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Tišma M, Kaljević J, Gruber S, Le TBK, Dekker C. Connecting the dots: key insights on ParB for chromosome segregation from single-molecule studies. FEMS Microbiol Rev 2024; 48:fuad067. [PMID: 38142222 PMCID: PMC10786196 DOI: 10.1093/femsre/fuad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 12/25/2023] Open
Abstract
Bacterial cells require DNA segregation machinery to properly distribute a genome to both daughter cells upon division. The most common system involved in chromosome and plasmid segregation in bacteria is the ParABS system. A core protein of this system - partition protein B (ParB) - regulates chromosome organization and chromosome segregation during the bacterial cell cycle. Over the past decades, research has greatly advanced our knowledge of the ParABS system. However, many intricate details of the mechanism of ParB proteins were only recently uncovered using in vitro single-molecule techniques. These approaches allowed the exploration of ParB proteins in precisely controlled environments, free from the complexities of the cellular milieu. This review covers the early developments of this field but emphasizes recent advances in our knowledge of the mechanistic understanding of ParB proteins as revealed by in vitro single-molecule methods. Furthermore, we provide an outlook on future endeavors in investigating ParB, ParB-like proteins, and their interaction partners.
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Affiliation(s)
- Miloš Tišma
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology; Van der Maasweg 9, Delft, the Netherlands
| | - Jovana Kaljević
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, NR4 7UH Norwich, United Kingdom
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, UNIL-Sorge, Biophore, CH-1015 Lausanne, Switzerland
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, NR4 7UH Norwich, United Kingdom
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology; Van der Maasweg 9, Delft, the Netherlands
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2
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Sutton JAF, Cooke M, Tinajero-Trejo M, Wacnik K, Salamaga B, Portman-Ross C, Lund VA, Hobbs JK, Foster SJ. The roles of GpsB and DivIVA in Staphylococcus aureus growth and division. Front Microbiol 2023; 14:1241249. [PMID: 37711690 PMCID: PMC10498921 DOI: 10.3389/fmicb.2023.1241249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/04/2023] [Indexed: 09/16/2023] Open
Abstract
The spheroid bacterium Staphylococcus aureus is often used as a model of morphogenesis due to its apparently simple cell cycle. S. aureus has many cell division proteins that are conserved across bacteria alluding to common functions. However, despite intensive study, we still do not know the roles of many of these components. Here, we have examined the functions of the paralogues DivIVA and GpsB in the S. aureus cell cycle. Cells lacking gpsB display a more spherical phenotype than the wild-type cells, which is associated with a decrease in peripheral cell wall peptidoglycan synthesis. This correlates with increased localization of penicillin-binding proteins at the developing septum, notably PBPs 2 and 3. Our results highlight the role of GpsB as an apparent regulator of cell morphogenesis in S. aureus.
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Affiliation(s)
- Joshua A. F. Sutton
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Mark Cooke
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Mariana Tinajero-Trejo
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Katarzyna Wacnik
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Bartłomiej Salamaga
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Callum Portman-Ross
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Victoria A. Lund
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Jamie K. Hobbs
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Simon J. Foster
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
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3
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Mishra D, Srinivasan R. Catching a Walker in the Act-DNA Partitioning by ParA Family of Proteins. Front Microbiol 2022; 13:856547. [PMID: 35694299 PMCID: PMC9178275 DOI: 10.3389/fmicb.2022.856547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/28/2022] [Indexed: 12/01/2022] Open
Abstract
Partitioning the replicated genetic material is a crucial process in the cell cycle program of any life form. In bacteria, many plasmids utilize cytoskeletal proteins that include ParM and TubZ, the ancestors of the eukaryotic actin and tubulin, respectively, to segregate the plasmids into the daughter cells. Another distinct class of cytoskeletal proteins, known as the Walker A type Cytoskeletal ATPases (WACA), is unique to Bacteria and Archaea. ParA, a WACA family protein, is involved in DNA partitioning and is more widespread. A centromere-like sequence parS, in the DNA is bound by ParB, an adaptor protein with CTPase activity to form the segregation complex. The ParA ATPase, interacts with the segregation complex and partitions the DNA into the daughter cells. Furthermore, the Walker A motif-containing ParA superfamily of proteins is associated with a diverse set of functions ranging from DNA segregation to cell division, cell polarity, chemotaxis cluster assembly, cellulose biosynthesis and carboxysome maintenance. Unifying principles underlying the varied range of cellular roles in which the ParA superfamily of proteins function are outlined. Here, we provide an overview of the recent findings on the structure and function of the ParB adaptor protein and review the current models and mechanisms by which the ParA family of proteins function in the partitioning of the replicated DNA into the newly born daughter cells.
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Affiliation(s)
- Dipika Mishra
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
- Homi Bhabha National Institutes, Mumbai, India
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
- Homi Bhabha National Institutes, Mumbai, India
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4
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Abstract
Cytoskeletal proteins are classified as a group that is defined functionally, whose members are capable of polymerizing into higher order structures, either dynamically or statically, to perform structural roles during a variety of cellular processes. In eukaryotes, the most well-studied cytoskeletal proteins are actin, tubulin, and intermediate filaments, and are essential for cell shape and movement, chromosome segregation, and intracellular cargo transport. Prokaryotes often harbor homologs of these proteins, but in bacterial cells, these homologs are usually not employed in roles that can be strictly defined as "cytoskeletal". However, several bacteria encode other proteins capable of polymerizing which, although they do not appear to have a eukaryotic counterpart, nonetheless appear to perform a more traditional "cytoskeletal" function. In this review, we discuss recent reports that cover the structure and functions of prokaryotic proteins that are broadly termed as cytoskeletal, either by sequence homology or by function, to highlight how the enzymatic properties of traditionally studied cytoskeletal proteins may be used for other types of cellular functions; and to demonstrate how truly "cytoskeletal" functions may be performed by uniquely bacterial proteins that do not display homology to eukaryotic proteins.
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Affiliation(s)
- Félix Ramos-León
- National Institutes of Health, 37 Convent Dr., Bldg 37, Room 5132, Bethesda, Maryland, 20892, UNITED STATES
| | - Kumaran Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, 37 Convent Dr, Bldg 37, Room 5132, Bethesda, Maryland, 20892, UNITED STATES
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5
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Garg R, Anand C, Ganguly S, Rao S, Verma R, Nagaraja V. Direct Interaction of Polar Scaffolding Protein Wag31 with Nucleoid-Associated Protein Rv3852 Regulates Its Polar Localization. Cells 2021; 10:1558. [PMID: 34203111 DOI: 10.3390/cells10061558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/12/2021] [Accepted: 06/16/2021] [Indexed: 11/25/2022] Open
Abstract
Rv3852 is a unique nucleoid-associated protein (NAP) found exclusively in Mycobacterium tuberculosis (Mtb) and closely related species. Although annotated as H-NS, we showed previously that it is very different from H-NS in its properties and is distinct from other NAPs, anchoring to cell membrane by virtue of possessing a C-terminal transmembrane helix. Here, we investigated the role of Rv3852 in Mtb in organizing architecture or synthesis machinery of cell wall by protein–protein interaction approach. We demonstrated a direct physical interaction of Rv3852 with Wag31, an important cell shape and cell wall integrity determinant essential in Mtb. Wag31 localizes to the cell poles and possibly acts as a scaffold for cell wall synthesis proteins, resulting in polar cell growth in Mtb. Ectopic expression of Rv3852 in M. smegmatis resulted in its interaction with Wag31 orthologue DivIVAMsm. Binding of the NAP to Wag31 appears to be necessary for fine-tuning Wag31 localization to the cell poles, enabling complex cell wall synthesis in Mtb. In Rv3852 knockout background, Wag31 is mislocalized resulting in disturbed nascent peptidoglycan synthesis, suggesting that the NAP acts as a driver for localization of Wag31 to the cell poles. While this novel association between these two proteins presents one of the mechanisms to structure the elaborate multi-layered cell envelope of Mtb, it also exemplifies a new function for a NAP in mycobacteria.
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Sharma K, Sultana T, Liao M, Dahms TES, Dillon JAR. EF1025, a Hypothetical Protein From Enterococcus faecalis, Interacts With DivIVA and Affects Cell Length and Cell Shape. Front Microbiol 2020; 11:83. [PMID: 32117116 PMCID: PMC7028823 DOI: 10.3389/fmicb.2020.00083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/15/2020] [Indexed: 01/22/2023] Open
Abstract
DivIVA plays multifaceted roles in Gram-positive organisms through its association with various cell division and non-cell division proteins. We report a novel DivIVA interacting protein in Enterococcus faecalis, named EF1025 (encoded by EF1025), which is conserved in Gram-positive bacteria. The interaction of EF1025 with DivIVAEf was confirmed by Bacterial Two-Hybrid, Glutathione S-Transferase pull-down, and co-immunoprecipitation assays. EF1025, which contains a DNA binding domain and two Cystathionine β-Synthase (CBS) domains, forms a decamer mediated by the two CBS domains. Viable cells were recovered after insertional inactivation or deletion of EF1025 only through complementation of EF1025 in trans. These cells were longer than the average length of E. faecalis cells and had distorted shapes. Overexpression of EF1025 also resulted in cell elongation. Immuno-staining revealed comparable localization patterns of EF1025 and DivIVAEf in the later stages of division in E. faecalis cells. In summary, EF1025 is a novel DivIVA interacting protein influencing cell length and morphology in E. faecalis.
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Affiliation(s)
- Kusum Sharma
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.,Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Taranum Sultana
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | - Mingmin Liao
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | - Jo-Anne R Dillon
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.,Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
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7
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Kawalek A, Wawrzyniak P, Bartosik AA, Jagura-Burdzy G. Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes. Microorganisms 2020; 8:E105. [PMID: 31940850 PMCID: PMC7022226 DOI: 10.3390/microorganisms8010105] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
The segregation of newly replicated chromosomes in bacterial cells is a highly coordinated spatiotemporal process. In the majority of bacterial species, a tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target(s) parS sequence(s), facilitates the initial steps of chromosome partitioning. ParB nucleates around parS(s) located in the vicinity of newly replicated oriCs to form large nucleoprotein complexes, which are subsequently relocated by ParA to distal cellular compartments. In this review, we describe the role of ParB in various processes within bacterial cells, pointing out interspecies differences. We outline recent progress in understanding the ParB nucleoprotein complex formation and its role in DNA segregation, including ori positioning and anchoring, DNA condensation, and loading of the structural maintenance of chromosome (SMC) proteins. The auxiliary roles of ParBs in the control of chromosome replication initiation and cell division, as well as the regulation of gene expression, are discussed. Moreover, we catalog ParB interacting proteins. Overall, this work highlights how different bacterial species adapt the DNA partitioning ParAB-parS system to meet their specific requirements.
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Affiliation(s)
| | | | | | - Grazyna Jagura-Burdzy
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (A.K.); (P.W.); (A.A.B.)
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8
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Abstract
Reproduction in the bacterial kingdom predominantly occurs through binary fission-a process in which one parental cell is divided into two similarly sized daughter cells. How cell division, in conjunction with cell elongation and chromosome segregation, is orchestrated by a multitude of proteins has been an active area of research spanning the past few decades. Together, the monumental endeavors of multiple laboratories have identified several cell division and cell shape regulators as well as their underlying regulatory mechanisms in rod-shaped Escherichia coli and Bacillus subtilis, which serve as model organisms for Gram-negative and Gram-positive bacteria, respectively. Yet our understanding of bacterial cell division and morphology regulation is far from complete, especially in noncanonical and non-rod-shaped organisms. In this review, we focus on two proteins that are highly conserved in Gram-positive organisms, DivIVA and its homolog GpsB, and attempt to summarize the recent advances in this area of research and discuss their various roles in cell division, cell growth, and chromosome segregation in addition to their interactome and posttranslational regulation.
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9
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Abstract
DivIVA proteins and their GpsB homologues are late cell division proteins found in Gram-positive bacteria. DivIVA/GpsB proteins associate with the inner leaflet of the cytosolic membrane and act as scaffolds for other proteins required for cell growth and division. DivIVA/GpsB proteins comprise an N-terminal lipid-binding domain for membrane association fused to C-terminal domains supporting oligomerization. Despite sharing the same domain organization, DivIVA and GpsB serve different cellular functions: DivIVA plays diverse roles in division site selection, chromosome segregation and controlling peptidoglycan homeostasis, whereas GpsB contributes to the spatiotemporal control of penicillin-binding protein activity. The crystal structures of the lipid-binding domains of DivIVA from Bacillus subtilis and GpsB from several species share a fold unique to this group of proteins, whereas the C-terminal domains of DivIVA and GpsB are radically different. A number of pivotal features identified from the crystal structures explain the functional differences between the proteins. Herein we discuss these structural and functional relationships and recent advances in our understanding of how DivIVA/GpsB proteins bind and recruit their interaction partners, knowledge that might be useful for future structure-based DivIVA/GpsB inhibitor design.
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Affiliation(s)
- Sven Halbedel
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, United Kingdom
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10
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Kaval KG, Hauf S, Rismondo J, Hahn B, Halbedel S. Genetic Dissection of DivIVA Functions in Listeria monocytogenes. J Bacteriol 2017; 199:e00421-17. [PMID: 28972021 DOI: 10.1128/JB.00421-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 09/22/2017] [Indexed: 12/30/2022] Open
Abstract
DivIVA is a membrane binding protein that clusters at curved membrane regions, such as the cell poles and the membrane invaginations occurring during cell division. DivIVA proteins recruit many other proteins to these subcellular sites through direct protein-protein interactions. DivIVA-dependent functions are typically associated with cell growth and division, even though species-specific differences in the spectrum of DivIVA functions and their causative interaction partners exist. DivIVA from the Gram-positive human pathogen Listeria monocytogenes has at least three different functions. In this bacterium, DivIVA is required for precise positioning of the septum at midcell, it contributes to the secretion of autolysins required for the breakdown of peptidoglycan at the septum after the completion of cell division, and it is essential for flagellar motility. While the DivIVA interaction partners for control of division site selection are well established, the proteins connecting DivIVA with autolysin secretion or swarming motility are completely unknown. We set out to identify divIVA alleles in which these three DivIVA functions could be separated, since the question of the degree to which the three functions of L. monocytogenes DivIVA are interlinked could not be answered before. Here, we identify such alleles, and our results show that division site selection, autolysin secretion, and swarming represent three discrete pathways that are independently influenced by DivIVA. These findings provide the required basis for the identification of DivIVA interaction partners controlling autolysin secretion and swarming in the future.IMPORTANCE DivIVA of the pathogenic bacterium Listeria monocytogenes is a central scaffold protein that influences at least three different cellular processes, namely, cell division, protein secretion, and bacterial motility. How DivIVA coordinates these rather unrelated processes is not known. We here identify variants of L. monocytogenes DivIVA, in which these functions are separated from each other. These results have important implications for the models explaining how DivIVA interacts with other proteins.
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11
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Lu H, Qian S, Muhammad U, Jiang X, Han J, Lu Z. Effect of fructose on promoting fengycin biosynthesis inBacillus amyloliquefaciensfmb-60. J Appl Microbiol 2016; 121:1653-1664. [DOI: 10.1111/jam.13291] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/05/2016] [Accepted: 08/30/2016] [Indexed: 11/28/2022]
Affiliation(s)
- H. Lu
- College of Food Science and Technology; Nanjing Agricultural University; Nanjing Jiangsu China
| | - S. Qian
- Department of Bioengineering and Food; Bengbu College; Bengbu Anhui China
| | - U. Muhammad
- College of Food Science and Technology; Nanjing Agricultural University; Nanjing Jiangsu China
| | - X. Jiang
- College of Food Science and Technology; Nanjing Agricultural University; Nanjing Jiangsu China
| | - J. Han
- College of Food Science and Technology; Nanjing Agricultural University; Nanjing Jiangsu China
| | - Z. Lu
- College of Food Science and Technology; Nanjing Agricultural University; Nanjing Jiangsu China
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12
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Kloosterman TG, Lenarcic R, Willis CR, Roberts DM, Hamoen LW, Errington J, Wu LJ. Complex polar machinery required for proper chromosome segregation in vegetative and sporulating cells of Bacillus subtilis. Mol Microbiol 2016; 101:333-50. [PMID: 27059541 PMCID: PMC4949633 DOI: 10.1111/mmi.13393] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 01/16/2023]
Abstract
Chromosome segregation is an essential process of cell multiplication. In prokaryotes, segregation starts with the newly replicated sister origins of replication, oriCs, which move apart to defined positions in the cell. We have developed a genetic screen to identify mutants defective in placement of oriC during spore development in the Gram‐positive bacterium Bacillus subtilis. In addition to the previously identified proteins Soj and DivIVA, our screen identified several new factors involved in polar recruitment of oriC: a reported regulator of competence ComN, and the regulators of division site selection MinD and MinJ. Previous work implicated Soj as an important regulator of oriC positioning in the cell. Our results suggest a model in which the DivIVA‐interacting proteins ComN and MinJ recruit MinD to the cell pole, and that these proteins work upstream of Soj to enable oriC placement. We show that these proteins form a polar complex, which acts in parallel with but distinct from the sporulation‐specific RacA pathway of oriC placement, and also functions during vegetative growth. Our study further shows that MinD has two distinct cell cycle roles, in cell division and chromosome segregation, and highlights that cell probably use multiple parallel mechanisms to ensure accurate chromosome segregation.
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Affiliation(s)
- Tomas G Kloosterman
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK.,Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Rok Lenarcic
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK.,Lek Pharmaceuticals d.d., Menges, Slovenia
| | - Clare R Willis
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - David M Roberts
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Leendert W Hamoen
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK.,Department of Cell Biology & Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Ling J Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
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13
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Garcia-Garcia T, Poncet S, Derouiche A, Shi L, Mijakovic I, Noirot-Gros MF. Role of Protein Phosphorylation in the Regulation of Cell Cycle and DNA-Related Processes in Bacteria. Front Microbiol 2016; 7:184. [PMID: 26909079 PMCID: PMC4754617 DOI: 10.3389/fmicb.2016.00184] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/02/2016] [Indexed: 11/26/2022] Open
Abstract
In all living organisms, the phosphorylation of proteins modulates various aspects of their functionalities. In eukaryotes, protein phosphorylation plays a key role in cell signaling, gene expression, and differentiation. Protein phosphorylation is also involved in the global control of DNA replication during the cell cycle, as well as in the mechanisms that cope with stress-induced replication blocks. Similar to eukaryotes, bacteria use Hanks-type kinases and phosphatases for signal transduction, and protein phosphorylation is involved in numerous cellular processes. However, it remains unclear whether protein phosphorylation in bacteria can also regulate the activity of proteins involved in DNA-mediated processes such as DNA replication or repair. Accumulating evidence supported by functional and biochemical studies suggests that phospho-regulatory mechanisms also take place during the bacterial cell cycle. Recent phosphoproteomics and interactomics studies identified numerous phosphoproteins involved in various aspect of DNA metabolism strongly supporting the existence of such level of regulation in bacteria. Similar to eukaryotes, bacterial scaffolding-like proteins emerged as platforms for kinase activation and signaling. This review reports the current knowledge on the phosphorylation of proteins involved in the maintenance of genome integrity and the regulation of cell cycle in bacteria that reveals surprising similarities to eukaryotes.
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Affiliation(s)
| | - Sandrine Poncet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - Abderahmane Derouiche
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | - Lei Shi
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | - Ivan Mijakovic
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of TechnologyGothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
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14
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Eswaramoorthy P, Winter PW, Wawrzusin P, York AG, Shroff H, Ramamurthi KS. Asymmetric division and differential gene expression during a bacterial developmental program requires DivIVA. PLoS Genet 2014; 10:e1004526. [PMID: 25101664 DOI: 10.1371/journal.pgen.1004526] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/05/2014] [Indexed: 11/24/2022] Open
Abstract
Sporulation in the bacterium Bacillus subtilis is a developmental program in which a progenitor cell differentiates into two different cell types, the smaller of which eventually becomes a dormant cell called a spore. The process begins with an asymmetric cell division event, followed by the activation of a transcription factor, σF, specifically in the smaller cell. Here, we show that the structural protein DivIVA localizes to the polar septum during sporulation and is required for asymmetric division and the compartment-specific activation of σF. Both events are known to require a protein called SpoIIE, which also localizes to the polar septum. We show that DivIVA copurifies with SpoIIE and that DivIVA may anchor SpoIIE briefly to the assembling polar septum before SpoIIE is subsequently released into the forespore membrane and recaptured at the polar septum. Finally, using super-resolution microscopy, we demonstrate that DivIVA and SpoIIE ultimately display a biased localization on the side of the polar septum that faces the smaller compartment in which σF is activated. A central feature of developmental programs is the establishment of asymmetry and the production of genetically identical daughter cells that display different cell fates. Sporulation in the bacterium Bacillus subtilis is a simple developmental program in which the cell divides asymmetrically to produce two daughter cells, after which the transcription factor σF is activated specifically in the smaller cell. Here we investigated DivIVA, which localizes to highly negatively curved membranes, and discovered that it localizes at the asymmetric division site. In the absence of DivIVA, cells failed to asymmetrically divide and prematurely activated σF in the predivisional cell, largely unreported phenotypes for any deletion mutant in a sporulation gene. We found that DivIVA copurifies with SpoIIE, a protein that is required for asymmetric division and σF activation, and that both proteins preferentially localize on the side of the septum facing the smaller daughter cell. DivIVA is therefore a previously overlooked structural factor that is required at the onset of sporulation to mediate both asymmetric division and compartment-specific transcription.
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15
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Abstract
Simple visual inspection of bacteria indicated that, at least in some otherwise symmetric cells, structures such as flagella were often seen at a single pole. Because these structures are composed of proteins, it was not clear how to reconcile these observations of morphological asymmetry with the widely held view of bacteria as unstructured "bags of enzymes." However, over the last decade, numerous GFP tagged proteins have been found at specific intracellular locations such as the poles of the cells, indicating that bacteria have a high degree of intracellular organization. Here we will explore the role of chromosomal asymmetry and the presence of "new" and "old" poles that result from the cytokinesis of rod-shaped cells in establishing bipolar and monopolar protein localization patterns. This article is intended to be illustrative, not exhaustive, so we have focused on examples drawn largely from Caulobacter crescentus and Bacillus subtilis, two bacteria that undergo dramatic morphological transformation. We will highlight how breaking monopolar symmetry is essential for the correct development of these organisms.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York 10032, USA.
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Chaudhuri RR, Allen AG, Owen PJ, Shalom G, Stone K, Harrison M, Burgis TA, Lockyer M, Garcia-Lara J, Foster SJ, Pleasance SJ, Peters SE, Maskell DJ, Charles IG. Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH). BMC Genomics 2009; 10:291. [PMID: 19570206 PMCID: PMC2721850 DOI: 10.1186/1471-2164-10-291] [Citation(s) in RCA: 214] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 07/01/2009] [Indexed: 11/10/2022] Open
Abstract
Background In recent years there has been an increasing problem with Staphylococcus aureus strains that are resistant to treatment with existing antibiotics. An important starting point for the development of new antimicrobial drugs is the identification of "essential" genes that are important for bacterial survival and growth. Results We have developed a robust microarray and PCR-based method, Transposon-Mediated Differential Hybridisation (TMDH), that uses novel bioinformatics to identify transposon inserts in genome-wide libraries. Following a microarray-based screen, genes lacking transposon inserts are re-tested using a PCR and sequencing-based approach. We carried out a TMDH analysis of the S. aureus genome using a large random mariner transposon library of around a million mutants, and identified a total of 351 S. aureus genes important for survival and growth in culture. A comparison with the essential gene list experimentally derived for Bacillus subtilis highlighted interesting differences in both pathways and individual genes. Conclusion We have determined the first comprehensive list of S. aureus essential genes. This should act as a useful starting point for the identification of potential targets for novel antimicrobial compounds. The TMDH methodology we have developed is generic and could be applied to identify essential genes in other bacterial pathogens.
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Affiliation(s)
- Roy R Chaudhuri
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
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Bowman GR, Comolli LR, Zhu J, Eckart M, Koenig M, Downing KH, Moerner WE, Earnest T, Shapiro L. A polymeric protein anchors the chromosomal origin/ParB complex at a bacterial cell pole. Cell 2008; 134:945-55. [PMID: 18805088 DOI: 10.1016/j.cell.2008.07.015] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 04/15/2008] [Accepted: 07/11/2008] [Indexed: 10/21/2022]
Abstract
Bacterial replication origins move towards opposite ends of the cell during DNA segregation. We have identified a proline-rich polar protein, PopZ, required to anchor the separated Caulobacter crescentus chromosome origins at the cell poles, a function that is essential for maintaining chromosome organization and normal cell division. PopZ interacts directly with the ParB protein bound to specific DNA sequences near the replication origin. As the origin/ParB complex is being replicated and moved across the cell, PopZ accumulates at the cell pole and tethers the origin in place upon arrival. The polar accumulation of PopZ occurs by a diffusion/capture mechanism that requires the MreB cytoskeleton. High molecular weight oligomers of PopZ assemble in vitro into a filamentous network with trimer junctions, suggesting that the PopZ network and ParB-bound DNA interact in an adhesive complex, fixing the chromosome origin at the cell pole.
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Affiliation(s)
- Grant R Bowman
- Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, Stanford, CA 94305, USA
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Simmons LA, Grossman AD, Walker GC. Clp and Lon proteases occupy distinct subcellular positions in Bacillus subtilis. J Bacteriol 2008; 190:6758-68. [PMID: 18689473 DOI: 10.1128/JB.00590-08] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among other functions, ATP-dependent proteases degrade misfolded proteins and remove several key regulatory proteins necessary to activate stress responses. In Bacillus subtilis, ClpX, ClpE, and ClpC form homohexameric ATPases that couple to the ClpP peptidase. To understand where these peptidases and ATPases localize in living cells, each protein was fused to a fluorescent moiety. We found that ClpX-GFP (green fluorescent protein) and ClpP-GFP localized as focal assemblies in areas that were not occupied by the nucleoid. We found that the percentage of cells with ClpP-GFP foci increased following heat shock independently of protein synthesis. We determined that ClpE-YFP (yellow fluorescent protein) and ClpC-YFP formed foci coincident with nucleoid edges, usually near cell poles. Furthermore, we found that ClpQ-YFP (HslV) localized as small foci, usually positioned near the cell membrane. We found that ClpQ-YFP foci were dependent on the presence of the cognate hexameric ATPase ClpY (HslU). Moreover, we found that LonA-GFP is coincident with the nucleoid during normal growth and that LonA-GFP also localized to the forespore during development. We also investigated LonB-GFP and found that this protein localized to the forespore membrane early in development, followed by localization throughout the forespore later in development. Our comprehensive study has shown that in B. subtilis several ATP-fueled proteases occupy distinct subcellular locations. With these data, we suggest that substrate specificity could be determined, in part, by the spatial and temporal organization of proteases in vivo.
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Kozbial P, Xu Q, Chiu HJ, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Carlton D, Clayton T, Deller M, Duan L, Elias Y, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Spraggon G, Trout CV, van den Bedem H, Weekes D, White A, Wolf G, Zubieta C, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold. Proteins 2008; 71:1589-96. [PMID: 18324683 DOI: 10.1002/prot.22020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Piotr Kozbial
- Joint Center for Structural Genomics, La Jolla, California, USA
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Affiliation(s)
- Miguel Vicente
- Centro Nacional de Biotecnología, CSIC Campus de Cantoblanco, 28049 Madrid, Spain.
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Fadda D, Santona A, D'Ulisse V, Ghelardini P, Ennas MG, Whalen MB, Massidda O. Streptococcus pneumoniae DivIVA: localization and interactions in a MinCD-free context. J Bacteriol 2006; 189:1288-98. [PMID: 17098892 PMCID: PMC1797354 DOI: 10.1128/jb.01168-06] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To clarify the function of DivIVA in Streptococcus pneumoniae, we localized this protein in exponentially growing cells by both immunofluorescence microscopy and immunoelectron microscopy and found that S. pneumoniae DivIVA (DivIVA(SPN)) had a unique localization profile: it was present simultaneously both as a ring at the division septum and as dots at the cell poles. Double-immunofluorescence analysis suggested that DivIVA is recruited to the septum at a later stage than FtsZ and is retained at the poles after cell separation. All the other cell division proteins that we tested were localized in the divIVA null mutant, although the percentage of cells having constricted Z rings was significantly reduced. In agreement with its localization profile and consistent with its coiled-coil nature, DivIVA interacted with itself and with a number of known or putative S. pneumoniae cell division proteins. Finally, a missense divIVA mutant, obtained by allelic replacement, allowed us to correlate, at the molecular level, the specific interactions and some of the facets of the divIVA mutant phenotype. Taken together, the results suggest that although the possibility of a direct role in chromosome segregation cannot be ruled out, DivIVA in S. pneumoniae seems to be primarily involved in the formation and maturation of the cell poles. The localization and the interaction properties of DivIVA(SPN) raise the intriguing possibility that a common, MinCD-independent function evolved differently in the various host backgrounds.
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Affiliation(s)
- Daniela Fadda
- Dipartimento di Scienze e Tecnologie Biomediche, Sez. Microbiologia Medica, Via Porcell, 4, 09100 Cagliari, Italy
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