjugation efficiency when determined by colony formation assay. In the current study, conjugation efficiencies were determined under different conditions using a two-color fluorescence-activated flow cytometry method and measuring a single-round of pLS20-mediated transfer of a mobilizable plasmid. Under standard conditions, the conjugation efficiency obtained by fluorescence-activated flow cytometry was 23-fold higher than that obtained by colony formation. Furthermore, the efficiency difference increased to 45-fold when rappLS20 was overexpressed.
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Affiliation(s)
- Kotaro Mori
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Valeria Verrone
- School of Computing, Newcastle University, 1 Science Square, Science Central, Newcastle upon Tyne NE4 5TG, UK; (V.V.); (A.W.)
| | - Ryotaro Amatsu
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Kaho Fukui
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Anil Wipat
- School of Computing, Newcastle University, 1 Science Square, Science Central, Newcastle upon Tyne NE4 5TG, UK; (V.V.); (A.W.)
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
- Correspondence: ; Tel.: +81-78-803-5891
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32
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Rillema R, Hoang Y, MacCready JS, Vecchiarelli AG. Carboxysome Mispositioning Alters Growth, Morphology, and Rubisco Level of the Cyanobacterium Synechococcus elongatus PCC 7942. mBio 2021; 12:e0269620. [PMID: 34340540 PMCID: PMC8406218 DOI: 10.1128/mbio.02696-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/01/2021] [Indexed: 12/23/2022] Open
Abstract
Cyanobacteria are the prokaryotic group of phytoplankton responsible for a significant fraction of global CO2 fixation. Like plants, cyanobacteria use the enzyme ribulose 1,5-bisphosphate carboxylase/oxidase (Rubisco) to fix CO2 into organic carbon molecules via the Calvin-Benson-Bassham cycle. Unlike plants, cyanobacteria evolved a carbon-concentrating organelle called the carboxysome-a proteinaceous compartment that encapsulates and concentrates Rubisco along with its CO2 substrate. In the rod-shaped cyanobacterium Synechococcus elongatus PCC 7942, we recently identified the McdAB system responsible for uniformly distributing carboxysomes along the cell length. It remains unknown what role carboxysome positioning plays with respect to cellular physiology. Here, we show that a failure to distribute carboxysomes leads to slower cell growth, cell elongation, asymmetric cell division, and elevated levels of cellular Rubisco. Unexpectedly, we also report that even wild-type S. elongatus undergoes cell elongation and asymmetric cell division when grown at the cool, but environmentally relevant, growth temperature of 20°C or when switched from a high- to ambient-CO2 environment. The findings suggest that carboxysome positioning by the McdAB system functions to maintain the carbon fixation efficiency of Rubisco by preventing carboxysome aggregation, which is particularly important under growth conditions where rod-shaped cyanobacteria adopt a filamentous morphology. IMPORTANCE Photosynthetic cyanobacteria are responsible for almost half of global CO2 fixation. Due to eutrophication, rising temperatures, and increasing atmospheric CO2 concentrations, cyanobacteria have gained notoriety for their ability to form massive blooms in both freshwater and marine ecosystems across the globe. Like plants, cyanobacteria use the most abundant enzyme on Earth, Rubisco, to provide the sole source of organic carbon required for its photosynthetic growth. Unlike plants, cyanobacteria have evolved a carbon-concentrating organelle called the carboxysome that encapsulates and concentrates Rubisco with its CO2 substrate to significantly increase carbon fixation efficiency and cell growth. We recently identified the positioning system that distributes carboxysomes in cyanobacteria. However, the physiological consequence of carboxysome mispositioning in the absence of this distribution system remains unknown. Here, we find that carboxysome mispositioning triggers changes in cell growth and morphology as well as elevated levels of cellular Rubisco.
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Affiliation(s)
- Rees Rillema
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Y Hoang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Joshua S. MacCready
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anthony G. Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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33
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Boudsocq F, Salhi M, Barbe S, Bouet JY. Three ParA Dimers Cooperatively Assemble on Type Ia Partition Promoters. Genes (Basel) 2021; 12:genes12091345. [PMID: 34573327 PMCID: PMC8465637 DOI: 10.3390/genes12091345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 02/03/2023] Open
Abstract
Accurate DNA segregation is essential for faithful inheritance of genetic material. In bacteria, this process is mainly ensured by partition systems composed of two proteins, ParA and ParB, and a centromere site. Auto-regulation of Par operon expression is important for efficient partitioning and is primarily mediated by ParA for type Ia plasmid partition systems. For the F-plasmid, four ParAF monomers were proposed to bind to four repeated sequences in the promoter region. By contrast, using quantitative surface-plasmon-resonance, we showed that three ParAF dimers bind to this region. We uncovered that one perfect inverted repeat (IR) motif, consisting of two hexamer sequences spaced by 28-bp, constitutes the primary ParAF DNA binding site. A similar but degenerated motif overlaps the former. ParAF binding to these motifs is well supported by biochemical and modeling analyses. Molecular dynamics simulations predict that the winged-HTH domain displays high flexibility, which may favor the cooperative ParA binding to the promoter. We propose that three ParAF dimers bind cooperatively to overlapping motifs, thus covering the promoter region. A similar organization is found on closely related and distant plasmid partition systems, suggesting that such promoter organization for auto-regulated Par operons is widespread and may have evolved from a common ancestor.
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Affiliation(s)
- François Boudsocq
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062 Toulouse, France; (M.S.); (J.-Y.B.)
- Correspondence:
| | - Maya Salhi
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062 Toulouse, France; (M.S.); (J.-Y.B.)
| | - Sophie Barbe
- CNRS, Toulouse Biotechnology Institute (TBI), Université de Toulouse, INRAE, INSA, F-31077 Toulouse, France;
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062 Toulouse, France; (M.S.); (J.-Y.B.)
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34
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The structure of the bacterial DNA segregation ATPase filament reveals the conformational plasticity of ParA upon DNA binding. Nat Commun 2021; 12:5166. [PMID: 34453062 PMCID: PMC8397727 DOI: 10.1038/s41467-021-25429-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/11/2021] [Indexed: 02/02/2023] Open
Abstract
The efficient segregation of replicated genetic material is an essential step for cell division. Bacterial cells use several evolutionarily-distinct genome segregation systems, the most common of which is the type I Par system. It consists of an adapter protein, ParB, that binds to the DNA cargo via interaction with the parS DNA sequence; and an ATPase, ParA, that binds nonspecific DNA and mediates cargo transport. However, the molecular details of how this system functions are not well understood. Here, we report the cryo-EM structure of the Vibrio cholerae ParA2 filament bound to DNA, as well as the crystal structures of this protein in various nucleotide states. These structures show that ParA forms a left-handed filament on DNA, stabilized by nucleotide binding, and that ParA undergoes profound structural rearrangements upon DNA binding and filament assembly. Collectively, our data suggest the structural basis for ParA’s cooperative binding to DNA and the formation of high ParA density regions on the nucleoid. ParA is an ATPase involved in the segregation of newly replicated DNA in bacteria. Here, structures of a ParA filament bound to DNA and of ParA in various nucleotide states offer insight into its conformational changes upon DNA binding and filament assembly, including the basis for ParA’s cooperative binding to DNA.
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Taylor JA, Seol Y, Budhathoki J, Neuman KC, Mizuuchi K. CTP and parS coordinate ParB partition complex dynamics and ParA-ATPase activation for ParABS-mediated DNA partitioning. eLife 2021; 10:65651. [PMID: 34286695 PMCID: PMC8357417 DOI: 10.7554/elife.65651] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
ParABS partition systems, comprising the centromere-like DNA sequence parS, the parS-binding ParB-CTPase, and the nucleoid-binding ParA-ATPase, ensure faithful segregation of bacterial chromosomes and low-copy-number plasmids. F-plasmid partition complexes containing ParBF and parSF move by generating and following a local concentration gradient of nucleoid-bound ParAF. However, the process through which ParBF activates ParAF-ATPase has not been defined. We studied CTP- and parSF-modulated ParAF-ParBF complex assembly, in which DNA-bound ParAF-ATP dimers are activated for ATP hydrolysis by interacting with two ParBF N-terminal domains. CTP or parSF enhances the ATPase rate without significantly accelerating ParAF-ParBF complex assembly. Together, parSF and CTP accelerate ParAF-ParBF assembly without further significant increase in ATPase rate. Magnetic-tweezers experiments showed that CTP promotes multiple ParBF loading onto parSF-containing DNA, generating condensed partition complex-like assemblies. We propose that ParBF in the partition complex adopts a conformation that enhances ParBF-ParBF and ParAF-ParBF interactions promoting efficient partitioning.
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Affiliation(s)
- James A Taylor
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Yeonee Seol
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jagat Budhathoki
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Keir C Neuman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Kiyoshi Mizuuchi
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
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Taylor JA, Seol Y, Budhathoki J, Neuman KC, Mizuuchi K. CTP and parS coordinate ParB partition complex dynamics and ParA-ATPase activation for ParABS-mediated DNA partitioning. eLife 2021; 10:65651. [PMID: 34286695 DOI: 10.1101/2021.01.24.427996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 07/20/2021] [Indexed: 05/25/2023] Open
Abstract
ParABS partition systems, comprising the centromere-like DNA sequence parS, the parS-binding ParB-CTPase, and the nucleoid-binding ParA-ATPase, ensure faithful segregation of bacterial chromosomes and low-copy-number plasmids. F-plasmid partition complexes containing ParBF and parSF move by generating and following a local concentration gradient of nucleoid-bound ParAF. However, the process through which ParBF activates ParAF-ATPase has not been defined. We studied CTP- and parSF-modulated ParAF-ParBF complex assembly, in which DNA-bound ParAF-ATP dimers are activated for ATP hydrolysis by interacting with two ParBF N-terminal domains. CTP or parSF enhances the ATPase rate without significantly accelerating ParAF-ParBF complex assembly. Together, parSF and CTP accelerate ParAF-ParBF assembly without further significant increase in ATPase rate. Magnetic-tweezers experiments showed that CTP promotes multiple ParBF loading onto parSF-containing DNA, generating condensed partition complex-like assemblies. We propose that ParBF in the partition complex adopts a conformation that enhances ParBF-ParBF and ParAF-ParBF interactions promoting efficient partitioning.
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Affiliation(s)
- James A Taylor
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Yeonee Seol
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jagat Budhathoki
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Keir C Neuman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Kiyoshi Mizuuchi
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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MacCready JS, Tran L, Basalla JL, Hakim P, Vecchiarelli AG. The McdAB system positions α-carboxysomes in proteobacteria. Mol Microbiol 2021; 116:277-297. [PMID: 33638215 PMCID: PMC8359340 DOI: 10.1111/mmi.14708] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023]
Abstract
Carboxysomes are protein-based organelles essential for carbon fixation in cyanobacteria and proteobacteria. Previously, we showed that the cyanobacterial nucleoid is used to equally space out β-carboxysomes across cell lengths by a two-component system (McdAB) in the model cyanobacterium Synechococcus elongatus PCC 7942. More recently, we found that McdAB systems are widespread among β-cyanobacteria, which possess β-carboxysomes, but are absent in α-cyanobacteria, which possess structurally and phyletically distinct α-carboxysomes. Cyanobacterial α-carboxysomes are thought to have arisen in proteobacteria and then horizontally transferred into cyanobacteria, which suggests that α-carboxysomes in proteobacteria may also lack the McdAB system. Here, using the model chemoautotrophic proteobacterium Halothiobacillus neapolitanus, we show that a McdAB system distinct from that of β-cyanobacteria operates to position α-carboxysomes across cell lengths. We further show that this system is widespread among α-carboxysome-containing proteobacteria and that cyanobacteria likely inherited an α-carboxysome operon from a proteobacterium lacking the mcdAB locus. These results demonstrate that McdAB is a cross-phylum two-component system necessary for positioning both α- and β-carboxysomes. The findings have further implications for understanding the positioning of other protein-based bacterial organelles involved in diverse metabolic processes. PLAIN LANGUAGE SUMMARY: Cyanobacteria are well known to fix atmospheric CO2 into sugars using the enzyme Rubisco. Less appreciated are the carbon-fixing abilities of proteobacteria with diverse metabolisms. Bacterial Rubisco is housed within organelles called carboxysomes that increase enzymatic efficiency. Here we show that proteobacterial carboxysomes are distributed in the cell by two proteins, McdA and McdB. McdA on the nucleoid interacts with McdB on carboxysomes to equidistantly space carboxysomes from one another, ensuring metabolic homeostasis and a proper inheritance of carboxysomes following cell division. This study illuminates how widespread carboxysome positioning systems are among diverse bacteria. Carboxysomes significantly contribute to global carbon fixation; therefore, understanding the spatial organization mechanism shared across the bacterial world is of great interest.
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Affiliation(s)
- Joshua S. MacCready
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMIUSA
| | - Lisa Tran
- Department of Microbiology and ImmunologyUniversity of MichiganAnn ArborMIUSA
| | - Joseph L. Basalla
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMIUSA
| | - Pusparanee Hakim
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMIUSA
| | - Anthony G. Vecchiarelli
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMIUSA
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Abstract
Bacterial microcompartments (BMCs) confine a diverse array of metabolic reactions within a selectively permeable protein shell, allowing for specialized biochemistry that would be less efficient or altogether impossible without compartmentalization. BMCs play critical roles in carbon fixation, carbon source utilization, and pathogenesis. Despite their prevalence and importance in bacterial metabolism, little is known about BMC “homeostasis,” a term we use here to encompass BMC assembly, composition, size, copy-number, maintenance, turnover, positioning, and ultimately, function in the cell. The carbon-fixing carboxysome is one of the most well-studied BMCs with regard to mechanisms of self-assembly and subcellular organization. In this minireview, we focus on the only known BMC positioning system to date—the maintenance of carboxysome distribution (Mcd) system, which spatially organizes carboxysomes. We describe the two-component McdAB system and its proposed diffusion-ratchet mechanism for carboxysome positioning. We then discuss the prevalence of McdAB systems among carboxysome-containing bacteria and highlight recent evidence suggesting how liquid-liquid phase separation (LLPS) may play critical roles in carboxysome homeostasis. We end with an outline of future work on the carboxysome distribution system and a perspective on how other BMCs may be spatially regulated. We anticipate that a deeper understanding of BMC organization, including nontraditional homeostasis mechanisms involving LLPS and ATP-driven organization, is on the horizon.
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Lysinibacillus sphaericus III(3)7 and Plasmid Vector pMK4: New Challenges in Cloning Platforms. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12020031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The acquisition and especially the maintenance of a plasmid usually brings a fitness cost that reduces the reproductive rate of the bacterial host; for strains like Lysinibacillus sphaericus III(3)7, which possesses important environmental properties, this alteration along with morphological changes and reduced sporulation rates may exert a negative effect on metabolic studies using plasmids as cloning platforms. The aim of this study is to approach the metabolic behavior of pMK4-bearing cells of L. sphaericus III(3)7 through the use of bioinformatic and in vitro analyses. An incompatibility model between the pMK4 vector and a predicted megaplasmid, pBsph, inside III(3)7 cells was constructed based on an incA region. Additionally, in vitro long-term plasmid stability was not found in plasmid-bearing cells. Alignments between replicons, mobile genetic elements and RNA-RNA interactions were assessed, pairwise alignment visualization, graphic models and morphological changes were evaluated by SEM. Metabolite analysis was done through HPLC coupled to a Q-TOF 6545, and electrospray ionization was used, finally, Aedes aegypti and Culex quinquefasciatus larvae were used for larvicidal activity assessment. Results found, a decreased growth rate, spore formation reduction and morphological changes, which supported the idea of metabolic cost exerted by pMK4. An incompatibility between pMK4 and pBsph appears to take place inside L. sphaericus III(3)7 cells, however, further in vitro studies are needed to confirm it.
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Azaldegui CA, Vecchiarelli AG, Biteen JS. The emergence of phase separation as an organizing principle in bacteria. Biophys J 2021; 120:1123-1138. [PMID: 33186556 PMCID: PMC8059088 DOI: 10.1016/j.bpj.2020.09.023] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Recent investigations in bacteria suggest that membraneless organelles play a crucial role in the subcellular organization of bacterial cells. However, the biochemical functions and assembly mechanisms of these compartments have not yet been completely characterized. This article assesses the current methodologies used in the study of membraneless organelles in bacteria, highlights the limitations in determining the phase of complexes in cells that are typically an order of magnitude smaller than a eukaryotic cell, and identifies gaps in our current knowledge about the functional role of membraneless organelles in bacteria. Liquid-liquid phase separation (LLPS) is one proposed mechanism for membraneless organelle assembly. Overall, we outline the framework to evaluate LLPS in vivo in bacteria, we describe the bacterial systems with proposed LLPS activity, and we comment on the general role LLPS plays in bacteria and how it may regulate cellular function. Lastly, we provide an outlook for super-resolution microscopy and single-molecule tracking as tools to assess condensates in bacteria.
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Affiliation(s)
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan.
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
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MacCready JS, Basalla JL, Vecchiarelli AG. Origin and Evolution of Carboxysome Positioning Systems in Cyanobacteria. Mol Biol Evol 2021; 37:1434-1451. [PMID: 31899489 PMCID: PMC7182216 DOI: 10.1093/molbev/msz308] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Carboxysomes are protein-based organelles that are essential for allowing cyanobacteria to fix CO2. Previously, we identified a two-component system, McdAB, responsible for equidistantly positioning carboxysomes in the model cyanobacterium Synechococcus elongatus PCC 7942 (MacCready JS, Hakim P, Young EJ, Hu L, Liu J, Osteryoung KW, Vecchiarelli AG, Ducat DC. 2018. Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria. eLife 7:pii:e39723). McdA, a ParA-type ATPase, nonspecifically binds the nucleoid in the presence of ATP. McdB, a novel factor that directly binds carboxysomes, displaces McdA from the nucleoid. Removal of McdA from the nucleoid in the vicinity of carboxysomes by McdB causes a global break in McdA symmetry, and carboxysome motion occurs via a Brownian-ratchet-based mechanism toward the highest concentration of McdA. Despite the importance for cyanobacteria to properly position their carboxysomes, whether the McdAB system is widespread among cyanobacteria remains an open question. Here, we show that the McdAB system is widespread among β-cyanobacteria, often clustering with carboxysome-related components, and is absent in α-cyanobacteria. Moreover, we show that two distinct McdAB systems exist in β-cyanobacteria, with Type 2 systems being the most ancestral and abundant, and Type 1 systems, like that of S. elongatus, possibly being acquired more recently. Lastly, all McdB proteins share the sequence signatures of a protein capable of undergoing liquid–liquid phase separation. Indeed, we find that representatives of both McdB types undergo liquid–liquid phase separation in vitro, the first example of a ParA-type ATPase partner protein to exhibit this behavior. Our results have broader implications for understanding carboxysome evolution, biogenesis, homeostasis, and positioning in cyanobacteria.
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Affiliation(s)
- Joshua S MacCready
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Joseph L Basalla
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
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Meijer WJJ, Boer DR, Ares S, Alfonso C, Rojo F, Luque-Ortega JR, Wu LJ. Multiple Layered Control of the Conjugation Process of the Bacillus subtilis Plasmid pLS20. Front Mol Biosci 2021; 8:648468. [PMID: 33816561 PMCID: PMC8014075 DOI: 10.3389/fmolb.2021.648468] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/08/2021] [Indexed: 11/24/2022] Open
Abstract
Bacterial conjugation is the main horizontal gene transfer route responsible for the spread of antibiotic resistance, virulence and toxin genes. During conjugation, DNA is transferred from a donor to a recipient cell via a sophisticated channel connecting the two cells. Conjugation not only affects many different aspects of the plasmid and the host, ranging from the properties of the membrane and the cell surface of the donor, to other developmental processes such as competence, it probably also poses a burden on the donor cell due to the expression of the large number of genes involved in the conjugation process. Therefore, expression of the conjugation genes must be strictly controlled. Over the past decade, the regulation of the conjugation genes present on the conjugative Bacillus subtilis plasmid pLS20 has been studied using a variety of methods including genetic, biochemical, biophysical and structural approaches. This review focuses on the interplay between RcopLS20, RappLS20 and Phr*pLS20, the proteins that control the activity of the main conjugation promoter Pc located upstream of the conjugation operon. Proper expression of the conjugation genes requires the following two fundamental elements. First, conjugation is repressed by default and an intercellular quorum-signaling system is used to sense conditions favorable for conjugation. Second, different layers of regulation act together to repress the Pc promoter in a strict manner but allowing rapid activation. During conjugation, ssDNA is exported from the cell by a membrane-embedded DNA translocation machine. Another membrane-embedded DNA translocation machine imports ssDNA in competent cells. Evidences are reviewed indicating that conjugation and competence are probably mutually exclusive processes. Some of the questions that remain unanswered are discussed.
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Affiliation(s)
- Wilfried J J Meijer
- Laboratory 402, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | | | - Saúl Ares
- Laboratory 35, C. Grupo Interdisciplinar de Sistemas Complejos and Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Carlos Alfonso
- Laboratory B08, Systems Biochemistry of Bacterial Division Lab, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Fernando Rojo
- Laboratory 216, Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Juan R Luque-Ortega
- Laboratory S07, Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom
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Adamczyk M, Lewicka E, Szatkowska R, Nieznanska H, Ludwiczak J, Jasiński M, Dunin-Horkawicz S, Sitkiewicz E, Swiderska B, Goch G, Jagura-Burdzy G. Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins. BMC Microbiol 2021; 21:32. [PMID: 33482722 PMCID: PMC7821693 DOI: 10.1186/s12866-020-02079-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/20/2020] [Indexed: 01/22/2023] Open
Abstract
Background DNA binding KfrA-type proteins of broad-host-range bacterial plasmids belonging to IncP-1 and IncU incompatibility groups are characterized by globular N-terminal head domains and long alpha-helical coiled-coil tails. They have been shown to act as transcriptional auto-regulators. Results This study was focused on two members of the growing family of KfrA-type proteins encoded by the broad-host-range plasmids, R751 of IncP-1β and RA3 of IncU groups. Comparative in vitro and in silico studies on KfrAR751 and KfrARA3 confirmed their similar biophysical properties despite low conservation of the amino acid sequences. They form a wide range of oligomeric forms in vitro and, in the presence of their cognate DNA binding sites, they polymerize into the higher order filaments visualized as “threads” by negative staining electron microscopy. The studies revealed also temperature-dependent changes in the coiled-coil segment of KfrA proteins that is involved in the stabilization of dimers required for DNA interactions. Conclusion KfrAR751 and KfrARA3 are structural homologues. We postulate that KfrA type proteins have moonlighting activity. They not only act as transcriptional auto-regulators but form cytoskeletal structures, which might facilitate plasmid DNA delivery and positioning in the cells before cell division, involving thermal energy. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02079-w.
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Affiliation(s)
- M Adamczyk
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Noakowskiego 3, 00-664, Warsaw, Poland.
| | - E Lewicka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - R Szatkowska
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - H Nieznanska
- Nencki Institute of Experimental Biology PAS, Laboratory of Electron Microscopy, Pasteura 3, 02-093, Warsaw, Poland
| | - J Ludwiczak
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland.,Nencki Institute of Experimental Biology, Laboratory of Bioinformatics, Pasteura 3, 02-093, Warsaw, Poland
| | - M Jasiński
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland
| | - S Dunin-Horkawicz
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland
| | - E Sitkiewicz
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - B Swiderska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - G Goch
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - G Jagura-Burdzy
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
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Mishra D, Pahujani S, Mitra N, Srivastava A, Srinivasan R. Identification of a Potential Membrane-Targeting Sequence in the C-Terminus of the F Plasmid Segregation Protein SopA. J Membr Biol 2021; 254:243-257. [PMID: 33427942 DOI: 10.1007/s00232-020-00157-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
Stable maintenance and partitioning of the 'Fertility' plasmid or the F plasmid in its host Escherichia coli require the function of a ParA superfamily of proteins known as SopA. The mechanism by which SopA mediates plasmid segregation is well studied. SopA is a nucleoid-binding protein and binds DNA in an ATP-dependent but sequence non-specific manner. ATP hydrolysis stimulated by the binding of the SopBC complex mediates the release of SopA from the nucleoid. Cycles of ATP-binding and hydrolysis generate an ATPase gradient that moves the plasmid through a chemophoresis force. Nucleoid binding of SopA thus assumes a central role in its plasmid-partitioning function. However, earlier work also suggests that the F plasmid can be partitioned into anucleate cells, thus implicating nucleoid independent partitioning. Interestingly, SopA is also reported to be associated with the inner membrane of the bacteria. Here, we report the identification of a possible membrane-targeting sequence, a predicted amphipathic helix, at the C-terminus of SopA. Molecular dynamics simulations indicate that the predicted amphipathic helical motif of SopA has weak affinity for membranes. Moreover, we experimentally show that SopA can associate with bacterial membranes, is detectable in the membrane fractions of bacterial lysates, and is sensitive to the membrane potential. Further, unlike the wild-type SopA, a deletion of the C-terminal 29 amino acids results in the loss of F plasmids from bacterial cells.
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Affiliation(s)
- Dipika Mishra
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institutes, Bhubaneswar, Odisha, 752050, India
| | - Sakshi Pahujani
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institutes, Bhubaneswar, Odisha, 752050, India.,Molecular Biophysics Unit, Indian Institute of Science-Bangalore, C. V. Raman Road, Bangalore, Karnataka, 560012, India
| | - Nivedita Mitra
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institutes, Bhubaneswar, Odisha, 752050, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science-Bangalore, C. V. Raman Road, Bangalore, Karnataka, 560012, India.
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institutes, Bhubaneswar, Odisha, 752050, India.
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46
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Birmes L, Freese HM, Petersen J. RepC_soli: a novel promiscuous plasmid type of Rhodobacteraceae mediates horizontal transfer of antibiotic resistances in the ocean. Environ Microbiol 2021; 23:5395-5411. [PMID: 33393148 DOI: 10.1111/1462-2920.15380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022]
Abstract
Alphaproteobacteria are typically characterized by a multipartite genome organization with a chromosome, stable chromids and accessory plasmids. Extrachromosomal elements determine the lifestyle of roseobacters and their horizontal transfer was previously correlated with rapid adaptations to novel ecological niches. We characterized the distribution and biology of a novel Rhodobacteraceae-specific plasmid type that was designated RepC_soli according to its diagnostic solitary replicase. This low copy number replicon exhibits an exceptional stability, which is likely ensured by non-canonical separate parA and parB partitioning genes. RepC_soli plasmids occur frequently in the surface-associated marine genus Phaeobacter and comparative genome analyses revealed the emergence of four compatibility groups. The universal presence of conserved type IV secretion systems in RepC_soli plasmids is indicative of their recurrent mobilization, a prediction that was experimentally validated by conjugation of the 57 kb Phaeobacter inhibens P72 plasmid (pP72_e) over genus borders. RepC_soli plasmids harbour a diverse collection of beneficial genes including transporters for heavy metal detoxification, prokaryotic defence systems and a conspicuous abundance of antibiotic resistance genes. The pP72_e-encoded efflux pump FloR conferred an about 50-fold increase of resistance against chloramphenicol. Its specific occurrence in Phaeobacter likely reflects a genetic footprint of (former) antimicrobial use in marine aquaculture.
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Affiliation(s)
- Lukas Birmes
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Inhoffenstraße 7 B, D-38124, Germany
| | - Heike M Freese
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Inhoffenstraße 7 B, D-38124, Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Inhoffenstraße 7 B, D-38124, Germany
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47
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Hayashi I. The C-terminal region of the plasmid partitioning protein TubY is a tetramer that can bind membranes and DNA. J Biol Chem 2020; 295:17770-17780. [PMID: 33454013 PMCID: PMC7762940 DOI: 10.1074/jbc.ra120.014705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/13/2020] [Indexed: 01/07/2023] Open
Abstract
Bacterial low-copy-number plasmids require partition (par) systems to ensure their stable inheritance by daughter cells. In general, these systems consist of three components: a centromeric DNA sequence, a centromere-binding protein and a nucleotide hydrolase that polymerizes and functions as a motor. Type III systems, however, segregate plasmids using three proteins: the FtsZ/tubulin-like GTPase TubZ, the centromere-binding protein TubR and the MerR-like transcriptional regulator TubY. Although the TubZ filament is sufficient to transport the TubR-centromere complex in vitro, TubY is still necessary for the stable maintenance of the plasmid. TubY contains an N-terminal DNA-binding helix-turn-helix motif and a C-terminal coiled-coil followed by a cluster of lysine residues. This study determined the crystal structure of the C-terminal domain of TubY from the Bacillus cereus pXO1-like plasmid and showed that it forms a tetrameric parallel four-helix bundle that differs from the typical MerR family proteins with a dimeric anti-parallel coiled-coil. Biochemical analyses revealed that the C-terminal tail with the conserved lysine cluster helps TubY to stably associate with the TubR-centromere complex as well as to nonspecifically bind DNA. Furthermore, this C-terminal tail forms an amphipathic helix in the presence of lipids but must oligomerize to localize the protein to the membrane in vivo. Taken together, these data suggest that TubY is a component of the nucleoprotein complex within the partitioning machinery, and that lipid membranes act as mediators of type III systems.
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Affiliation(s)
- Ikuko Hayashi
- Department of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Kanagawa, Japan
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48
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Baxter JC, Waples WG, Funnell BE. Nonspecific DNA binding by P1 ParA determines the distribution of plasmid partition and repressor activities. J Biol Chem 2020; 295:17298-17309. [PMID: 33055234 PMCID: PMC7863886 DOI: 10.1074/jbc.ra120.015642] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/10/2020] [Indexed: 12/13/2022] Open
Abstract
The faithful segregation, or "partition," of many low-copy number bacterial plasmids is driven by plasmid-encoded ATPases that are represented by the P1 plasmid ParA protein. ParA binds to the bacterial nucleoid via an ATP-dependent nonspecific DNA (nsDNA)-binding activity, which is essential for partition. ParA also has a site-specific DNA-binding activity to the par operator (parOP), which requires either ATP or ADP, and which is essential for it to act as a transcriptional repressor but is dispensable for partition. Here we examine how DNA binding by ParA contributes to the relative distribution of its plasmid partition and repressor activities, using a ParA with an alanine substitution at Arg351, a residue previously predicted to participate in site-specific DNA binding. In vivo, the parAR351A allele is compromised for partition, but its repressor activity is dramatically improved so that it behaves as a "super-repressor." In vitro, ParAR351A binds and hydrolyzes ATP, and undergoes a specific conformational change required for nsDNA binding, but its nsDNA-binding activity is significantly damaged. This defect in turn significantly reduces the assembly and stability of partition complexes formed by the interaction of ParA with ParB, the centromere-binding protein, and DNA. In contrast, the R351A change shows only a mild defect in site-specific DNA binding. We conclude that the partition defect is due to altered nsDNA binding kinetics and affinity for the bacterial chromosome. Furthermore, the super-repressor phenotype is explained by an increased pool of non-nucleoid bound ParA that is competent to bind parOP and repress transcription.
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Affiliation(s)
- Jamie C Baxter
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada
| | - William G Waples
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada
| | - Barbara E Funnell
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada.
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49
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Groaz A, Moghimianavval H, Tavella F, Giessen TW, Vecchiarelli AG, Yang Q, Liu AP. Engineering spatiotemporal organization and dynamics in synthetic cells. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 13:e1685. [PMID: 33219745 DOI: 10.1002/wnan.1685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/13/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022]
Abstract
Constructing synthetic cells has recently become an appealing area of research. Decades of research in biochemistry and cell biology have amassed detailed part lists of components involved in various cellular processes. Nevertheless, recreating any cellular process in vitro in cell-sized compartments remains ambitious and challenging. Two broad features or principles are key to the development of synthetic cells-compartmentalization and self-organization/spatiotemporal dynamics. In this review article, we discuss the current state of the art and research trends in the engineering of synthetic cell membranes, development of internal compartmentalization, reconstitution of self-organizing dynamics, and integration of activities across scales of space and time. We also identify some research areas that could play a major role in advancing the impact and utility of engineered synthetic cells. This article is categorized under: Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
| | | | | | | | | | - Qiong Yang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Allen P Liu
- University of Michigan, Ann Arbor, Michigan, USA
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50
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Nußbaum P, Ithurbide S, Walsh JC, Patro M, Delpech F, Rodriguez-Franco M, Curmi PMG, Duggin IG, Quax TEF, Albers SV. An Oscillating MinD Protein Determines the Cellular Positioning of the Motility Machinery in Archaea. Curr Biol 2020; 30:4956-4972.e4. [PMID: 33125862 DOI: 10.1016/j.cub.2020.09.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/28/2020] [Accepted: 09/23/2020] [Indexed: 01/14/2023]
Abstract
MinD proteins are well studied in rod-shaped bacteria such as E. coli, where they display self-organized pole-to-pole oscillations that are important for correct positioning of the Z-ring at mid-cell for cell division. Archaea also encode proteins belonging to the MinD family, but their functions are unknown. MinD homologous proteins were found to be widespread in Euryarchaeota and form a sister group to the bacterial MinD family, distinct from the ParA and other related ATPase families. We aimed to identify the function of four archaeal MinD proteins in the model archaeon Haloferax volcanii. Deletion of the minD genes did not cause cell division or size defects, and the Z-ring was still correctly positioned. Instead, one of the deletions (ΔminD4) reduced swimming motility and hampered the correct formation of motility machinery at the cell poles. In ΔminD4 cells, there is reduced formation of the motility structure and chemosensory arrays, which are essential for signal transduction. In bacteria, several members of the ParA family can position the motility structure and chemosensory arrays via binding to a landmark protein, and consequently these proteins do not oscillate along the cell axis. However, GFP-MinD4 displayed pole-to-pole oscillation and formed polar patches or foci in H. volcanii. The MinD4 membrane-targeting sequence (MTS), homologous to the bacterial MinD MTS, was essential for the oscillation. Surprisingly, mutant MinD4 proteins failed to form polar patches. Thus, MinD4 from H. volcanii combines traits of different bacterial ParA/MinD proteins.
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Affiliation(s)
- Phillip Nußbaum
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Solenne Ithurbide
- The ithree institute, University of Technology, Sydney, Ultimo, NSW 2007, Australia
| | - James C Walsh
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, NSW 2052, Australia
| | - Megha Patro
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Floriane Delpech
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Marta Rodriguez-Franco
- Cell Biology, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Paul M G Curmi
- School of Physics, University of New South Wales, Sydney, NSW 2052, Australia
| | - Iain G Duggin
- The ithree institute, University of Technology, Sydney, Ultimo, NSW 2007, Australia.
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
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