1
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Hinrichs R, Graumann PL. Visual Evidence for the Recruitment of Four Enzymes with RNase Activity to the Bacillus subtilis Replication Forks. Cells 2024; 13:1381. [PMID: 39195267 DOI: 10.3390/cells13161381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 08/29/2024] Open
Abstract
Removal of RNA/DNA hybrids for the maturation of Okazaki fragments on the lagging strand, or due to misincorporation of ribonucleotides by DNA polymerases, is essential for all types of cells. In prokaryotic cells such as Escherichia coli, DNA polymerase 1 and RNase HI are supposed to remove RNA from Okazaki fragments, but many bacteria lack HI-type RNases, such as Bacillus subtilis. Previous work has demonstrated in vitro that four proteins are able to remove RNA from RNA/DNA hybrids, but their actual contribution to DNA replication is unclear. We have studied the dynamics of DNA polymerase A (similar to Pol 1), 5'->3' exonuclease ExoR, and the two endoribonucleases RNase HII and HIII in B. subtilis using single-molecule tracking. We found that all four enzymes show a localization pattern similar to that of replicative DNA helicase. By scoring the distance of tracks to replication forks, we found that all four enzymes are enriched at DNA replication centers. After inducing UV damage, RNase HIII was even more strongly recruited to the replication forks, and PolA showed a more static behavior, indicative of longer binding events, whereas RNase HII and ExoR showed no response. Inhibition of replication by 6(p hydroxyphenylazo)-uracil (HPUra) demonstrated that both RNase HII and RNase HIII are directly involved in the replication. We found that the absence of ExoR increases the likelihood of RNase HIII at the forks, indicating that substrate availability rather than direct protein interactions may be a major driver for the recruitment of RNases to the lagging strands. Thus, B. subtilis replication forks appear to be an intermediate between E. coli type and eukaryotic replication forks and employ a multitude of RNases, rather than any dedicated enzyme for RNA/DNA hybrid removal.
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Affiliation(s)
- Rebecca Hinrichs
- Centre for Synthetic Microbiology (SYNMIKRO), Philipps Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
| | - Peter L Graumann
- Centre for Synthetic Microbiology (SYNMIKRO), Philipps Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
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2
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Fiedler SM, Graumann PL. Dynamics of cell wall-binding proteins at a single molecule level: B. subtilis autolysins show different kinds of motion. Mol Biol Cell 2024; 35:ar55. [PMID: 38381561 PMCID: PMC11064672 DOI: 10.1091/mbc.e23-10-0387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/23/2024] [Accepted: 02/13/2024] [Indexed: 02/23/2024] Open
Abstract
The bacterial cell wall is a meshwork of crosslinked peptidoglycan strands, with a thickness of up to 50 nm in Firmicutes. Little is known about how proteins move through the cell wall to find sites of enzymatic activity. Cell wall synthesis for cell elongation involves the integration of new peptidoglycan strands by integral membrane proteins, as well as the degradation of existing strands by so-called autolysins, soluble proteins that are secreted through the cell membrane. Autolysins comprise different classes of proteases and glucanases and mostly contain cell-wall binding domains in addition to their catalytic domain. We have studied dynamics of Bacillus subtilis autolysins LytC, a major endopeptidase required for lateral cell wall growth, and LytF, a peptidase acting at the newly formed division site in order to achieve separation of daughter cells. We show that both proteins, fused to moxVenus are present as three distinct populations of different diffusion constants. The fastest population is compatible with free diffusion in a crowded liquid environment, that is similar to that of cytosolic enzymes, likely reflecting autolysins diffusing through the periplasm. The medium mobile fraction can be explained by constrained motion through a polymeric substance, indicating mobility of autolysins through the wall similar to that of DNA-binding proteins within the nucleoid. The slow-mobile fraction are most likely autolysins bound to their specific substrate sites. We show that LytF is more static during exponential phase, while LytC appears to be more active during the transition to stationary phase. Both autolysins became more static in backgrounds lacking redundant other autolysins, suggesting stochastic competition for binding sites. On the other hand, lack of inhibitor IseA or autolysin CwlS lead to an altered preference for polar localization of LytF within the cell wall, revealing that inhibitors and autolysins also affect each other's pattern of localization, in addition to their activity.
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Affiliation(s)
- Svenja M. Fiedler
- Fachbereich Chemie und Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein Strasse 4, 35043 Marburg, Germany
| | - Peter L. Graumann
- Fachbereich Chemie und Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein Strasse 4, 35043 Marburg, Germany
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3
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Fiedler SM, Graumann PL. B. subtilis Sec and Srp Systems Show Dynamic Adaptations to Different Conditions of Protein Secretion. Cells 2024; 13:377. [PMID: 38474341 DOI: 10.3390/cells13050377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/04/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
SecA is a widely conserved ATPase that drives the secretion of proteins across the cell membrane via the SecYEG translocon, while the SRP system is a key player in the insertion of membrane proteins via SecYEG. How SecA gains access to substrate proteins in Bacillus subtilis cells and copes with an increase in substrate availability during biotechnologically desired, high-level expression of secreted proteins is poorly understood. Using single molecule tracking, we found that SecA localization closely mimics that of ribosomes, and its molecule dynamics change similarly to those of ribosomes after inhibition of transcription or translation. These data suggest that B. subtilis SecA associates with signal peptides as they are synthesized at the ribosome, similar to the SRP system. In agreement with this, SecA is a largely mobile cytosolic protein; only a subset is statically associated with the cell membrane, i.e., likely with the Sec translocon. SecA dynamics were considerably different during the late exponential, transition, and stationary growth phases, revealing that single molecule dynamics considerably alter during different genetic programs in cells. During overproduction of a secretory protein, AmyE, SecA showed the strongest changes during the transition phase, i.e., where general protein secretion is high. To investigate whether the overproduction of AmyE also has an influence on other proteins that interact with SecYEG, we analyzed the dynamics of SecDF, YidC, and FtsY with and without AmyE overproduction. SecDF and YidC did not reveal considerable differences in single molecule dynamics during overexpression, while the SRP component FtsY changed markedly in its behavior and became more statically engaged. These findings indicate that the SRP pathway becomes involved in protein secretion upon an overload of proteins carrying a signal sequence. Thus, our data reveal high plasticity of the SecA and SRP systems in dealing with different needs for protein secretion.
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Affiliation(s)
- Svenja M Fiedler
- Fachbereich Chemie und Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein Straße 4, 35043 Marburg, Germany
| | - Peter L Graumann
- Fachbereich Chemie und Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein Straße 4, 35043 Marburg, Germany
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4
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Pöhl S, Osorio-Valeriano M, Cserti E, Harberding J, Hernandez-Tamayo R, Biboy J, Sobetzko P, Vollmer W, Graumann PL, Thanbichler M. A dynamic bactofilin cytoskeleton cooperates with an M23 endopeptidase to control bacterial morphogenesis. eLife 2024; 12:RP86577. [PMID: 38294932 PMCID: PMC10945521 DOI: 10.7554/elife.86577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
Bactofilins have emerged as a widespread family of cytoskeletal proteins with important roles in bacterial morphogenesis, but their precise mode of action is still incompletely understood. In this study, we identify the bactofilin cytoskeleton as a key regulator of cell growth in the stalked budding alphaproteobacterium Hyphomonas neptunium. We show that, in this species, bactofilin polymers localize dynamically to the stalk base and the bud neck, with their absence leading to unconstrained growth of the stalk and bud compartments, indicating a central role in the spatial regulation of cell wall biosynthesis. Database searches reveal that bactofilin genes are often clustered with genes for cell wall hydrolases of the M23 peptidase family, suggesting a functional connection between these two types of proteins. In support of this notion, we find that the H. neptunium M23 peptidase homolog LmdC interacts directly with bactofilin in vitro and is required for proper cell shape in vivo. Complementary studies in the spiral-shaped alphaproteobacterium Rhodospirillum rubrum again reveal a close association of its bactofilin and LmdC homologs, which co-localize at the inner curve of the cell, modulating the degree of cell curvature. Collectively, these findings demonstrate that bactofilins and M23 peptidases form a conserved functional module that promotes local changes in the mode of cell wall biosynthesis, thereby driving cell shape determination in morphologically complex bacteria.
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Affiliation(s)
- Sebastian Pöhl
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
| | - Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Emöke Cserti
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
| | - Jannik Harberding
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
| | - Rogelio Hernandez-Tamayo
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Department of Chemistry, University of MarburgMarburgGermany
- Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle UniversityNewcastle upon TyneUnited Kingdom
| | | | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle UniversityNewcastle upon TyneUnited Kingdom
- Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
| | - Peter L Graumann
- Department of Chemistry, University of MarburgMarburgGermany
- Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
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5
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Hammerl DR, Graumann PL. Visualization, Quantification, and Statistical Evaluation of Dynamics for DNA-Binding Proteins in Bacteria by Single-Molecule Tracking. Methods Mol Biol 2024; 2819:189-223. [PMID: 39028508 DOI: 10.1007/978-1-0716-3930-6_10] [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] [Indexed: 07/20/2024]
Abstract
All DNA-binding proteins in vivo exist as a population of freely diffusing molecules and of DNA-bound molecules. The molecules bound to DNA can be split into specifically/tightly and nonspecifically bound proteins. Single-molecule tracking (SMT) is a method allowing to visualize protein dynamics in living cells, revealing their behavior in terms of mode of motion, diffusion coefficient/speed, change of dwell times, and unveiling preferred subcellular sites of dwelling. Bleaching-type SMT or fluorescent protein-tagged SMT involves rapid laser-induced bleaching of most fluorophore-labeled molecules. The remaining single fluorescent proteins are then continuously tracked. The trajectories of several fluorescent molecules per cell for a population of cells are analyzed and combined to permit a robust analysis of average behavior of single molecules in live cells, including analyses of protein dynamics in mutant cells or cells exposed to changes in environmental conditions.In this chapter, we describe the preparation of Bacillus subtilis cells, the recording of movies of those cells expressing a monomeric variant of a yellow fluorescent protein (mNeonGreen) fused to a protein of choice, and the subsequent curation of the movie data including the statistical analysis of the protein dynamics. We present a short overview of the analysis program SMTracker 2.0, highlighting its ability to analyze SMT data by non-expert scientists.
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Affiliation(s)
- Daniel R Hammerl
- Zentrum für Synthetische Mikrobiologie (SYNMIKRO), AG Graumann, Marburg, Germany
| | - Peter L Graumann
- Zentrum für Synthetische Mikrobiologie (SYNMIKRO), AG Graumann, Marburg, Germany.
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6
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Haq IU, Müller P, Brantl S. A comprehensive study of the interactions in the B. subtilis degradosome with special emphasis on the role of the small proteins SR1P and SR7P. Mol Microbiol 2024; 121:40-52. [PMID: 37994189 DOI: 10.1111/mmi.15195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/24/2023]
Abstract
Here, we employ coelution experiments and far-western blotting to identify stable interactions between the main components of the B. subtilis degradosome and the small proteins SR1P and SR7P. Our data indicate that B. subtilis has a degradosome comprising at least RNases Y and PnpA, enolase, phosphofructokinase, glycerol-3-phosphate dehydrogenase GapA, and helicase CshA that can be co-purified without cross-linking. All interactions were corroborated by far-western blotting with proteins purified from E. coli. Previously, we discovered that stress-induced SR7P binds enolase to enhance its interaction with and activity of enolase-bound RNase Y (RnY), while SR1P transcribed under gluconeogenic conditions interacts with GapA to stimulate its interaction with and the activity of RnjA (RnjA). We show that SR1P can directly bind RnjA, RnY, and PnpA independently of GapA, whereas SR7P only interacts with enolase. Northern blotting suggests that the degradation of individual RNAs in B. subtilis under gluconeogenic or stress conditions depends on either RnjA or RnY alone or on RnjA-SR1P, RnY-SR1P, or RnY-Eno. In vitro degradation assays with RnY or RnjA substrates corroborate the in vivo role of SR1P. Currently, it is unknown which substrate property is decisive for the utilization of one of the complexes.
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Affiliation(s)
- Inam Ul Haq
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut, AG Bakteriengenetik, Jena, Germany
| | - Peter Müller
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut, AG Bakteriengenetik, Jena, Germany
| | - Sabine Brantl
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut, AG Bakteriengenetik, Jena, Germany
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7
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Strach M, Koch F, Fiedler S, Liebeton K, Graumann PL. Protein secretion zones during overexpression of amylase within the Gram-positive cell wall. BMC Biol 2023; 21:206. [PMID: 37794427 PMCID: PMC10552229 DOI: 10.1186/s12915-023-01684-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 08/16/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Whereas the translocation of proteins across the cell membrane has been thoroughly investigated, it is still unclear how proteins cross the cell wall in Gram-positive bacteria, which are widely used for industrial applications. We have studied the secretion of α-amylase AmyE within two different Bacillus strains, B. subtilis and B. licheniformis. RESULTS We show that a C-terminal fusion of AmyE with the fluorescent reporter mCherry is secreted via discrete patches showing very low dynamics. These are visible at many places within the cell wall for many minutes. Expression from a high copy number plasmid was required to be able to see these structures we term "secretion zones". Zones corresponded to visualized AmyE activity on the surface of cells, showing that they release active enzymes. They overlapped with SecA signals but did not frequently co-localize with the secretion ATPase. Single particle tracking showed higher dynamics of SecA and of SecDF, involved in AmyE secretion, at the cell membrane than AmyE. These experiments suggest that SecA initially translocates AmyE molecules through the cell membrane, and then diffuses to a different translocon. Single molecule tracking of SecA suggests the existence of three distinct diffusive states of SecA, which change during AmyE overexpression, but increased AmyE secretion does not appear to overwhelm the system. CONCLUSIONS Because secretion zones were only found during the transition to and within the stationary phase, diffusion rather than passive transport based on cell wall growth from inside to outside may release AmyE and, thus, probably secreted proteins in general. Our findings suggest active transport through the cell membrane and slow, passive transition through the cell wall, at least for overexpressed proteins, in bacteria of the genus Bacillus.
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Affiliation(s)
- Manuel Strach
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, Marburg, 35032, Germany
| | - Felicitas Koch
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, Marburg, 35032, Germany
| | - Svenja Fiedler
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, Marburg, 35032, Germany
| | - Klaus Liebeton
- BRAIN Biotech AG, Darmstädter Str. 34-36, Zwingenberg, 64673, Germany
| | - Peter L Graumann
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, Marburg, 35032, Germany.
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8
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Kilb A, Burghard-Schrod M, Holtrup S, Graumann PL. Uptake of environmental DNA in Bacillus subtilis occurs all over the cell surface through a dynamic pilus structure. PLoS Genet 2023; 19:e1010696. [PMID: 37816065 PMCID: PMC10564135 DOI: 10.1371/journal.pgen.1010696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/28/2023] [Indexed: 10/12/2023] Open
Abstract
At the transition to stationary phase, a subpopulation of Bacillus subtilis cells can enter the developmental state of competence, where DNA is taken up through the cell envelope, and is processed to single stranded DNA, which is incorporated into the genome if sufficient homology between sequences exists. We show here that the initial step of transport across the cell wall occurs via a true pilus structure, with an average length of about 500 nm, which assembles at various places on the cell surface. Once assembled, the pilus remains at one position and can be retracted in a time frame of seconds. The major pilin, ComGC, was studied at a single molecule level in live cells. ComGC was found in two distinct populations, one that would correspond to ComGC freely diffusing throughout the cell membrane, and one that is relatively stationary, likely reflecting pilus-incorporated molecules. The ratio of 65% diffusing and 35% stationary ComGC molecules changed towards more stationary molecules upon addition of external DNA, while the number of pili in the population did not strongly increase. These findings suggest that the pilus assembles stochastically, but engages more pilin monomers from the membrane fraction in the presence of transport substrate. Our data support a model in which transport of environmental DNA occurs through the entire cell surface by a dynamic pilus, mediating efficient uptake through the cell wall into the periplasm, where DNA diffuses to a cell pole containing the localized transport machinery mediating passage into the cytosol.
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Affiliation(s)
- Alexandra Kilb
- Fachbereich Chemie und Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Marie Burghard-Schrod
- Fachbereich Chemie und Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Sven Holtrup
- Fachbereich Chemie und Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Peter L. Graumann
- Fachbereich Chemie und Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
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9
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Izquierdo-Martinez A, Billini M, Miguel-Ruano V, Hernández-Tamayo R, Richter P, Biboy J, Batuecas MT, Glatter T, Vollmer W, Graumann PL, Hermoso JA, Thanbichler M. DipM controls multiple autolysins and mediates a regulatory feedback loop promoting cell constriction in Caulobacter crescentus. Nat Commun 2023; 14:4095. [PMID: 37433794 DOI: 10.1038/s41467-023-39783-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Proteins with a catalytically inactive LytM-type endopeptidase domain are important regulators of cell wall-degrading enzymes in bacteria. Here, we study their representative DipM, a factor promoting cell division in Caulobacter crescentus. We show that the LytM domain of DipM interacts with multiple autolysins, including the soluble lytic transglycosylases SdpA and SdpB, the amidase AmiC and the putative carboxypeptidase CrbA, and stimulates the activities of SdpA and AmiC. Its crystal structure reveals a conserved groove, which is predicted to represent the docking site for autolysins by modeling studies. Mutations in this groove indeed abolish the function of DipM in vivo and its interaction with AmiC and SdpA in vitro. Notably, DipM and its targets SdpA and SdpB stimulate each other's recruitment to midcell, establishing a self-reinforcing cycle that gradually increases autolytic activity as cytokinesis progresses. DipM thus coordinates different peptidoglycan-remodeling pathways to ensure proper cell constriction and daughter cell separation.
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Affiliation(s)
- Adrian Izquierdo-Martinez
- Department of Biology, University of Marburg, Marburg, Germany
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Maria Billini
- Department of Biology, University of Marburg, Marburg, Germany
| | - Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Rogelio Hernández-Tamayo
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Pia Richter
- Department of Biology, University of Marburg, Marburg, Germany
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - María T Batuecas
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Timo Glatter
- Mass Spectrometry and Proteomics Facility, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Peter L Graumann
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, Germany.
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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10
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Köhler R, Sadhir I, Murray SM. ★Track: Inferred counting and tracking of replicating DNA loci. Biophys J 2023; 122:1577-1585. [PMID: 36966362 PMCID: PMC10183378 DOI: 10.1016/j.bpj.2023.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/10/2023] [Accepted: 03/22/2023] [Indexed: 03/27/2023] Open
Abstract
Fluorescent microscopy is the primary method to study DNA organization within cells. However, the variability and low signal/noise commonly associated with live-cell time-lapse imaging challenges quantitative measurements. In particular, obtaining quantitative or mechanistic insight often depends on the accurate tracking of fluorescent particles. Here, we present ★Track, an inference method that determines the most likely temporal tracking of replicating intracellular particles such DNA loci while accounting for missing, merged, and spurious detections. It allows the accurate prediction of particle copy numbers as well as the timing of replication events. We demonstrate ★Track's abilities and gain new insight into plasmid copy number control and the volume dependence of bacterial chromosome replication initiation. By enabling the accurate tracking of DNA loci, ★Track can help to uncover the mechanistic principles of chromosome organization and dynamics across a range of systems.
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Affiliation(s)
- Robin Köhler
- Max Planck Institute for Terrestrial Microbiology and LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ismath Sadhir
- Max Planck Institute for Terrestrial Microbiology and LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Seán M Murray
- Max Planck Institute for Terrestrial Microbiology and LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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11
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Hołówka J, Łebkowski T, Feddersen H, Giacomelli G, Drużka K, Makowski Ł, Trojanowski D, Broda N, Bramkamp M, Zakrzewska-Czerwińska J. Mycobacterial IHF is a highly dynamic nucleoid-associated protein that assists HupB in organizing chromatin. Front Microbiol 2023; 14:1146406. [PMID: 36960278 PMCID: PMC10028186 DOI: 10.3389/fmicb.2023.1146406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) crucially contribute to organizing bacterial chromatin and regulating gene expression. Among the most highly expressed NAPs are the HU and integration host factor (IHF) proteins, whose functional homologues, HupB and mycobacterial integration host factor (mIHF), are found in mycobacteria. Despite their importance for the pathogenicity and/or survival of tubercle bacilli, the role of these proteins in mycobacterial chromosome organization remains unknown. Here, we used various approaches, including super-resolution microscopy, to perform a comprehensive analysis of the roles of HupB and mIHF in chromosome organization. We report that HupB is a structural agent that maintains chromosome integrity on a local scale, and that the lack of this protein alters chromosome morphology. In contrast, mIHF is a highly dynamic protein that binds DNA only transiently, exhibits susceptibility to the chromosomal DNA topology changes and whose depletion leads to the growth arrest of tubercle bacilli. Additionally, we have shown that depletion of Mycobacterium smegmatis integration host factor (msIHF) leads to chromosome shrinkage and replication inhibition.
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Affiliation(s)
- Joanna Hołówka
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
- *Correspondence: Joanna Hołówka,
| | - Tomasz Łebkowski
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Helge Feddersen
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Giacomo Giacomelli
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Karolina Drużka
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Łukasz Makowski
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Damian Trojanowski
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Natalia Broda
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Marc Bramkamp
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
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12
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ATPase Activity of Bacillus subtilis RecA Affects the Dynamic Formation of RecA Filaments at DNA Double Strand Breaks. mSphere 2022; 7:e0041222. [PMID: 36321831 PMCID: PMC9769622 DOI: 10.1128/msphere.00412-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
RecA plays a central role in DNA repair and is a main actor involved in homologous recombination (HR). In vivo, RecA forms filamentous structures termed "threads," which are essential for HR, but whose nature is still ill defined. We show that RecA from Bacillus subtilis having lower ATP binding activity can still form nucleoprotein filaments in vitro, features lower dsDNA binding activity, but still retains most of wild type RecA activity in vivo. Contrarily, loss of ATPase activity strongly reduced formation of nucleoprotein filaments in vitro, and effectivity to repair double strand breaks (DSBs) in vivo. In the presence of wild type RecA protein, additionally expressed RecA with lowered ATPbinding activity only moderately affected RecA dynamics, while loss of ATPase activity leads to a large reduction of the formation of threads, as well as of their dynamic changes observed in a seconds-scale. Single molecule tracking of RecA revealed incorporation of freely diffusing and nonspecifically DNA-bound molecules into threads upon induction of a single DSB. This change of dynamics was highly perturbed in the absence of ATPase activity, revealing that filamentous forms of RecA as well as their dynamics depend on ATPase activity. Based on the idea that ATPase activity of RecA is most important for DNA strand exchange activity, our data suggest that extension and retraction of threads due is to many local strand invasion events during the search for sequences homologous to the induced DNA break site. IMPORTANCE Single-strand (ss) DNA binding ATPase RecA is the central recombinase in homologous recombination, and therefore essential for DNA repair pathways involving DNA strand exchange reactions. In several bacterial, RecA forms filamentous structures along the long axis of cells after induction of double strand breaks (DSBs) in the chromosome. These striking assemblies likely reflect RecA/ssDNA nucleoprotein filaments, which can extend and remodel within a time frame of few minutes. We show that ATPase activity of RecA is pivotal for these dynamic rearrangements, which include recruitment of freely diffusing molecules into low-mobile molecules within filaments. Our data suggest that ssDNA binding- and unbinding reactions are at the heart of RecA dynamics that power the dynamics of subcellular filamentous assemblies, leading to strand exchange reactions over a distance of several micrometers.
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13
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Stoll J, Zegarra V, Bange G, Graumann PL. Single-molecule dynamics suggest that ribosomes assemble at sites of translation in Bacillus subtilis. Front Microbiol 2022; 13:999176. [PMID: 36406443 PMCID: PMC9670183 DOI: 10.3389/fmicb.2022.999176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 04/07/2024] Open
Abstract
Eukaryotic cells transcribe ribosomal RNA and largely assemble ribosomes in a structure called the nucleolus, where chromosomal regions containing rRNA operons are clustered. In bacteria, many rRNA operons cluster close to the origin regions that are positioned on the outer borders of nucleoids, close to polar areas, where translating 70S ribosomes are located. Because outer regions of the nucleoids contain the highest accumulation of RNA polymerase, it has been hypothesized that bacteria contain "nucleolus-like" structures. However, ribosome subunits freely diffuse through the entire cells, and could thus be assembled and matured throughout the non-compartmentalized cell. By tracking single molecules of two GTPases that play an essential role in ribosomal folding and processing in Bacillus subtilis, we show that this process takes place at sites of translation, i.e., predominantly at the cell poles. Induction of the stringent response led to a change in the population of GTPases assumed to be active in maturation, but did not abolish nucleoid occlusion of ribosomes or of GTPases. Our findings strongly support the idea of the conceptualization of nucleolus-like structures in bacteria, i.e., rRNA synthesis, ribosomal protein synthesis and subunit assembly occurring in close proximity at the cell poles, facilitating the efficiency of ribosome maturation even under conditions of transient nutrient deprivation.
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Affiliation(s)
| | | | | | - Peter L. Graumann
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
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14
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Wisniewska A, Wons E, Potrykus K, Hinrichs R, Gucwa K, Graumann PL, Mruk I. Molecular basis for lethal cross-talk between two unrelated bacterial transcription factors - the regulatory protein of a restriction-modification system and the repressor of a defective prophage. Nucleic Acids Res 2022; 50:10964-10980. [PMID: 36271797 DOI: 10.1093/nar/gkac914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial gene expression depends on the efficient functioning of global transcriptional networks, however their interconnectivity and orchestration rely mainly on the action of individual DNA binding proteins called transcription factors (TFs). TFs interact not only with their specific target sites, but also with secondary (off-target) sites, and vary in their promiscuity. It is not clear yet what mechanisms govern the interactions with secondary sites, and how such rewiring affects the overall regulatory network, but this could clearly constrain horizontal gene transfer. Here, we show the molecular mechanism of one such off-target interaction between two unrelated TFs in Escherichia coli: the C regulatory protein of a Type II restriction-modification system, and the RacR repressor of a defective prophage. We reveal that the C protein interferes with RacR repressor expression, resulting in derepression of the toxic YdaT protein. These results also provide novel insights into regulation of the racR-ydaST operon. We mapped the C regulator interaction to a specific off-target site, and also visualized C protein dynamics, revealing intriguing differences in single molecule dynamics in different genetic contexts. Our results demonstrate an apparent example of horizontal gene transfer leading to adventitious TF cross-talk with negative effects on the recipient's viability. More broadly, this study represents an experimentally-accessible model of a regulatory constraint on horizontal gene transfer.
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Affiliation(s)
- Aleksandra Wisniewska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Rebecca Hinrichs
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Katarzyna Gucwa
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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15
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Characterization of the self-targeting Type IV CRISPR interference system in Pseudomonas oleovorans. Nat Microbiol 2022; 7:1870-1878. [PMID: 36175516 DOI: 10.1038/s41564-022-01229-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/04/2022] [Indexed: 11/08/2022]
Abstract
Bacterial Type IV CRISPR-Cas systems are thought to rely on multi-subunit ribonucleoprotein complexes to interfere with mobile genetic elements, but the substrate requirements and potential DNA nuclease activities for many systems within this type are uncharacterized. Here we show that the native Pseudomonas oleovorans Type IV-A CRISPR-Cas system targets DNA in a PAM-dependent manner and elicits interference without showing DNA nuclease activity. We found that the first crRNA of P. oleovorans contains a perfect match in the host gene coding for the Type IV pilus biogenesis protein PilN. Deletion of the native Type IV CRISPR array resulted in upregulation of pilN operon transcription in the absence of genome cleavage, indicating that Type IV-A CRISPR-Cas systems can function in host gene regulation. These systems resemble CRISPR interference (CRISPRi) methodology but represent a natural CRISPRi-like system that is found in many Pseudomonas and Klebsiella species and allows for gene silencing using engineered crRNAs.
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16
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Tight Complex Formation of the Fumarate Sensing DcuS-DcuR Two-Component System at the Membrane and Target Promoter Search by Free DcuR Diffusion. mSphere 2022; 7:e0023522. [PMID: 35862816 PMCID: PMC9429925 DOI: 10.1128/msphere.00235-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Signaling of two-component systems by phosphoryl transfer requires interaction of the sensor kinase with the response regulator. Interaction of the C4-dicarboxylate-responsive and membrane-integral sensor kinase DcuS with the response regulator DcuR was studied. In vitro, the cytoplasmic part of DcuS (PASC-Kin) was employed. Stable complexes were formed, when either DcuS or DcuR were phosphorylated (Kd 22 ± 11 and 28 ± 7 nM, respectively). The unphosphorylated proteins produced a more labile complex (Kd 1380 ± 395 nM). Bacterial two-hybrid studies confirm interaction of DcuR with DcuS (and PASC-Kin) in vivo. The absolute contents of DcuR (197-979 pmol mg−1 protein) in the bacteria exceeded those of DcuS by more than 1 order of magnitude. According to the Kd values, DcuS exists in complex, with phosphorylated but also unphosphorylated DcuR. In live cell imaging, the predominantly freely diffusing DcuR becomes markedly less mobile after phosphorylation and activation of DcuS by fumarate. Portions of the low mobility fraction accumulated at the cell poles, the preferred location of DcuS, and other portions within the cell, representing phosphorylated DcuR bound to promoters. In the model, acitvation of DcuS increases the affinity toward DcuR, leading to DcuS-P × DcuR formation and phosphorylation of DcuR. The complex is stable enough for phosphate-transfer, but labile enough to allow exchange between DcuR from the cytosol and DcuR-P of the complex. Released DcuR-P diffuses to target promoters and binds. Uncomplexed DcuR-P in the cytosol binds to nonactivated DcuS and becomes dephosphorylated. The lower affinity between DcuR and DcuS avoids blocking of DcuS and allows rapid exchange of DcuR. IMPORTANCE Complex formation of membrane-bound sensor kinases with the response regulators represents an inherent step of signaling from the membrane to the promoters on the DNA. In the C4-dicarboxylate-sensing DcuS-DcuR two-component system, complex formation is strengthened by activation (phosphorylation) in vitro and in vivo, with trapping of the response regulator DcuR at the membrane. Single-molecule tracking of DcuR in the bacterial cell demonstrates two populations of DcuR with decreased mobility in the bacteria after activation: one at the membrane, but a second in the cytosol, likely representing DNA-bound DcuR. The data suggest a model with binding of DcuR to DcuS-P for phosphorylation, and of DcuR-P to DcuS for dephosphorylation, allowing rapid adaptation of the DcuR phosphorylation state. DcuR-P is released and transferred to DNA by 3D diffusion.
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17
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Rotter DAO, Heger C, Kühm C, Schmidt N, Schäfer A, Heimerl T, Mack M, Graumann PL. The Acetyltransferase RibT From Bacillus subtilis Affects in vivo Dynamics of the Multimeric Heavy Riboflavin Synthase Complex. Front Microbiol 2022; 13:856820. [PMID: 35495702 PMCID: PMC9048828 DOI: 10.3389/fmicb.2022.856820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
Flavins are ubiquitous molecules in life as they serve as important enzyme cofactors. In the Gram-positive, soil-dwelling bacterium Bacillus subtilis, four well-characterized gene products (the enzymes RibDG, RibE, RibAB, and RibH) catalyze the biosynthesis of riboflavin (RF) from guanosine-triphosphate (GTP) and ribulose-5-phosphate (R5P). The corresponding genes form an operon together with the gene ribT (ribDG-E-AB-H-T), wherein the function of this terminal gene remained enigmatic. RibT has been structurally characterized as a GCN5-like acetyltransferase (GNAT), however, with unidentified target molecules. Bacterial two-hybrid system revealed interactions between RibT, RibH, and RibE, forming the heavy RF synthase complex. Applying single particle tracking (SPT), we found that confined (sub)diffusion of RibT is largely dependent on interacting RibE and, to a lesser degree, on interacting RibH. By induced expression of otherwise low-expressed ribT from an ectopic locus, we observed a decrease in the subpopulation considered to represent capsids of the heavy RF synthase and an increase in the subpopulation thought to represent pentamers of RibH, pointing to a putative role for RibT in capsid disassembly. Complementarily, either deletion of ribT or mutation of a key residue from RibH (K29) suspected to be the substrate of RibT for acetylation leads to increased levels of subpopulations considered as capsids of RibH-mVenus (RibH-mV) in comparison to wild-type (wt)-like cells. Thus, we provide evidence for an indirect involvement of RibT in RF biosynthesis by a putative capsid disassembling mechanism considered to involve acetylation of RibH residue K29 at the three-fold symmetry axis of 60-mer capsids.
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Affiliation(s)
- Daniel Andreas Orlando Rotter
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
- BioNTech Manufacturing Marburg GmbH, Marburg, Germany
| | - Christoph Heger
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
- BioSpringBiotechnolgie GmbH, Frankfurt am Main, Germany
| | - Christian Kühm
- Institute of Technical Microbiology, University of Applied Sciences Mannheim, Mannheim, Germany
| | - Nina Schmidt
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Antje Schäfer
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Thomas Heimerl
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Matthias Mack
- Institute of Technical Microbiology, University of Applied Sciences Mannheim, Mannheim, Germany
| | - Peter L. Graumann
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
- *Correspondence: Peter L. Graumann
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18
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Hinrichs R, Pozhydaieva N, Höfer K, Graumann PL. Y-Complex Proteins Show RNA-Dependent Binding Events at the Cell Membrane and Distinct Single-Molecule Dynamics. Cells 2022; 11:cells11060933. [PMID: 35326384 PMCID: PMC8945944 DOI: 10.3390/cells11060933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/07/2023] Open
Abstract
Bacteria are dependent on rapid alterations in gene expression. A prerequisite for rapid adaptations is efficient RNA turnover, with endonuclease RNase Y playing a crucial role in mRNA stability as well as in maturation. In Bacillus subtilis, RNase Y in turn interacts with the so-called “Y-complex” consisting of three proteins, which play important functions in sporulation, natural transformation and biofilm formation. It is thought that the Y-complex acts as an accessory factor in RNase Y regulation but might also have independent functions. Using single-molecule tracking, we show that all three Y-complex proteins exhibit three distinct mobilities, including movement through the cytosol and confined motion, predominantly at membrane-proximal sites but also within the cell center. A transcriptional arrest leads to a strong change in localization and dynamics of YmcA, YlbF and YaaT, supporting their involvement in global RNA degradation. However, Y-complex proteins show distinguishable protein dynamics, and the deletion of yaaT or ylbF shows a minor effect on the dynamics of YmcA. Cell fractionation reveals that YaaT displays a mixture of membrane association and presence in the cytosol, while YlbF and YmcA do not show direct membrane attachment. Taken together, our experiments reveal membrane-associated and membrane-independent activities of Y-complex proteins and a dynamic interplay between them with indirect membrane association of YmcA and YlbF via YaaT.
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Affiliation(s)
- Rebecca Hinrichs
- SYNMIKRO, Zentrum für Synthetische Mikrobiologie, Philipps Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany; (R.H.); (N.P.); (K.H.)
- Fachbereich Chemie, Philipps Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
| | - Nadiia Pozhydaieva
- SYNMIKRO, Zentrum für Synthetische Mikrobiologie, Philipps Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany; (R.H.); (N.P.); (K.H.)
- Max-Planck-Institut für Terrestrische Mikrobiologie, Karl-von-Frisch Straße 16, 35043 Marburg, Germany
| | - Katharina Höfer
- SYNMIKRO, Zentrum für Synthetische Mikrobiologie, Philipps Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany; (R.H.); (N.P.); (K.H.)
- Max-Planck-Institut für Terrestrische Mikrobiologie, Karl-von-Frisch Straße 16, 35043 Marburg, Germany
| | - Peter L. Graumann
- SYNMIKRO, Zentrum für Synthetische Mikrobiologie, Philipps Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany; (R.H.); (N.P.); (K.H.)
- Fachbereich Chemie, Philipps Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
- Correspondence: ; Tel.: +49-6421-282-2210
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19
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Subcellular Dynamics of a Conserved Bacterial Polar Scaffold Protein. Genes (Basel) 2022; 13:genes13020278. [PMID: 35205323 PMCID: PMC8872289 DOI: 10.3390/genes13020278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 02/05/2023] Open
Abstract
In order to survive, bacterial cells rely on precise spatiotemporal organization and coordination of essential processes such as cell growth, chromosome segregation, and cell division. Given the general lack of organelles, most bacteria are forced to depend on alternative localization mechanisms, such as, for example, geometrical cues. DivIVA proteins are widely distributed in mainly Gram-positive bacteria and were shown to bind the membrane, typically in regions of strong negative curvature, such as the cell poles and division septa. Here, they have been shown to be involved in a multitude of processes: from apical cell growth and chromosome segregation in actinobacteria to sporulation and inhibition of division re-initiation in firmicutes. Structural analyses revealed that DivIVA proteins can form oligomeric assemblies that constitute a scaffold for recruitment of other proteins. However, it remained unclear whether interaction with partner proteins influences DivIVA dynamics. Using structured illumination microscopy (SIM), single-particle tracking (SPT) microscopy, and fluorescent recovery after photobleaching (FRAP) experiments, we show that DivIVA from Corynebacterium glutamicum is mobilized by its binding partner ParB. In contrast, we show that the interaction between Bacillus subtilis DivIVA and its partner protein MinJ reduces DivIVA mobility. Furthermore, we show that the loss of the rod-shape leads to an increase in DivIVA dynamics in both organisms. Taken together, our study reveals the modulation of the polar scaffold protein by protein interactors and cell morphology. We reason that this leads to a very simple, yet robust way for actinobacteria to maintain polar growth and their rod-shape. In B. subtilis, however, the DivIVA protein is tailored towards a more dynamic function that allows quick relocalization from poles to septa upon division.
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20
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Condon C, Pellegrini O, Gilet L, Durand S, Braun F. Walking from E. coli to B. subtilis, one ribonuclease at a time. C R Biol 2021; 344:357-371. [DOI: 10.5802/crbiol.70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022]
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21
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Single molecule dynamics of DNA receptor ComEA, membrane permease ComEC and taken up DNA in competent Bacillus subtilis cells. J Bacteriol 2021; 204:e0057221. [PMID: 34928178 DOI: 10.1128/jb.00572-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In competent Gram-negative and Gram-positive bacteria, double stranded DNA is taken up through the outer cell membrane and/or the cell wall, and is bound by ComEA, which in Bacillus subtilis is a membrane protein. DNA is converted to single stranded DNA, and transported through the cell membrane via ComEC. We show that in Bacillus subtilis, the C-terminus of ComEC, thought to act as a nuclease, is not only important for DNA uptake, as judged from a loss of transformability, but also for the localization of ComEC to the cell pole and its mobility within the cell membrane. Using single molecule tracking, we show that only 13% of ComEC molecules are statically localised at the pole, while 87% move throughout the cell membrane. These experiments suggest that recruitment of ComEC to the cell pole is mediated by a diffusion/capture mechanism. Mutation of a conserved aspartate residue in the C-terminus, likely affecting metal binding, strongly impairs transformation efficiency, suggesting that this periplasmic domain of ComEC could indeed serve a catalytic function as nuclease. By tracking fluorescently labeled DNA, we show that taken up DNA has a similar mobility as a protein, in spite of being a large polymer. DNA dynamics are similar within the periplasm as those of ComEA, suggesting that most taken up molecules are bound to ComEA. We show that DNA can be highly mobile within the periplasm, indicating that this subcellular space can act as reservoir for taken up DNA, before its entry into the cytosol. Importance Bacteria can take up DNA from the environment and incorporate it into their chromosome, termed "natural competence" that can result in the uptake of novel genetic information. We show that fluorescently labelled DNA moves within the periplasm of competent Bacillus subtilis cells, with similar dynamics as DNA receptor ComEA. This indicates that DNA can accumulate in the periplasm, likely bound by ComEA, and thus can be stored before uptake at the cell pole, via integral membrane DNA permease ComEC. Assembly of the latter assembles at the cell pole likely occurs by a diffusion-capture mechanism. DNA uptake into cells thus takes a detour through the entire periplasm, and involves a high degree of free diffusion along and within the cell membrane.
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22
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Osorio-Valeriano M, Altegoer F, Das CK, Steinchen W, Panis G, Connolley L, Giacomelli G, Feddersen H, Corrales-Guerrero L, Giammarinaro PI, Hanßmann J, Bramkamp M, Viollier PH, Murray S, Schäfer LV, Bange G, Thanbichler M. The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes. Mol Cell 2021; 81:3992-4007.e10. [PMID: 34562373 DOI: 10.1016/j.molcel.2021.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/27/2021] [Accepted: 08/31/2021] [Indexed: 01/29/2023]
Abstract
ParB-like CTPases mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded at parS motifs in the centromere of target DNA molecules and spread laterally to form large nucleoprotein complexes serving as docking points for the DNA segregation machinery. Here, we solve crystal structures of ParB in the pre- and post-hydrolysis state and illuminate the catalytic mechanism of nucleotide hydrolysis. Moreover, we identify conformational changes that underlie the CTP- and parS-dependent closure of ParB clamps. The study of CTPase-deficient ParB variants reveals that CTP hydrolysis serves to limit the sliding time of ParB clamps and thus drives the establishment of a well-defined ParB diffusion gradient across the centromere whose dynamics are critical for DNA segregation. These findings clarify the role of the ParB CTPase cycle in partition complex assembly and function and thus advance our understanding of this prototypic CTP-dependent molecular switch.
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Affiliation(s)
- Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Florian Altegoer
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Lara Connolley
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Giacomo Giacomelli
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Helge Feddersen
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | | | - Pietro I Giammarinaro
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Juri Hanßmann
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | - Marc Bramkamp
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Seán Murray
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gert Bange
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany.
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