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Dehghani B, Rodrigues CDA. SpoIIQ-dependent localization of SpoIIE contributes to septal stability and compartmentalization during the engulfment stage of Bacillus subtilis sporulation. J Bacteriol 2024; 206:e0022024. [PMID: 38904397 PMCID: PMC11270862 DOI: 10.1128/jb.00220-24] [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: 05/23/2024] [Accepted: 06/01/2024] [Indexed: 06/22/2024] Open
Abstract
During spore development in bacteria, a polar septum separates two transcriptionally distinct cellular compartments, the mother cell and the forespore. The conserved serine phosphatase SpoIIE is known for its critical role in the formation of this septum and activation of compartment-specific transcription in the forespore. Signaling between the mother cell and forespore then leads to activation of mother cell transcription and a phagocytic-like process called engulfment, which involves dramatic remodeling of the septum and requires a balance between peptidoglycan synthesis and hydrolysis to ensure septal stability and compartmentalization. Using Bacillus subtilis, we identify an additional role for SpoIIE in maintaining septal stability and compartmentalization at the onset of engulfment. This role for SpoIIE is mediated by SpoIIQ, which anchors SpoIIE in the engulfing membrane. A SpoIIQ mutant (SpoIIQ Y28A) that fails to anchor SpoIIE, results in septal instability and miscompartmentalization during septal peptidoglycan hydrolysis, when other septal stabilization factors are absent. Our data support a model whereby SpoIIE and its interactions with the peptidoglycan synthetic machinery contribute to the stabilization of the asymmetric septum early in engulfment, thereby ensuring compartmentalization during spore development.IMPORTANCEBacterial sporulation is a complex process involving a vast array of proteins. Some of these proteins are absolutely critical and regulate key points in the developmental process. Once such protein is SpoIIE, known for its role in the formation of the polar septum, a hallmark of the early stages of sporulation, and activation of the first sporulation-specific sigma factor, σF, in the developing spore. Interestingly, SpoIIE has been shown to interact with SpoIIQ, an important σF-regulated protein that functions during the engulfment stage. However, the significance of this interaction has remained unclear. Here, we unveil the importance of the SpoIIQ-SpoIIE interaction and identify a role for SpoIIE in the stabilization of the polar septum and maintenance of compartmentalization at the onset of engulfment. In this way, we demonstrate that key sporulation proteins, like SpoIIQ and SpoIIE, function in multiple processes during spore development.
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Affiliation(s)
- Behzad Dehghani
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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2
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Muchová K, Pospíšil J, Kalocsaiová E, Chromiková Z, Žarnovičanová S, Šanderová H, Krásný L, Barák I. Spatio-temporal control of asymmetric septum positioning during sporulation in Bacillus subtilis. J Biol Chem 2024; 300:107339. [PMID: 38705388 PMCID: PMC11154705 DOI: 10.1016/j.jbc.2024.107339] [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: 03/19/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024] Open
Abstract
During sporulation, Bacillus subtilis forms an asymmetric septum, dividing the cell into two compartments, a mother cell and a forespore. The site of asymmetric septation is linked to the membrane where FtsZ and SpoIIE initiate the formation of the Z-ring and the E-ring, respectively. These rings then serve as a scaffold for the other cell division and peptidoglycan synthesizing proteins needed to build the septum. However, despite decades of research, not enough is known about how the asymmetric septation site is determined. Here, we identified and characterized the interaction between SpoIIE and RefZ. We show that these two proteins transiently colocalize during the early stages of asymmetric septum formation when RefZ localizes primarily from the mother cell side of the septum. We propose that these proteins and their interplay with the spatial organization of the chromosome play a role in controlling asymmetric septum positioning.
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Affiliation(s)
- Katarína Muchová
- Department of Microbial Genetics, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jiří Pospíšil
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Evelína Kalocsaiová
- Department of Microbial Genetics, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zuzana Chromiková
- Department of Microbial Genetics, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Silvia Žarnovičanová
- Department of Microbial Genetics, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Imrich Barák
- Department of Microbial Genetics, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia.
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Zhao N, Xu J, Jiao L, Liu M, Zhang T, Li J, Wei X, Fan M. Acid adaptive response of Alicyclobacillus acidoterrestris: A strategy to survive lethal heat and acid stresses. Food Res Int 2022; 157:111364. [DOI: 10.1016/j.foodres.2022.111364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 11/26/2022]
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Abstract
Many pathogens or symbionts of animals and plants contain multiple replicons, a configuration called a multipartite genome. Multipartite genomes enable those species to replicate their genomes faster and better adapt to new niches. Despite their prevalence, the mechanisms by which multipartite genomes are stably maintained are poorly understood. Agrobacterium tumefaciens is a plant pathogen that contains four replicons: a circular chromosome (Ch1), a linear chromosome (Ch2), and two large plasmids. Recent work indicates that their replication origins are clustered at the cell poles in a manner that depends on their ParB family centromeric proteins: ParB1 for Ch1 and individual RepB paralogs for Ch2 and the plasmids. However, understanding of these interactions and how they contribute to genome maintenance is limited. By combining genome-wide chromosome conformation capture (Hi-C) assays, chromatin-immunoprecipitation sequencing (ChIP-seq), and live cell fluorescence microscopy, we provide evidence here that centromeric clustering is mediated by interactions between these centromeric proteins. We further show that the disruption of centromere clustering results in the loss of replicons. Our data establish the role of centromeric clustering in multipartite genome stability. IMPORTANCE About 10% of sequenced bacteria have multiple replicons, also known as multipartite genomes. How these multipartite genomes are maintained is still poorly understood. Here, we use Agrobacterium tumefaciens as a model and show that the replication origins of the four replicons are clustered through direct interactions between the centromeric proteins; disruption of origin clustering leads to the loss of replicons. Thus, our study provided evidence that centromeric clustering is important for maintaining multipartite genomes.
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Parrell D, Kroos L. Channels modestly impact compartment-specific ATP levels during Bacillus subtilis sporulation and a rise in the mother cell ATP level is not necessary for Pro-σ K cleavage. Mol Microbiol 2020; 114:563-581. [PMID: 32515031 DOI: 10.1111/mmi.14560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 01/13/2023]
Abstract
Starvation of Bacillus subtilis initiates endosporulation involving formation of mother cell (MC) and forespore (FS) compartments. During engulfment, the MC membrane migrates around the FS and protein channels connect the two compartments. The channels are necessary for postengulfment FS gene expression, which relieves inhibition of SpoIVFB, an intramembrane protease that cleaves Pro-σK , releasing σK into the MC. SpoIVFB has an ATP-binding domain exposed to the MC cytoplasm, but the role of ATP in regulating Pro-σK cleavage has been unclear, as has the impact of the channels on MC and FS ATP levels. Using luciferase produced separately in each compartment to measure relative ATP concentrations during sporulation, we found that the MC ATP concentration rises about twofold coincident with increasing cleavage of Pro-σK , and the FS ATP concentration does not decline. Mutants lacking a channel protein or defective in channel protein turnover exhibited modest and varied effects on ATP levels, which suggested that low ATP concentration does not explain the lack of postengulfment FS gene expression in channel mutants. Furthermore, a rise in the MC ATP level was not necessary for Pro-σK cleavage by SpoIVFB, based on analysis of mutants that bypass the need for relief of SpoIVFB inhibition.
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Affiliation(s)
- Daniel Parrell
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Lee Kroos
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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Linking the Peptidoglycan Synthesis Protein Complex with Asymmetric Cell Division during Bacillus subtilis Sporulation. Int J Mol Sci 2020; 21:ijms21124513. [PMID: 32630428 PMCID: PMC7349982 DOI: 10.3390/ijms21124513] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022] Open
Abstract
Peptidoglycan is generally considered one of the main determinants of cell shape in bacteria. In rod-shaped bacteria, cell elongation requires peptidoglycan synthesis to lengthen the cell wall. In addition, peptidoglycan is synthesized at the division septum during cell division. Sporulation of Bacillus subtilis begins with an asymmetric cell division. Formation of the sporulation septum requires almost the same set of proteins as the vegetative septum; however, these two septa are significantly different. In addition to their differences in localization, the sporulation septum is thinner and it contains SpoIIE, a crucial sporulation specific protein. Here we show that peptidoglycan biosynthesis is linked to the cell division machinery during sporulation septum formation. We detected a direct interaction between SpoIIE and GpsB and found that both proteins co-localize during the early stages of asymmetric septum formation. We propose that SpoIIE is part of a multi-protein complex which includes GpsB, other division proteins and peptidoglycan synthesis proteins, and could provide a link between the peptidoglycan synthesis machinery and the complex morphological changes required for forespore formation during B. subtilis sporulation.
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Wollman AJ, Muchová K, Chromiková Z, Wilkinson AJ, Barák I, Leake MC. Single-molecule optical microscopy of protein dynamics and computational analysis of images to determine cell structure development in differentiating Bacillus subtilis. Comput Struct Biotechnol J 2020; 18:1474-1486. [PMID: 32637045 PMCID: PMC7327415 DOI: 10.1016/j.csbj.2020.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022] Open
Abstract
Here we use singe-molecule optical proteomics and computational analysis of live cell bacterial images, using millisecond super-resolved tracking and quantification of fluorescently labelled protein SpoIIE in single live Bacillus subtilis bacteria to understand its crucial role in cell development. Asymmetric cell division during sporulation in Bacillus subtilis presents a model system for studying cell development. SpoIIE is a key integral membrane protein phosphatase that couples morphological development to differential gene expression. However, the basic mechanisms behind its operation remain unclear due to limitations of traditional tools and technologies. We instead used advanced single-molecule imaging of fluorescently tagged SpoIIE in real time on living cells to reveal vital changes to the patterns of expression, localization, mobility and stoichiometry as cells undergo asymmetric cell division then engulfment of the smaller forespore by the larger mother cell. We find, unexpectedly, that SpoIIE forms tetramers capable of cell- and stage-dependent clustering, its copy number rising to ~ 700 molecules as sporulation progresses. We observed that slow moving SpoIIE clusters initially located at septa are released as mobile clusters at the forespore pole as phosphatase activity is manifested and compartment-specific RNA polymerase sigma factor, σF, becomes active. Our findings reveal that information captured in its quaternary organization enables one protein to perform multiple functions, extending an important paradigm for regulatory proteins in cells. Our findings more generally demonstrate the utility of rapid live cell single-molecule optical proteomics for enabling mechanistic insight into the complex processes of cell development during the cell cycle.
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Affiliation(s)
- Adam J.M. Wollman
- Departments of Physics and Biology, University of York, York YO10 5DD, United Kingdom
| | - Katarína Muchová
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zuzana Chromiková
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Anthony J. Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Imrich Barák
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Mark C. Leake
- Departments of Physics and Biology, University of York, York YO10 5DD, United Kingdom
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Brunet YR, Wang X, Rudner DZ. SweC and SweD are essential co-factors of the FtsEX-CwlO cell wall hydrolase complex in Bacillus subtilis. PLoS Genet 2019; 15:e1008296. [PMID: 31437162 PMCID: PMC6705773 DOI: 10.1371/journal.pgen.1008296] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/08/2019] [Indexed: 01/10/2023] Open
Abstract
The peptidoglycan (PG) sacculus is composed of long glycan strands cross-linked together by short peptides forming a covalently closed meshwork that protects the bacterial cell from osmotic lysis and specifies its shape. PG hydrolases play essential roles in remodeling this three-dimensional network during growth and division but how these autolytic enzymes are regulated remains poorly understood. The FtsEX ABC transporter-like complex has emerged as a broadly conserved regulatory module in controlling cell wall hydrolases in diverse bacterial species. In most characterized examples, this complex regulates distinct PG hydrolases involved in cell division and is intimately associated with the cytokinetic machinery called the divisome. However, in the gram-positive bacterium Bacillus subtilis the FtsEX complex is required for cell wall elongation where it regulates the PG hydrolase CwlO that acts along the lateral cell wall. To investigate whether additional factors are required for FtsEX function outside the divisome, we performed a synthetic lethal screen taking advantage of the conditional essentiality of CwlO. This screen identified two uncharacterized factors (SweD and SweC) that are required for CwlO activity. We demonstrate that these proteins reside in a membrane complex with FtsX and that amino acid substitutions in residues adjacent to the ATPase domain of FtsE partially bypass the requirement for them. Collectively our data indicate that SweD and SweC function as essential co-factors of FtsEX in controlling CwlO during cell wall elongation. We propose that factors analogous to SweDC function to support FtsEX activity outside the divisome in other bacteria.
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Affiliation(s)
- Yannick R. Brunet
- Department of Microbiology, Harvard Medical School, Boston, MA, United States of America
| | - Xindan Wang
- Department of Microbiology, Harvard Medical School, Boston, MA, United States of America
| | - David Z. Rudner
- Department of Microbiology, Harvard Medical School, Boston, MA, United States of America
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Barák I, Muchová K, Labajová N. Asymmetric cell division during Bacillus subtilis sporulation. Future Microbiol 2019; 14:353-363. [PMID: 30855188 DOI: 10.2217/fmb-2018-0338] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacillus subtilis is a rod-shaped bacterium which divides precisely at mid-cell during vegetative growth. Unlike Escherichia coli, another model organism used for studying cell division, B. subtilis can also divide asymmetrically during sporulation, the simplest cell differentiation process. The asymmetrically positioned sporulation septum serves as a morphological foundation for establishing differential gene expression in the smaller forespore and larger mother cell. Both vegetative and sporulation septation events are fine-tuned with cell cycle, and placement of both septa are highly precise. We understand in some detail how this is achieved during vegetative growth but have limited information about how the asymmetric septation site is determined during sporulation.
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Affiliation(s)
- Imrich Barák
- Department of Microbial Genetics, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Katarína Muchová
- Department of Microbial Genetics, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Naďa Labajová
- Department of Microbial Genetics, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
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Ramírez-Guadiana FH, Rodrigues CDA, Marquis KA, Campo N, Barajas-Ornelas RDC, Brock K, Marks DS, Kruse AC, Rudner DZ. Evidence that regulation of intramembrane proteolysis is mediated by substrate gating during sporulation in Bacillus subtilis. PLoS Genet 2018; 14:e1007753. [PMID: 30403663 PMCID: PMC6242693 DOI: 10.1371/journal.pgen.1007753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 11/19/2018] [Accepted: 10/10/2018] [Indexed: 01/11/2023] Open
Abstract
During the morphological process of sporulation in Bacillus subtilis two adjacent daughter cells (called the mother cell and forespore) follow different programs of gene expression that are linked to each other by signal transduction pathways. At a late stage in development, a signaling pathway emanating from the forespore triggers the proteolytic activation of the mother cell transcription factor σK. Cleavage of pro-σK to its mature and active form is catalyzed by the intramembrane cleaving metalloprotease SpoIVFB (B), a Site-2 Protease (S2P) family member. B is held inactive by two mother-cell membrane proteins SpoIVFA (A) and BofA. Activation of pro-σK processing requires a site-1 signaling protease SpoIVB (IVB) that is secreted from the forespore into the space between the two cells. IVB cleaves the extracellular domain of A but how this cleavage activates intramembrane proteolysis has remained unclear. Structural studies of the Methanocaldococcus jannaschii S2P homolog identified closed (substrate-occluded) and open (substrate-accessible) conformations of the protease, but the biological relevance of these conformations has not been established. Here, using co-immunoprecipitation and fluorescence microscopy, we show that stable association between the membrane-embedded protease and its substrate requires IVB signaling. We further show that the cytoplasmic cystathionine-β-synthase (CBS) domain of the B protease is not critical for this interaction or for pro-σK processing, suggesting the IVB-dependent interaction site is in the membrane protease domain. Finally, we provide evidence that the B protease domain adopts both open and closed conformations in vivo. Collectively, our data support a substrate-gating model in which IVB-dependent cleavage of A on one side of the membrane triggers a conformational change in the membrane-embedded protease from a closed to an open state allowing pro-σK access to the caged interior of the protease. Regulated Intramembrane Proteolysis is a broadly conserved mechanism for transducing information across lipid bilayers. In these signaling pathways a protease on one side of the membrane triggers the activation of a membrane-embedded protease that cleaves its substrate within or adjacent to the cytoplasmic face of the membrane. Site-2 metalloproteases (S2P) are the most commonly used intramembrane cleaving proteases in these pathways but the mechanism by which cleavage on one side of the membrane triggers intramembrane proteolysis remains poorly understood. Here, we provide evidence for a substrate-gating model in which an extracellular signaling protease triggers a conformational change in a S2P family member from a closed to an open conformation allowing its substrate access to the catalytic center of the enzyme.
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Affiliation(s)
| | | | - Kathleen A. Marquis
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA United States of America
| | - Nathalie Campo
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA United States of America
| | | | - Kelly Brock
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - David Z. Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA United States of America
- * E-mail:
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Ramírez-Guadiana FH, Meeske AJ, Rodrigues CDA, Barajas-Ornelas RDC, Kruse AC, Rudner DZ. A two-step transport pathway allows the mother cell to nurture the developing spore in Bacillus subtilis. PLoS Genet 2017; 13:e1007015. [PMID: 28945739 PMCID: PMC5629000 DOI: 10.1371/journal.pgen.1007015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/05/2017] [Accepted: 09/09/2017] [Indexed: 11/18/2022] Open
Abstract
One of the hallmarks of bacterial endospore formation is the accumulation of high concentrations of pyridine-2,6-dicarboxylic acid (dipicolinic acid or DPA) in the developing spore. This small molecule comprises 5–15% of the dry weight of dormant spores and plays a central role in resistance to both wet heat and desiccation. DPA is synthesized in the mother cell at a late stage in sporulation and must be translocated across two membranes (the inner and outer forespore membranes) that separate the mother cell and forespore. The enzymes that synthesize DPA and the proteins required to translocate it across the inner forespore membrane were identified over two decades ago but the factors that transport DPA across the outer forespore membrane have remained mysterious. Here, we report that SpoVV (formerly YlbJ) is the missing DPA transporter. SpoVV is produced in the mother cell during the morphological process of engulfment and specifically localizes in the outer forespore membrane. Sporulating cells lacking SpoVV produce spores with low levels of DPA and cells engineered to express SpoVV and the DPA synthase during vegetative growth accumulate high levels of DPA in the culture medium. SpoVV resembles concentrative nucleoside transporters and mutagenesis of residues predicted to form the substrate-binding pocket supports the idea that SpoVV has a similar structure and could therefore function similarly. These findings provide a simple two-step transport mechanism by which the mother cell nurtures the developing spore. DPA produced in the mother cell is first translocated into the intermembrane space by SpoVV and is then imported into the forespore by the SpoVA complex. This pathway is likely to be broadly conserved as DPA synthase, SpoVV, and SpoVA proteins can be found in virtually all endospore forming bacteria. All pathogenic and non-pathogenic bacteria that differentiate into dormant endospores including Clostridium difficile, Bacillus anthracis, and Bacillus subtilis, contain very high concentrations of the small molecule dipicolinic acid (DPA). This molecule displaces water in the spore core where it plays an integral role in spore resistance and dormancy. DPA and its contribution to spore dehydration were discovered in 1953 but the molecular basis for its accumulation in the spore has remained unclear. The developing endospore resides within a mother cell that assembles protective layers around the spore and nurtures it by providing mother-cell-produced molecules. DPA is produced in the mother cell at a late stage in development and then must be translocated across two membranes into the spore core. Here, we report the discovery of the missing DPA transporter, homologs of which are present in virtually all endospore-forming bacteria. Our data provide evidence for a simple two-step transport pathway in which the mother cell nurtures the developing spore by sequentially moving DPA across the two membranes that surround it.
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Affiliation(s)
| | - Alexander J. Meeske
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | | | | | - Andrew C. Kruse
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - David Z. Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
- * E-mail:
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12
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Abstract
Bacillus subtilis is the best described member of the Gram positive bacteria. It is a typical rod shaped bacterium and grows by elongation in its long axis, before dividing at mid cell to generate two similar daughter cells. B. subtilis is a particularly interesting model for cell cycle studies because it also carries out a modified, asymmetrical division during endospore formation, which can be simply induced by starvation. Cell growth occurs strictly by elongation of the rod, which maintains a constant diameter at all growth rates. This process involves expansion of the cell wall, requiring intercalation of new peptidoglycan and teichoic acid material, as well as controlled hydrolysis of existing wall material. Actin-like MreB proteins are the key spatial regulators that orchestrate the plethora of enzymes needed for cell elongation, many of which are thought to assemble into functional complexes called elongasomes. Cell division requires a switch in the orientation of cell wall synthesis and is organised by a tubulin-like protein FtsZ. FtsZ forms a ring-like structure at the site of impending division, which is specified by a range of mainly negative regulators. There it recruits a set of dedicated division proteins to form a structure called the divisome, which brings about the process of division. During sporulation, both the positioning and fine structure of the division septum are altered, and again, several dedicated proteins that contribute specifically to this process have been identified. This chapter summarises our current understanding of elongation and division in B. subtilis, with particular emphasis on the cytoskeletal proteins MreB and FtsZ, and highlights where the major gaps in our understanding remain.
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Defeu Soufo HJ. A Novel Cell Type Enables B. subtilis to Escape from Unsuccessful Sporulation in Minimal Medium. Front Microbiol 2016; 7:1810. [PMID: 27891124 PMCID: PMC5104909 DOI: 10.3389/fmicb.2016.01810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/27/2016] [Indexed: 11/28/2022] Open
Abstract
Sporulation is the most enduring survival strategy developed by several bacterial species. However, spore development of the model organism Bacillus subtilis has mainly been studied by means of media or conditions optimized for the induction of sporogenesis. Here, I show that during prolonged growth during stationary phase in minimal medium, B. subtilis undergoes an asymmetric cell division that produces small and round-shaped, DNA containing cells. In contrast to wild-type cells, mutants harboring spo0A or spoIIIE/sftA double mutations neither sporulate nor produce this special cell type, providing evidence that the small round cells emerge from the abortion of endospore formation. In most cases observed, the small round cells arise in the presence of sigma H but absence of sigma F activity, different from cases of abortive sporulation described for rich media. These data suggest that in minimal media, many cells are able to initiate but fail to complete spore development, and therefore return to normal growth as rods. This work reveals that the continuation of asymmetric cell division, which results in the formation of the small round cells, is a way for cells to delay or escape from—unsuccessful—sporulation. Based on these findings, I suggest to name the here described cell type as “dwarf cells” to distinguish them from the well-known minicells observed in mutants defective in septum placement or proper chromosome partitioning.
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14
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Rodrigues CDA, Ramírez-Guadiana FH, Meeske AJ, Wang X, Rudner DZ. GerM is required to assemble the basal platform of the SpoIIIA-SpoIIQ transenvelope complex during sporulation in Bacillus subtilis. Mol Microbiol 2016; 102:260-273. [PMID: 27381174 DOI: 10.1111/mmi.13457] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2016] [Indexed: 11/29/2022]
Abstract
Sporulating Bacillus subtilis cells assemble a multimeric membrane complex connecting the mother cell and developing spore that is required to maintain forespore differentiation. An early step in the assembly of this transenvelope complex (called the A-Q complex) is an interaction between the extracellular domains of the forespore membrane protein SpoIIQ and the mother cell membrane protein SpoIIIAH. This interaction provides a platform onto which the remaining components of the complex assemble and also functions as an anchor for cell-cell signalling and morphogenetic proteins involved in spore development. SpoIIQ is required to recruit SpoIIIAH to the sporulation septum on the mother cell side; however, the mechanism by which SpoIIQ specifically localizes to the septal membranes on the forespore side has remained enigmatic. Here, we identify GerM, a lipoprotein previously implicated in spore germination, as the missing factor required for SpoIIQ localization. Our data indicate that GerM and SpoIIIAH, derived from the mother cell, and SpoIIQ, from the forespore, have reciprocal localization dependencies suggesting they constitute a tripartite platform for the assembly of the A-Q complex and a hub for the localization of mother cell and forespore proteins.
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Affiliation(s)
- Christopher D A Rodrigues
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Fernando H Ramírez-Guadiana
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Alexander J Meeske
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Xindan Wang
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
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Muchová K, Chromiková Z, Bradshaw N, Wilkinson AJ, Barák I. Morphogenic Protein RodZ Interacts with Sporulation Specific SpoIIE in Bacillus subtilis. PLoS One 2016; 11:e0159076. [PMID: 27415800 PMCID: PMC4945075 DOI: 10.1371/journal.pone.0159076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/27/2016] [Indexed: 12/02/2022] Open
Abstract
The first landmark in sporulation of Bacillus subtilis is the formation of an asymmetric septum followed by selective activation of the transcription factor σF in the resulting smaller cell. How the morphological transformations that occur during sporulation are coupled to cell-specific activation of transcription is largely unknown. The membrane protein SpoIIE is a constituent of the asymmetric sporulation septum and is a crucial determinant of σF activation. Here we report that the morphogenic protein, RodZ, which is essential for cell shape determination, is additionally required for asymmetric septum formation and sporulation. In cells depleted of RodZ, formation of asymmetric septa is disturbed and σF activation is perturbed. During sporulation, we found that SpoIIE recruits RodZ to the asymmetric septum. Moreover, we detected a direct interaction between SpoIIE and RodZ in vitro and in vivo, indicating that SpoIIE-RodZ may form a complex to coordinate asymmetric septum formation and σF activation. We propose that RodZ could provide a link between the cell shape machinery and the coordinated morphological and developmental transitions required to form a resistant spore.
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Affiliation(s)
- Katarína Muchová
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zuzana Chromiková
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Niels Bradshaw
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Anthony J. Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Imrich Barák
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
- * E-mail:
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16
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A Membrane-Embedded Amino Acid Couples the SpoIIQ Channel Protein to Anti-Sigma Factor Transcriptional Repression during Bacillus subtilis Sporulation. J Bacteriol 2016; 198:1451-63. [PMID: 26929302 DOI: 10.1128/jb.00958-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/22/2016] [Indexed: 01/19/2023] Open
Abstract
UNLABELLED SpoIIQ is an essential component of a channel connecting the developing forespore to the adjacent mother cell during Bacillus subtilis sporulation. This channel is generally required for late gene expression in the forespore, including that directed by the late-acting sigma factor σ(G) Here, we present evidence that SpoIIQ also participates in a previously unknown gene regulatory circuit that specifically represses expression of the gene encoding the anti-sigma factor CsfB, a potent inhibitor of σ(G) The csfB gene is ordinarily transcribed in the forespore only by the early-acting sigma factor σ(F) However, in a mutant lacking the highly conserved SpoIIQ transmembrane amino acid Tyr-28, csfB was also aberrantly transcribed later by σ(G), the very target of CsfB inhibition. This regulation of csfB by SpoIIQ Tyr-28 is specific, given that the expression of other σ(F)-dependent genes was unaffected. Moreover, we identified a conserved element within the csfB promoter region that is both necessary and sufficient for SpoIIQ Tyr-28-mediated inhibition. These results indicate that SpoIIQ is a bifunctional protein that not only generally promotes σ(G)activity in the forespore as a channel component but also specifically maximizes σ(G)activity as part of a gene regulatory circuit that represses σ(G)-dependent expression of its own inhibitor, CsfB. Finally, we demonstrate that SpoIIQ Tyr-28 is required for the proper localization and stability of the SpoIIE phosphatase, raising the possibility that these two multifunctional proteins cooperate to fine-tune developmental gene expression in the forespore at late times. IMPORTANCE Cellular development is orchestrated by gene regulatory networks that activate or repress developmental genes at the right time and place. Late gene expression in the developing Bacillus subtilis spore is directed by the alternative sigma factor σ(G) The activity of σ(G)requires a channel apparatus through which the adjacent mother cell provides substrates that generally support gene expression. Here we report that the channel protein SpoIIQ also specifically maximizes σ(G)activity as part of a previously unknown regulatory circuit that prevents σ(G)from activating transcription of the gene encoding its own inhibitor, the anti-sigma factor CsfB. The discovery of this regulatory circuit significantly expands our understanding of the gene regulatory network controlling late gene expression in the developing B. subtilis spore.
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17
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Bradshaw N, Losick R. Asymmetric division triggers cell-specific gene expression through coupled capture and stabilization of a phosphatase. eLife 2015; 4. [PMID: 26465112 PMCID: PMC4714977 DOI: 10.7554/elife.08145] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 10/13/2015] [Indexed: 11/13/2022] Open
Abstract
Formation of a division septum near a randomly chosen pole during sporulation in Bacillus subtilis creates unequal sized daughter cells with dissimilar programs of gene expression. An unanswered question is how polar septation activates a transcription factor (σ(F)) selectively in the small cell. We present evidence that the upstream regulator of σ(F), the phosphatase SpoIIE, is compartmentalized in the small cell by transfer from the polar septum to the adjacent cell pole where SpoIIE is protected from proteolysis and activated. Polar recognition, protection from proteolysis, and stimulation of phosphatase activity are linked to oligomerization of SpoIIE. This mechanism for initiating cell-specific gene expression is independent of additional sporulation proteins; vegetative cells engineered to divide near a pole sequester SpoIIE and activate σ(F) in small cells. Thus, a simple model explains how SpoIIE responds to a stochastically-generated cue to activate σ(F) at the right time and in the right place.
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Affiliation(s)
- Niels Bradshaw
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
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18
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Schneider J, Klein T, Mielich-Süss B, Koch G, Franke C, Kuipers OP, Kovács ÁT, Sauer M, Lopez D. Spatio-temporal remodeling of functional membrane microdomains organizes the signaling networks of a bacterium. PLoS Genet 2015; 11:e1005140. [PMID: 25909364 PMCID: PMC4409396 DOI: 10.1371/journal.pgen.1005140] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 03/11/2015] [Indexed: 11/18/2022] Open
Abstract
Lipid rafts are membrane microdomains specialized in the regulation of numerous cellular processes related to membrane organization, as diverse as signal transduction, protein sorting, membrane trafficking or pathogen invasion. It has been proposed that this functional diversity would require a heterogeneous population of raft domains with varying compositions. However, a mechanism for such diversification is not known. We recently discovered that bacterial membranes organize their signal transduction pathways in functional membrane microdomains (FMMs) that are structurally and functionally similar to the eukaryotic lipid rafts. In this report, we took advantage of the tractability of the prokaryotic model Bacillus subtilis to provide evidence for the coexistence of two distinct families of FMMs in bacterial membranes, displaying a distinctive distribution of proteins specialized in different biological processes. One family of microdomains harbors the scaffolding flotillin protein FloA that selectively tethers proteins specialized in regulating cell envelope turnover and primary metabolism. A second population of microdomains containing the two scaffolding flotillins, FloA and FloT, arises exclusively at later stages of cell growth and specializes in adaptation of cells to stationary phase. Importantly, the diversification of membrane microdomains does not occur arbitrarily. We discovered that bacterial cells control the spatio-temporal remodeling of microdomains by restricting the activation of FloT expression to stationary phase. This regulation ensures a sequential assembly of functionally specialized membrane microdomains to strategically organize signaling networks at the right time during the lifespan of a bacterium. Cellular membranes organize proteins related to signal transduction, protein sorting and membrane trafficking into the so-called lipid rafts. It has been proposed that the functional diversity of lipid rafts would require a heterogeneous population of raft domains with varying compositions. However, a mechanism for such diversification is not known due in part to the complexity that entails the manipulation of eukaryotic cells. The recent discovery that bacteria organize many cellular processes in membrane microdomains (FMMs), functionally similar to the eukaryotic lipid rafts, prompted us to explore FMMs diversity in the bacterial model Bacillus subtilis. We show that diversification of FMMs occurs in cells and gives rise to functionally distinct microdomains, which compartmentalize distinct signal transduction pathways and regulate the expression of different genetic programs. We discovered that FMMs diversification does not occur randomly. Cells sequentially regulate the specialization of the FMMs during cell growth to ensure an effective and diverse activation of signaling processes.
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Affiliation(s)
- Johannes Schneider
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
| | - Teresa Klein
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Benjamin Mielich-Süss
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
| | - Gudrun Koch
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
| | - Christian Franke
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Oscar P. Kuipers
- Molecular Genetics Group,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ákos T. Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Daniel Lopez
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- * E-mail:
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19
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Asymmetric division and differential gene expression during a bacterial developmental program requires DivIVA. PLoS Genet 2014; 10:e1004526. [PMID: 25101664 PMCID: PMC4125091 DOI: 10.1371/journal.pgen.1004526] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [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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20
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Pérez Rodriguez MA, Guo X. Biomacromolecular localization in bacterial cells by the diffusion and capture mechanism. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-012-0596-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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21
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Pedrido ME, de Oña P, Ramirez W, Leñini C, Goñi A, Grau R. Spo0A links de novo fatty acid synthesis to sporulation and biofilm development in Bacillus subtilis. Mol Microbiol 2012; 87:348-67. [PMID: 23170957 DOI: 10.1111/mmi.12102] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2012] [Indexed: 11/25/2022]
Abstract
During sporulation in Bacillus subtilis, the committed-cell undergoes substantial membrane rearrangements to generate two cells of different sizes and fates: the mother cell and the forespore. Here, we demonstrate that the master transcription factor Spo0A reactivates lipid synthesis during development. Maximal Spo0A-dependent lipid synthesis occurs during the key stages of asymmetric division and forespore engulfment. Spo0A reactivates the accDA operon that encodes the carboxylase component of the acetyl-CoA carboxylase enzyme, which catalyses the first and rate-limiting step in de novo lipid biosynthesis, malonyl-CoA formation. The disruption of the Spo0A-binding box in the promoter region of accDA impairs its transcriptional reactivation and blocks lipid synthesis. The Spo0A-insensitive accDA(0A) cells were proficient in planktonic growth but defective in sporulation (σ(E) activation) and biofilm development (cell cluster formation and water repellency). Exogenous fatty acid supplementation to accDA(0A) cells overcomes their inability to synthesize lipids during development and restores sporulation and biofilm proficiencies. The transient exclusion of the lipid synthesis regulon from the forespore and the known compartmentalization of Spo0A and ACP in the mother cell suggest that de novo lipid synthesis is confined to the mother cell. The significance of the Spo0A-controlled de novo lipid synthesis during B. subtilis development is discussed.
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Affiliation(s)
- María E Pedrido
- Departamento de Microbiología, Universidad Nacional de Rosario, CONICET, Argentina
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22
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Galperin MY, Mekhedov SL, Puigbo P, Smirnov S, Wolf YI, Rigden DJ. Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ Microbiol 2012; 14:2870-90. [PMID: 22882546 PMCID: PMC3533761 DOI: 10.1111/j.1462-2920.2012.02841.x] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Three classes of low-G+C Gram-positive bacteria (Firmicutes), Bacilli, Clostridia and Negativicutes, include numerous members that are capable of producing heat-resistant endospores. Spore-forming firmicutes include many environmentally important organisms, such as insect pathogens and cellulose-degrading industrial strains, as well as human pathogens responsible for such diseases as anthrax, botulism, gas gangrene and tetanus. In the best-studied model organism Bacillus subtilis, sporulation involves over 500 genes, many of which are conserved among other bacilli and clostridia. This work aimed to define the genomic requirements for sporulation through an analysis of the presence of sporulation genes in various firmicutes, including those with smaller genomes than B. subtilis. Cultivable spore-formers were found to have genomes larger than 2300 kb and encompass over 2150 protein-coding genes of which 60 are orthologues of genes that are apparently essential for sporulation in B. subtilis. Clostridial spore-formers lack, among others, spoIIB, sda, spoVID and safA genes and have non-orthologous displacements of spoIIQ and spoIVFA, suggesting substantial differences between bacilli and clostridia in the engulfment and spore coat formation steps. Many B. subtilis sporulation genes, particularly those encoding small acid-soluble spore proteins and spore coat proteins, were found only in the family Bacillaceae, or even in a subset of Bacillus spp. Phylogenetic profiles of sporulation genes, compiled in this work, confirm the presence of a common sporulation gene core, but also illuminate the diversity of the sporulation processes within various lineages. These profiles should help further experimental studies of uncharacterized widespread sporulation genes, which would ultimately allow delineation of the minimal set(s) of sporulation-specific genes in Bacilli and Clostridia.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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23
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Weak transcription of the cry1Ac gene in nonsporulating Bacillus thuringiensis cells. Appl Environ Microbiol 2012; 78:6466-74. [PMID: 22773626 DOI: 10.1128/aem.01229-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cry1Ac gene of Bacillus thuringiensis subsp. kurstaki HD-73 (B. thuringiensis HD-73) is a typical example of a sporulation-dependent crystal gene and is controlled by sigma E and sigma K during sporulation. To monitor the production and accumulation of Cry1Ac at the cellular level, we developed a green fluorescent protein-based reporter system. The production of Cry1Ac was monitored in spo0A, sigE, and sigK mutants, and these mutants were able to express the Cry1Ac-green fluorescent protein fusion protein. In nonsporulating B. thuringiensis HD-73 cells, low-level expression of cry1Ac was also observed. Reverse transcription-PCR and Western blotting results confirmed that the cry1Ac promoter has low activity in nonsporulating B. thuringiensis cells. A beta-galactosidase assay demonstrated that the transcription of the cry1Ac gene during exponential and transition phases is positively regulated by Spo0A. Additional bioassay results indicated that spo0A and sigE mutants containing the cry1Ac-gfp fusion exhibited insecticidal activity against Plutella xylostella larvae.
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24
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RefZ facilitates the switch from medial to polar division during spore formation in Bacillus subtilis. J Bacteriol 2012; 194:4608-18. [PMID: 22730127 DOI: 10.1128/jb.00378-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During sporulation, Bacillus subtilis redeploys the division protein FtsZ from midcell to the cell poles, ultimately generating an asymmetric septum. Here, we describe a sporulation-induced protein, RefZ, that facilitates the switch from a medial to a polar FtsZ ring placement. The artificial expression of RefZ during vegetative growth converts FtsZ rings into FtsZ spirals, arcs, and foci, leading to filamentation and lysis. Mutations in FtsZ specifically suppress RefZ-dependent division inhibition, suggesting that RefZ may target FtsZ. During sporulation, cells lacking RefZ are delayed in polar FtsZ ring formation, spending more time in the medial and transition stages of FtsZ ring assembly. A RefZ-green fluorescent protein (GFP) fusion localizes in weak polar foci at the onset of sporulation and as a brighter midcell focus at the time of polar division. RefZ has a TetR DNA binding motif, and point mutations in the putative recognition helix disrupt focus formation and abrogate cell division inhibition. Finally, chromatin immunoprecipitation assays identified sites of RefZ enrichment in the origin region and near the terminus. Collectively, these data support a model in which RefZ helps promote the switch from medial to polar division and is guided by the organization of the chromosome. Models in which RefZ acts as an activator of FtsZ ring assembly near the cell poles or as an inhibitor of the transient medial ring at midcell are discussed.
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25
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Iber D. Inferring Biological Mechanisms by Data-Based Mathematical Modelling: Compartment-Specific Gene Activation during Sporulation in Bacillus subtilis as a Test Case. Adv Bioinformatics 2012; 2011:124062. [PMID: 22312331 PMCID: PMC3270535 DOI: 10.1155/2011/124062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 10/12/2011] [Accepted: 11/03/2011] [Indexed: 11/27/2022] Open
Abstract
Biological functionality arises from the complex interactions of simple components. Emerging behaviour is difficult to recognize with verbal models alone, and mathematical approaches are important. Even few interacting components can give rise to a wide range of different responses, that is, sustained, transient, oscillatory, switch-like responses, depending on the values of the model parameters. A quantitative comparison of model predictions and experiments is therefore important to distinguish between competing hypotheses and to judge whether a certain regulatory behaviour is at all possible and plausible given the observed type and strengths of interactions and the speed of reactions. Here I will review a detailed model for the transcription factor σ(F), a regulator of cell differentiation during sporulation in Bacillus subtilis. I will focus in particular on the type of conclusions that can be drawn from detailed, carefully validated models of biological signaling networks. For most systems, such detailed experimental information is currently not available, but accumulating biochemical data through technical advances are likely to enable the detailed modelling of an increasing number of pathways. A major challenge will be the linking of such detailed models and their integration into a multiscale framework to enable their analysis in a larger biological context.
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Affiliation(s)
- Dagmar Iber
- Department for Biosystems Science and Engineering, Switzerland and Swiss Institute of Bioinformatics (SIB), ETH Zurich, Mattenstraße 26, Basel 4058, Switzerland
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26
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Radhakrishnan SK, Viollier P. Two-in-one: bifunctional regulators synchronizing developmental events in bacteria. Trends Cell Biol 2012; 22:14-21. [DOI: 10.1016/j.tcb.2011.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 09/15/2011] [Accepted: 09/15/2011] [Indexed: 10/16/2022]
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27
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Abstract
Spores of Bacillus subtilis are encased in a protective coat made up of at least 70 proteins. The structure of the spore coat has been examined using a variety of genetic, imaging and biochemical techniques; however, the majority of these studies have focused on mature spores. In this study we use a library of 41 spore coat proteins fused to the green fluorescent protein to examine spore coat morphogenesis over the time-course of sporulation. We found considerable diversity in the localization dynamics of coat proteins and were able to establish six classes based on localization kinetics. Localization dynamics correlate well with the known transcriptional regulators of coat gene expression. Previously, we described the existence of multiple layers in the mature spore coat. Here, we find that the spore coat initially assembles a scaffold that is organized into multiple layers on one pole of the spore. The coat then encases the spore in multiple co-ordinated waves. Encasement is driven, at least partially, by transcription of coat genes and deletion of sporulation transcription factors arrests encasement. We also identify the trans-compartment SpoIIIAH-SpoIIQ channel as necessary for encasement. This is the first demonstration of a forespore contribution to spore coat morphogenesis.
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Affiliation(s)
- Peter T McKenney
- New York University, Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place, 8th floor, New York, NY 10003, USA
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28
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Levdikov VM, Blagova EV, Rawlings AE, Jameson K, Tunaley J, Hart DJ, Barak I, Wilkinson AJ. Structure of the phosphatase domain of the cell fate determinant SpoIIE from Bacillus subtilis. J Mol Biol 2011; 415:343-58. [PMID: 22115775 PMCID: PMC3517971 DOI: 10.1016/j.jmb.2011.11.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 11/30/2022]
Abstract
Sporulation in Bacillus subtilis begins with an asymmetric cell division producing two genetically identical cells with different fates. SpoIIE is a membrane protein that localizes to the polar cell division sites where it causes FtsZ to relocate from mid-cell to form polar Z-rings. Following polar septation, SpoIIE establishes compartment-specific gene expression in the smaller forespore cell by dephosphorylating the anti-sigma factor antagonist SpoIIAA, leading to the release of the RNA polymerase sigma factor σF from an inhibitory complex with the anti-sigma factor SpoIIAB. SpoIIE therefore couples morphological development to differential gene expression. Here, we determined the crystal structure of the phosphatase domain of SpoIIE to 2.6 Å spacing, revealing a domain-swapped dimer. SEC-MALLS (size-exclusion chromatography with multi-angle laser light scattering) analysis however suggested a monomer as the principal form in solution. A model for the monomer was derived from the domain-swapped dimer in which 2 five-stranded β-sheets are packed against one another and flanked by α-helices in an αββα arrangement reminiscent of other PP2C-type phosphatases. A flap region that controls access of substrates to the active site in other PP2C phosphatases is diminished in SpoIIE, and this observation correlates with the presence of a single manganese ion in the active site of SpoIIE in contrast to the two or three metal ions present in other PP2C enzymes. Mapping of a catalogue of mutational data onto the structure shows a clustering of sites whose point mutation interferes with the proper coupling of asymmetric septum formation to sigma factor activation and identifies a surface involved in intramolecular signaling.
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Affiliation(s)
- Vladimir M Levdikov
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
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29
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Kuchina A, Espinar L, Garcia-Ojalvo J, Süel GM. Reversible and noisy progression towards a commitment point enables adaptable and reliable cellular decision-making. PLoS Comput Biol 2011; 7:e1002273. [PMID: 22102806 PMCID: PMC3213189 DOI: 10.1371/journal.pcbi.1002273] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Accepted: 09/29/2011] [Indexed: 02/07/2023] Open
Abstract
Cells must make reliable decisions under fluctuating extracellular conditions, but also be flexible enough to adapt to such changes. How cells reconcile these seemingly contradictory requirements through the dynamics of cellular decision-making is poorly understood. To study this issue we quantitatively measured gene expression and protein localization in single cells of the model organism Bacillus subtilis during the progression to spore formation. We found that sporulation proceeded through noisy and reversible steps towards an irreversible, all-or-none commitment point. Specifically, we observed cell-autonomous and spontaneous bursts of gene expression and transient protein localization events during sporulation. Based on these measurements we developed mathematical population models to investigate how the degree of reversibility affects cellular decision-making. In particular, we evaluated the effect of reversibility on the 1) reliability in the progression to sporulation, and 2) adaptability under changing extracellular stress conditions. Results show that reversible progression allows cells to remain responsive to long-term environmental fluctuations. In contrast, the irreversible commitment point supports reliable execution of cell fate choice that is robust against short-term reductions in stress. This combination of opposite dynamic behaviors (reversible and irreversible) thus maximizes both adaptable and reliable decision-making over a broad range of changes in environmental conditions. These results suggest that decision-making systems might employ a general hybrid strategy to cope with unpredictably fluctuating environmental conditions. Cells must continuously make decisions in response to changes in their environment. These decisions must be irreversible, to prevent cells from reverting back to unfit cellular states, but also be flexible, to allow cells to go back to their previous state upon environmental changes. Using single-cell time-lapse fluorescence microscopy, we show that these seemingly contradictory properties coexist in Bacillus subtilis cells during their progression to spore formation. We suggest, on the basis of a mathematical population model, that reversible progression towards the irreversible decision to sporulate optimizes respectively adaptability and reliability of decision-making over a broad range of changes in environmental conditions.
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Affiliation(s)
- Anna Kuchina
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Lorena Espinar
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Terrassa, Spain
| | - Jordi Garcia-Ojalvo
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Terrassa, Spain
| | - Gürol M. Süel
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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Localization and cellular amounts of the WalRKJ (VicRKX) two-component regulatory system proteins in serotype 2 Streptococcus pneumoniae. J Bacteriol 2010; 192:4388-94. [PMID: 20622066 DOI: 10.1128/jb.00578-10] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The WalRK two-component regulatory system coordinates gene expression that maintains cell wall homeostasis and responds to antibiotic stress in low-GC Gram-positive bacteria. Phosphorylated WalR (VicR) of the major human respiratory pathogen Streptococcus pneumoniae (WalR(Spn)) positively regulates transcription of several surface virulence genes and, most critically, pcsB, which encodes an essential cell division protein. Despite numerous studies of several species, little is known about the signals sensed by the WalK histidine kinase or the function of the WalJ ancillary protein encoded in the walRK(Spn) operon. To better understand the functions of the WalRKJ(Spn) proteins in S. pneumoniae, we performed experiments to determine their cellular localization and amounts. In contrast to WalK from Bacillus subtilis (WalK(Bsu)), which is localized at division septa, immunofluorescence microscopy showed that WalK(Spn) is distributed throughout the cell periphery. WalJ(Spn) is also localized to the cell surface periphery, whereas WalR(Spn) was found to be localized in the cytoplasm around the nucleoid. In fractionation experiments, WalR(Spn) was recovered from the cytoplasmic fraction, while WalK(Spn) and the majority of WalJ(Spn) were recovered from the cell membrane fraction. This fractionation is consistent with the localization patterns observed. Lastly, we determined the cellular amounts of WalRKJ(Spn) by quantitative Western blotting. The WalR(Spn) response regulator is relatively abundant and present at levels of approximately 6,200 monomers per cell, which are approximately 14-fold greater than the amount of the WalK(Spn) histidine kinase, which is present at approximately 460 dimers (920 monomers) per cell. We detected approximately 1,200 monomers per cell of WalJ(Spn) ancillary protein, similar to the amount of WalK(Spn).
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Abstract
Like their eukaryotic counterparts, bacterial cells have a highly organized internal architecture. Here, we address the question of how proteins localize to particular sites in the cell and how they do so in a dynamic manner. We consider the underlying mechanisms that govern the positioning of proteins and protein complexes in the examples of the divisome, polar assemblies, cytoplasmic clusters, cytoskeletal elements, and organelles. We argue that geometric cues, self-assembly, and restricted sites of assembly are all exploited by the cell to specifically localize particular proteins that we refer to as anchor proteins. These anchor proteins in turn govern the localization of a whole host of additional proteins. Looking ahead, we speculate on the existence of additional mechanisms that contribute to the organization of bacterial cells, such as the nucleoid, membrane microdomains enriched in specific lipids, and RNAs with positional information.
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García Véscovi E, Sciara MI, Castelli ME. Two component systems in the spatial program of bacteria. Curr Opin Microbiol 2010; 13:210-8. [PMID: 20138002 DOI: 10.1016/j.mib.2009.12.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 12/29/2009] [Accepted: 12/31/2009] [Indexed: 11/26/2022]
Abstract
Despite being considered a relatively simple form of life, bacteria have revealed a high degree of structural organization, with the spatial destination of their components precisely regulated within the cell. Nevertheless, the primary signals that dictate differential distribution of cellular building blocks and physiological processes remain in most cases largely undisclosed. Signal transduction systems are no exception within this three-dimensional organization and two-component systems (TCS) involved in controlling cell division, differentiation, chemotaxis and virulence show specific and/or dynamic localization, engaging in the spatial program of the bacterial cell.
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Affiliation(s)
- Eleonora García Véscovi
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina.
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33
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Doan T, Morlot C, Meisner J, Serrano M, Henriques AO, Moran CP, Rudner DZ. Novel secretion apparatus maintains spore integrity and developmental gene expression in Bacillus subtilis. PLoS Genet 2009; 5:e1000566. [PMID: 19609349 PMCID: PMC2703783 DOI: 10.1371/journal.pgen.1000566] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 06/18/2009] [Indexed: 11/23/2022] Open
Abstract
Sporulation in Bacillus subtilis involves two cells that follow separate but coordinately regulated developmental programs. Late in sporulation, the developing spore (the forespore) resides within a mother cell. The regulation of the forespore transcription factor σG that acts at this stage has remained enigmatic. σG activity requires eight mother-cell proteins encoded in the spoIIIA operon and the forespore protein SpoIIQ. Several of the SpoIIIA proteins share similarity with components of specialized secretion systems. One of them resembles a secretion ATPase and we demonstrate that the ATPase motifs are required for σG activity. We further show that the SpoIIIA proteins and SpoIIQ reside in a multimeric complex that spans the two membranes surrounding the forespore. Finally, we have discovered that these proteins are all required to maintain forespore integrity. In their absence, the forespore develops large invaginations and collapses. Importantly, maintenance of forespore integrity does not require σG. These results support a model in which the SpoIIIA-SpoIIQ proteins form a novel secretion apparatus that allows the mother cell to nurture the forespore, thereby maintaining forespore physiology and σG activity during spore maturation. During development, cell–cell signaling pathways coordinate programs of gene expression in neighboring cells. Cell–cell signaling is typically achieved by the secretion of a signaling ligand followed by its binding to a membrane receptor on the surface of a neighboring cell (or cells). The ligand-bound receptor directly or indirectly triggers transcription factor activation. Here we present evidence for a non-canonical signaling pathway that links developmental gene expression in the forespore and mother cell during spore formation in Bacillus subtilis. Our data support a model in which a novel secretion system is assembled in the double membrane that encases the spore within the mother cell. This apparatus is not involved in transducing a specific activating signal but rather allows the mother cell to nurture the spore and thereby maintain the spore program of developmental gene expression.
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Affiliation(s)
- Thierry Doan
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Cecile Morlot
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jeffrey Meisner
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Monica Serrano
- Microbial Development Group, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriano O. Henriques
- Microbial Development Group, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Charles P. Moran
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - David Z. Rudner
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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34
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Bacterial landlines: contact-dependent signaling in bacterial populations. Curr Opin Microbiol 2009; 12:177-81. [PMID: 19246237 DOI: 10.1016/j.mib.2009.01.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Accepted: 01/27/2009] [Indexed: 11/21/2022]
Abstract
Bacterial populations utilize a variety of signaling strategies to exchange information, including the secretion of quorum-sensing molecules and contact-dependent signaling cascades. Although quorum sensing has received the bulk of attention for many years, contact-dependent signaling is forging a niche in the research world with the identification of novel systems and the emergence of more mechanistic data. Contact-dependent signaling is probably a common strategy by which bacteria in close contact, such as within biofilms, can modulate the growth and behavior of both siblings and competitors. Ongoing work with diverse bacterial systems, including Myxococcus xanthus, pathogenic Escherichia coli strains, Bacillus subtilis, and dissimilatory metal-reducing soil bacteria, is providing increasingly detailed insight into the dynamic mechanisms and potential of contact-dependent signaling processes.
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Guberman JM, Fay A, Dworkin J, Wingreen NS, Gitai Z. PSICIC: noise and asymmetry in bacterial division revealed by computational image analysis at sub-pixel resolution. PLoS Comput Biol 2008; 4:e1000233. [PMID: 19043544 PMCID: PMC2581597 DOI: 10.1371/journal.pcbi.1000233] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Accepted: 10/17/2008] [Indexed: 11/18/2022] Open
Abstract
Live-cell imaging by light microscopy has demonstrated that all cells are spatially and temporally organized. Quantitative, computational image analysis is an important part of cellular imaging, providing both enriched information about individual cell properties and the ability to analyze large datasets. However, such studies are often limited by the small size and variable shape of objects of interest. Here, we address two outstanding problems in bacterial cell division by developing a generally applicable, standardized, and modular software suite termed Projected System of Internal Coordinates from Interpolated Contours (PSICIC) that solves common problems in image quantitation. PSICIC implements interpolated-contour analysis for accurate and precise determination of cell borders and automatically generates internal coordinate systems that are superimposable regardless of cell geometry. We have used PSICIC to establish that the cell-fate determinant, SpoIIE, is asymmetrically localized during Bacillus subtilis sporulation, thereby demonstrating the ability of PSICIC to discern protein localization features at sub-pixel scales. We also used PSICIC to examine the accuracy of cell division in Esherichia coli and found a new role for the Min system in regulating division-site placement throughout the cell length, but only prior to the initiation of cell constriction. These results extend our understanding of the regulation of both asymmetry and accuracy in bacterial division while demonstrating the general applicability of PSICIC as a computational approach for quantitative, high-throughput analysis of cellular images.
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Affiliation(s)
- Jonathan M. Guberman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Allison Fay
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Jonathan Dworkin
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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