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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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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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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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Membrane protein engineering to the rescue. Biochem Soc Trans 2018; 46:1541-1549. [PMID: 30381335 DOI: 10.1042/bst20180140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023]
Abstract
The inherent hydrophobicity of membrane proteins is a major barrier to membrane protein research and understanding. Their low stability and solubility in aqueous environments coupled with poor expression levels make them a challenging area of research. For many years, the only way of working with membrane proteins was to optimise the environment to suit the protein, through the use of different detergents, solubilising additives, and other adaptations. However, with innovative protein engineering methodologies, the membrane proteins themselves are now being adapted to suit the environment. This mini-review looks at the types of adaptations which are applied to membrane proteins from a variety of different fields, including water solubilising fusion tags, thermostabilising mutation screening, scaffold proteins, stabilising protein chimeras, and isolating water-soluble domains.
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Cendrowicz E, de Sousa Borges A, Kopacz M, Scheffers DJ. Metal-dependent SpoIIE oligomerization stabilizes FtsZ during asymmetric division in Bacillus subtilis. PLoS One 2017; 12:e0174713. [PMID: 28358838 PMCID: PMC5373596 DOI: 10.1371/journal.pone.0174713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 03/14/2017] [Indexed: 11/26/2022] Open
Abstract
SpoIIE is a bifunctional protein involved in asymmetric septum formation and in activation of the forespore compartment-specific transcription factor σF through dephosphorylation of SpoIIAA-P. The phosphatase activity of SpoIIE requires Mn2+ as a metal cofactor. Here, we show that the presence of a metal cofactor also influences SpoIIE oligomerization and asymmetric septum formation. Absence of Mn2+ from sporulation medium results in a delay of the formation of polar FtsZ-rings, similar to a spoIIE null mutant. We purified the entire cytoplasmic part of the SpoIIE protein, and show that the protein copurifies with bound metals. Metal binding both stimulates SpoIIE oligomerization, and results in the formation of larger oligomeric structures. The presence of SpoIIE oligomers reduces FtsZ GTP hydrolysis activity and stabilizes FtsZ polymers in a light scattering assay. Combined, these results indicate that metal binding is not just required for SpoIIE phosphatase activity but also is important for SpoIIE's role in asymmetric septum formation.
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Affiliation(s)
- Ewa Cendrowicz
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Anabela de Sousa Borges
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Malgorzata Kopacz
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Dirk-Jan Scheffers
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- * E-mail:
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ESPRIT: A Method for Defining Soluble Expression Constructs in Poorly Understood Gene Sequences. Methods Mol Biol 2017; 1586:45-63. [PMID: 28470598 DOI: 10.1007/978-1-4939-6887-9_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Production of soluble, purifiable domains or multi-domain fragments of proteins is a prerequisite for structural biology and other applications. When target sequences are poorly annotated, or when there are few similar sequences available for alignments, identification of domains can be problematic. A method called expression of soluble proteins by random incremental truncation (ESPRIT) addresses this problem by high-throughput automated screening of tens of thousands of enzymatically truncated gene fragments. Rare soluble constructs are identified by experimental screening, and the boundaries revealed by DNA sequencing.
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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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Hart DJ, Waldo GS. Library methods for structural biology of challenging proteins and their complexes. Curr Opin Struct Biol 2013; 23:403-8. [PMID: 23602357 DOI: 10.1016/j.sbi.2013.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 03/18/2013] [Accepted: 03/19/2013] [Indexed: 02/08/2023]
Abstract
Genetic engineering of constructs to improve solubility or stability is a common approach, but it is often unclear how to obtain improvements. When the domain composition of a target is poorly understood, or if there are insufficient structure data to guide sited directed mutagenesis, long iterative phases of subcloning or mutation and expression often prove unsuccessful despite much effort. Random library approaches can offer a solution to this problem and involve construction of large libraries of construct variants that are analysed via screens or selections for the desired phenotype. Huge improvements in construct behaviour can be achieved rapidly with no requirement for prior knowledge of the target. Here we review the development of these experimental strategies and recent successes.
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Affiliation(s)
- Darren J Hart
- EMBL Grenoble Outstation and Unit of Virus Host-Cell Interactions, UMI3265 UJF-EMBL-CNRS, Grenoble, France.
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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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Yumerefendi H, Desravines DC, Hart DJ. Library-based methods for identification of soluble expression constructs. Methods 2011; 55:38-43. [DOI: 10.1016/j.ymeth.2011.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 06/09/2011] [Accepted: 06/11/2011] [Indexed: 01/10/2023] Open
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An Y, Meresse P, Mas PJ, Hart DJ. CoESPRIT: a library-based construct screening method for identification and expression of soluble protein complexes. PLoS One 2011; 6:e16261. [PMID: 21364980 PMCID: PMC3043051 DOI: 10.1371/journal.pone.0016261] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Accepted: 12/13/2010] [Indexed: 11/29/2022] Open
Abstract
Structural and biophysical studies of protein complexes require multi-milligram quantities of soluble material. Subunits are often unstable when expressed separately so co-expression strategies are commonly employed since in vivo complex formation can provide stabilising effects. Defining constructs for subunit co-expression experiments is difficult if the proteins are poorly understood. Even more problematic is when subunit polypeptide chains co-fold since individually they do not have predictable domains. We have developed CoESPRIT, a modified version of the ESPRIT random library construct screen used previously on single proteins, to express soluble protein complexes. A random library of target constructs is screened against a fixed bait protein to identify stable complexes. In a proof-of-principle study, C-terminal fragments of the influenza polymerase PB2 subunit containing folded domains were isolated using importin alpha as bait. Separately, a C-terminal fragment of the PB1 subunit was used as bait to trap N-terminal fragments of PB2 resulting in co-folded complexes. Subsequent expression of the target protein without the bait indicates whether the target is independently stable, or co-folds with its partner. This highly automated method provides an efficient strategy for obtaining recombinant protein complexes at yields compatible with structural, biophysical and functional studies.
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Affiliation(s)
- Yingfeng An
- Grenoble Outstation, European Molecular Biology Laboratory, BP181, Grenoble, France
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
| | - Patrick Meresse
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
| | - Philippe J. Mas
- Grenoble Outstation, European Molecular Biology Laboratory, BP181, Grenoble, France
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
| | - Darren J. Hart
- Grenoble Outstation, European Molecular Biology Laboratory, BP181, Grenoble, France
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
- * E-mail:
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