101
|
MinD directly interacting with FtsZ at the H10 helix suggests a model for robust activation of MinC to destabilize FtsZ polymers. Biochem J 2017; 474:3189-3205. [PMID: 28743721 DOI: 10.1042/bcj20170357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/10/2017] [Accepted: 07/25/2017] [Indexed: 12/30/2022]
Abstract
Cell division in bacteria is a highly controlled and regulated process. FtsZ, a bacterial cytoskeletal protein, forms a ring-like structure known as the Z-ring and recruits more than a dozen other cell division proteins. The Min system oscillates between the poles and inhibits the Z-ring formation at the poles by perturbing FtsZ assembly. This leads to an increase in the FtsZ concentration at the mid-cell and helps in Z-ring positioning. MinC, the effector protein, interferes with Z-ring formation through two different mechanisms mediated by its two domains with the help of MinD. However, the mechanism by which MinD triggers MinC activity is not yet known. We showed that MinD directly interacts with FtsZ with an affinity stronger than the reported MinC-FtsZ interaction. We determined the MinD-binding site of FtsZ using computational, mutational and biochemical analyses. Our study showed that MinD binds to the H10 helix of FtsZ. Single-point mutations at the charged residues in the H10 helix resulted in a decrease in the FtsZ affinity towards MinD. Based on our findings, we propose a novel model for MinCD-FtsZ interaction, where MinD through its direct interaction with FtsZ would trigger MinC activity to inhibit FtsZ functions.
Collapse
|
102
|
Skagia A, Zografou C, Venieraki A, Fasseas C, Katinakis P, Dimou M. Functional analysis of the cyclophilin PpiB role in bacterial cell division. Genes Cells 2017; 22:810-824. [DOI: 10.1111/gtc.12514] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/20/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Aggeliki Skagia
- Laboratory of General and Agricultural Microbiology; Faculty of Crop Science; Agricultural University of Athens; Iera Odos 75 11855 Athens Greece
| | - Chrysoula Zografou
- Laboratory of General and Agricultural Microbiology; Faculty of Crop Science; Agricultural University of Athens; Iera Odos 75 11855 Athens Greece
| | - Anastasia Venieraki
- Laboratory of General and Agricultural Microbiology; Faculty of Crop Science; Agricultural University of Athens; Iera Odos 75 11855 Athens Greece
| | - Costas Fasseas
- Laboratory of Electron Microscopy; Faculty of Crop Science; Agricultural University of Athens; Iera Odos 75 11855 Athens Greece
| | - Panagiotis Katinakis
- Laboratory of General and Agricultural Microbiology; Faculty of Crop Science; Agricultural University of Athens; Iera Odos 75 11855 Athens Greece
| | - Maria Dimou
- Laboratory of General and Agricultural Microbiology; Faculty of Crop Science; Agricultural University of Athens; Iera Odos 75 11855 Athens Greece
| |
Collapse
|
103
|
Abstract
The bacterial cytoplasmic membrane is composed of roughly equal proportions of lipids and proteins. The main lipid components are phospholipids, which vary in acyl chain length, saturation, and branching and carry head groups that vary in size and charge. Phospholipid variants determine membrane properties such as fluidity and charge that in turn modulate interactions with membrane-associated proteins. We summarize recent advances in understanding bacterial membrane structure and function, focusing particularly on the possible existence and significance of specialized membrane domains. We review the role of membrane curvature as a spatial cue for recruitment and regulation of proteins involved in morphogenic functions, especially elongation and division. Finally, we examine the role of the membrane, especially regulation of synthesis and fluid properties, in the life cycle of cell wall-deficient L-form bacteria.
Collapse
Affiliation(s)
- Henrik Strahl
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, NE2 4AX United Kingdom; ,
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, NE2 4AX United Kingdom; ,
| |
Collapse
|
104
|
MinE conformational dynamics regulate membrane binding, MinD interaction, and Min oscillation. Proc Natl Acad Sci U S A 2017; 114:7497-7504. [PMID: 28652337 DOI: 10.1073/pnas.1707385114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Escherichia coli MinE induces MinC/MinD to oscillate between the ends of the cell, contributing to the precise placement of the Z ring at midcell. To do this, MinE undergoes a remarkable conformational change from a latent 6β-stranded form that diffuses in the cytoplasm to an active 4β-stranded form bound to the membrane and MinD. How this conformational switch occurs is not known. Here, using hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) we rule out a model in which the two forms are in rapid equilibrium. Furthermore, HDX-MS revealed that a MinE mutant (D45A/V49A), previously shown to produce an aberrant oscillation and unable to assemble a MinE ring, is more rigid than WT MinE. This mutant has a defect in interaction with MinD, suggesting it has difficulty in switching to the active form. Analysis of intragenic suppressors of this mutant suggests it has difficulty in releasing the N-terminal membrane targeting sequences (MTS). These results indicate that the dynamic association of the MTS with the β-sheet is fine-tuned to balance MinE's need to sense MinD on the membrane with its need to diffuse in the cytoplasm, both of which are necessary for the oscillation. The results lead to models for MinE activation and MinE ring formation.
Collapse
|
105
|
Ruiz-Martinez A, Bartol TM, Sejnowski TJ, Tartakovsky DM. Efficient Multiscale Models of Polymer Assembly. Biophys J 2017; 111:185-96. [PMID: 27410746 DOI: 10.1016/j.bpj.2016.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/24/2016] [Accepted: 05/09/2016] [Indexed: 12/25/2022] Open
Abstract
Protein polymerization and bundling play a central role in cell physiology. Predictive modeling of these processes remains an open challenge, especially when the proteins involved become large and their concentrations high. We present an effective kinetics model of filament formation, bundling, and depolymerization after GTP hydrolysis, which involves a relatively small number of species and reactions, and remains robust over a wide range of concentrations and timescales. We apply this general model to study assembly of FtsZ protein, a basic element in the division process of prokaryotic cells such as Escherichia coli, Bacillus subtilis, or Caulobacter crescentus. This analysis demonstrates that our model outperforms its counterparts in terms of both accuracy and computational efficiency. Because our model comprises only 17 ordinary differential equations, its computational cost is orders-of-magnitude smaller than the current alternatives consisting of up to 1000 ordinary differential equations. It also provides, to our knowledge, a new insight into the characteristics and functioning of FtsZ proteins at high concentrations. The simplicity and versatility of our model render it a powerful computational tool, which can be used either as a standalone descriptor of other biopolymers' assembly or as a component in more complete kinetic models.
Collapse
Affiliation(s)
- Alvaro Ruiz-Martinez
- Department of Mechanical and Aerospace Engineering, University of California-San Diego, La Jolla, California
| | - Thomas M Bartol
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Terrence J Sejnowski
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, California; Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California; The Division of Biological Studies Sciences, University of California-San Diego, La Jolla, California.
| | - Daniel M Tartakovsky
- Department of Mechanical and Aerospace Engineering, University of California-San Diego, La Jolla, California.
| |
Collapse
|
106
|
In Situ Molecular Architecture of the Salmonella Type III Secretion Machine. Cell 2017; 168:1065-1074.e10. [PMID: 28283062 DOI: 10.1016/j.cell.2017.02.022] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/07/2017] [Accepted: 02/08/2017] [Indexed: 11/21/2022]
Abstract
Type III protein secretion systems have specifically evolved to deliver bacterially encoded proteins into target eukaryotic cells. The core elements of this multi-protein machine are the envelope-associated needle complex, the inner membrane export apparatus, and a large cytoplasmic sorting platform. Here, we report a high-resolution in situ structure of the Salmonella Typhimurium type III secretion machine obtained by high-throughput cryo-electron tomography and sub-tomogram averaging. Through molecular modeling and comparative analysis of machines assembled with protein-tagged components or from different deletion mutants, we determined the molecular architecture of the secretion machine in situ and localized its structural components. We also show that docking of the sorting platform results in significant conformational changes in the needle complex to provide the symmetry adaptation required for the assembly of the entire secretion machine. These studies provide major insight into the structure and assembly of a broadly distributed protein secretion machine.
Collapse
|
107
|
Du S, Lutkenhaus J. Assembly and activation of the Escherichia coli divisome. Mol Microbiol 2017; 105:177-187. [PMID: 28419603 DOI: 10.1111/mmi.13696] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/10/2017] [Accepted: 04/13/2017] [Indexed: 12/20/2022]
Abstract
Cell division in Escherichia coli is mediated by a large protein complex called the divisome. Most of the divisome proteins have been identified, but how they assemble onto the Z ring scaffold to form the divisome and work together to synthesize the septum is not well understood. In this review, we summarize the latest findings on divisome assembly and activation as well as provide our perspective on how these two processes might be regulated.
Collapse
Affiliation(s)
- Shishen Du
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Joe Lutkenhaus
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| |
Collapse
|
108
|
Du S, Lutkenhaus J. The N-succinyl-l,l-diaminopimelic acid desuccinylase DapE acts through ZapB to promote septum formation in Escherichia coli. Mol Microbiol 2017; 105:326-345. [PMID: 28470834 DOI: 10.1111/mmi.13703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Spatial regulation of cell division in Escherichia coli occurs at the stage of Z ring formation. It consists of negative (the Min and NO systems) and positive (Ter signal mediated by MatP/ZapA/ZapB) regulators. Here, we find that N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) facilitates functional Z ring formation by strengthening the Ter signal via ZapB. DapE depends on ZapB to localize to the Z ring and its overproduction suppresses the division defect caused by loss of both the Min and NO systems. DapE shows a strong interaction with ZapB and requires the presence of ZapB to exert its function in division. Consistent with the idea that DapE strengthens the Ter signal, overproduction of DapE supports cell division with reduced FtsZ levels and provides some resistance to the FtsZ inhibitors MinCD and SulA, while deletion of dapE, like deletion of zapB, exacerbates the phenotypes of cells impaired in Z ring formation such as ftsZ84 or a min mutant. Taken together, our results report DapE as a new component of the divisome that promotes the integrity of the Z ring by acting through ZapB and raises the possibility of the existence of additional divisome proteins that also function in other cellular processes.
Collapse
Affiliation(s)
- Shishen Du
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Joe Lutkenhaus
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| |
Collapse
|
109
|
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.
Collapse
|
110
|
Wagstaff JM, Tsim M, Oliva MA, García-Sanchez A, Kureisaite-Ciziene D, Andreu JM, Löwe J. A Polymerization-Associated Structural Switch in FtsZ That Enables Treadmilling of Model Filaments. mBio 2017; 8:e00254-17. [PMID: 28465423 PMCID: PMC5414002 DOI: 10.1128/mbio.00254-17] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/13/2017] [Indexed: 02/07/2023] Open
Abstract
Bacterial cell division in many organisms involves a constricting cytokinetic ring that is orchestrated by the tubulin-like protein FtsZ. FtsZ forms dynamic filaments close to the membrane at the site of division that have recently been shown to treadmill around the division ring, guiding septal wall synthesis. Here, using X-ray crystallography of Staphylococcus aureus FtsZ (SaFtsZ), we reveal how an FtsZ can adopt two functionally distinct conformations, open and closed. The open form is found in SaFtsZ filaments formed in crystals and also in soluble filaments of Escherichia coli FtsZ as deduced by electron cryomicroscopy. The closed form is found within several crystal forms of two nonpolymerizing SaFtsZ mutants and corresponds to many previous FtsZ structures from other organisms. We argue that FtsZ's conformational switch is polymerization-associated, driven by the formation of the longitudinal intersubunit interfaces along the filament. We show that such a switch provides explanations for both how treadmilling may occur within a single-stranded filament and why filament assembly is cooperative.IMPORTANCE The FtsZ protein is a key molecule during bacterial cell division. FtsZ forms filaments that organize cell membrane constriction, as well as remodeling of the cell wall, to divide cells. FtsZ functions through nucleotide-driven filament dynamics that are poorly understood at the molecular level. In particular, mechanisms for cooperative assembly (nonlinear dependency on concentration) and treadmilling (preferential growth at one filament end and loss at the other) have remained elusive. Here, we show that most likely all FtsZ proteins have two distinct conformations, a "closed" form in monomeric FtsZ and an "open" form in filaments. The conformational switch that occurs upon polymerization explains cooperativity and, in concert with polymerization-dependent nucleotide hydrolysis, efficient treadmilling of FtsZ polymers.
Collapse
Affiliation(s)
| | - Matthew Tsim
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - María A Oliva
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | | | | | | | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| |
Collapse
|
111
|
Late assembly of the Vibrio cholerae cell division machinery postpones septation to the last 10% of the cell cycle. Sci Rep 2017; 7:44505. [PMID: 28300142 PMCID: PMC5353653 DOI: 10.1038/srep44505] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/08/2017] [Indexed: 12/26/2022] Open
Abstract
Bacterial cell division is a highly regulated process, which involves the formation of a complex apparatus, the divisome, by over a dozen proteins. In the few model bacteria in which the division process was detailed, divisome assembly occurs in two distinct steps: a few proteins, including the FtsZ tubulin-like protein, form a membrane associated contractile ring, the Z-ring, at ~30% of the cell cycle. The Z-ring serves as a scaffold for the recruitment of a second series of proteins, including integral membrane and periplasmic cell wall remodelling enzymes, at ~50% of the cell cycle. Actual septation occupies most of the remaining half of the cell cycle. In contrast, we present evidence suggesting that early pre-divisional Z-rings form between 40 and 50% of the cell cycle and mature into fully assembled divisome at about 80% of the cell cycle in Vibrio cholerae. Thus, actual septation is restricted to a very short amount of time. Our results further suggest that late assembly of the divisome probably helps maintain the asymmetric polar organisation of V. cholerae cells by limiting the accumulation of a cell pole marker, HubP, at the nascent cell poles.
Collapse
|
112
|
Lin X, Li N, Kudo H, Zhang Z, Li J, Wang L, Zhang W, Takechi K, Takano H. Genes Sufficient for Synthesizing Peptidoglycan are Retained in Gymnosperm Genomes, and MurE from Larix gmelinii can Rescue the Albino Phenotype of Arabidopsis MurE Mutation. PLANT & CELL PHYSIOLOGY 2017; 58:587-597. [PMID: 28158764 DOI: 10.1093/pcp/pcx005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 01/10/2017] [Indexed: 05/08/2023]
Abstract
The endosymbiotic theory states that plastids are derived from a single cyanobacterial ancestor that possessed a cell wall. Peptidoglycan (PG), the main component of the bacteria cell wall, gradually degraded during plastid evolution. PG-synthesizing Mur genes have been found to be retained in the genomes of basal streptophyte plants, although many of them have been lost from the genomes of angiosperms. The enzyme encoded by bacterial MurE genes catalyzes the formation of the UDP-N-acetylmuramic acid (UDP-MurNAc) tripeptide in bacterial PG biosynthesis. Knockout of the MurE gene in the moss Physcomitrella patens resulted in defects of chloroplast division, whereas T-DNA-tagged mutants of Arabidopsis thaliana for MurE revealed inhibition of chloroplast development but not of plastid division, suggesting that AtMurE is functionally divergent from the bacterial and moss MurE proteins. Here, we could identify 10 homologs of bacterial Mur genes, including MurE, in the recently sequenced genomes of Picea abies and Pinus taeda, suggesting the retention of the plastid PG system in gymnosperms. To investigate the function of gymnosperm MurE, we isolated an ortholog of MurE from the larch, Larix gmelinii (LgMurE) and confirmed its presence as a single copy per genome, as well as its abundant expression in the leaves of larch seedlings. Analysis with a fusion protein combining green fluorescent protein and LgMurE suggested that it localizes in chloroplasts. Cross-species complementation assay with MurE mutants of A. thaliana and P. patens showed that the expression of LgMurE cDNA completely rescued the albefaction defects in A. thaliana but did not rescue the macrochloroplast phenotype in P. patens. The evolution of plastid PG and the mechanism behind the functional divergence of MurE genes are discussed in the context of information about plant genomes at different evolutionary stages.
Collapse
Affiliation(s)
- Xiaofei Lin
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Ningning Li
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Hiromi Kudo
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555 Japan
| | - Zhe Zhang
- College of Biological Science, China Agriculture University, Beijing, 100083, China
| | - Jinyu Li
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Li Wang
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Wenbo Zhang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Katsuaki Takechi
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, 860-8555 Japan
| | - Hiroyoshi Takano
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, 860-8555 Japan
- Institute of Pulsed Power Science, Kumamoto University, Kumamoto, 860-8555 Japan
| |
Collapse
|
113
|
Kinetics of large-scale chromosomal movement during asymmetric cell division in Escherichia coli. PLoS Genet 2017; 13:e1006638. [PMID: 28234902 PMCID: PMC5345879 DOI: 10.1371/journal.pgen.1006638] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/10/2017] [Accepted: 02/15/2017] [Indexed: 11/19/2022] Open
Abstract
Coordination between cell division and chromosome replication is essential for a cell to produce viable progeny. In the commonly accepted view, Escherichia coli realize this coordination via the accurate positioning of its cell division apparatus relative to the nucleoids. However, E. coli lacking proper positioning of its cell division planes can still successfully propagate. Here, we characterize how these cells partition their chromosomes into daughters during such asymmetric divisions. Using quantitative time-lapse imaging, we show that DNA translocase, FtsK, can pump as much as 80% (3.7 Mb) of the chromosome between daughters at an average rate of 1700±800 bp/s. Pauses in DNA translocation are rare, and in no occasions did we observe reversals at experimental time scales of a few minutes. The majority of DNA movement occurs at the latest stages of cell division when the cell division protein ZipA has already dissociated from the septum, and the septum has closed to a narrow channel with a diameter much smaller than the resolution limit of the microscope (~250 nm). Our data suggest that the narrow constriction is necessary for effective translocation of DNA by FtsK. DNA translocases are conserved throughout bacteria. While at atomic and molecular levels they have been well characterized, their ability to partition DNA in vegetatively growing cells has remained less clear. Here we show that E. coli translocase, FtsK, can move as much as 80% (3.7 Mb) of the chromosomal DNA across the closing septum in asymmetrically dividing cells at an average rate of 1700 bp/s. The majority of DNA movement occurs at the latest stages of cell division when the septum has closed to a narrow channel. Our data implies that a narrow septal opening is needed for effective translocation of DNA by FtsK.
Collapse
|
114
|
Gangan MS, Athale CA. Threshold effect of growth rate on population variability of Escherichia coli cell lengths. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160417. [PMID: 28386413 PMCID: PMC5367290 DOI: 10.1098/rsos.160417] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 01/23/2017] [Indexed: 05/24/2023]
Abstract
A long-standing question in biology is the effect of growth on cell size. Here, we estimate the effect of Escherichia coli growth rate (r) on population cell size distributions by estimating the coefficient of variation of cell lengths (CVL) from image analysis of fixed cells in DIC microscopy. We find that the CVL is constant at growth rates less than one division per hour, whereas above this threshold, CVL increases with an increase in the growth rate. We hypothesize that stochastic inhibition of cell division owing to replication stalling by a RecA-dependent mechanism, combined with the growth rate threshold of multi-fork replication (according to Cooper and Helmstetter), could form the basis of such a threshold effect. We proceed to test our hypothesis by increasing the frequency of stochastic stalling of replication forks with hydroxyurea (HU) treatment and find that cell length variability increases only when the growth rate exceeds this threshold. The population effect is also reproduced in single-cell studies using agar-pad cultures and 'mother machine'-based experiments to achieve synchrony. To test the role of RecA, critical for the repair of stalled replication forks, we examine the CVL of E. coli ΔrecA cells. We find cell length variability in the mutant to be greater than wild-type, a phenotype that is rescued by plasmid-based RecA expression. Additionally, we find that RecA-GFP protein recruitment to nucleoids is more frequent at growth rates exceeding the growth rate threshold and is further enhanced on HU treatment. Thus, we find growth rates greater than a threshold result in increased E. coli cell lengths in the population, and this effect is, at least in part, mediated by RecA recruitment to the nucleoid and stochastic inhibition of division.
Collapse
|
115
|
Gangan MS, Athale CA. Threshold effect of growth rate on population variability of Escherichia coli cell lengths. ROYAL SOCIETY OPEN SCIENCE 2017. [PMID: 28386413 DOI: 10.5061/dryad.2bs69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A long-standing question in biology is the effect of growth on cell size. Here, we estimate the effect of Escherichia coli growth rate (r) on population cell size distributions by estimating the coefficient of variation of cell lengths (CVL) from image analysis of fixed cells in DIC microscopy. We find that the CVL is constant at growth rates less than one division per hour, whereas above this threshold, CVL increases with an increase in the growth rate. We hypothesize that stochastic inhibition of cell division owing to replication stalling by a RecA-dependent mechanism, combined with the growth rate threshold of multi-fork replication (according to Cooper and Helmstetter), could form the basis of such a threshold effect. We proceed to test our hypothesis by increasing the frequency of stochastic stalling of replication forks with hydroxyurea (HU) treatment and find that cell length variability increases only when the growth rate exceeds this threshold. The population effect is also reproduced in single-cell studies using agar-pad cultures and 'mother machine'-based experiments to achieve synchrony. To test the role of RecA, critical for the repair of stalled replication forks, we examine the CVL of E. coli ΔrecA cells. We find cell length variability in the mutant to be greater than wild-type, a phenotype that is rescued by plasmid-based RecA expression. Additionally, we find that RecA-GFP protein recruitment to nucleoids is more frequent at growth rates exceeding the growth rate threshold and is further enhanced on HU treatment. Thus, we find growth rates greater than a threshold result in increased E. coli cell lengths in the population, and this effect is, at least in part, mediated by RecA recruitment to the nucleoid and stochastic inhibition of division.
Collapse
Affiliation(s)
- Manasi S Gangan
- Division of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr Homi Bhabha Road, Pashan, Pune 411008 , India
| | - Chaitanya A Athale
- Division of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr Homi Bhabha Road, Pashan, Pune 411008 , India
| |
Collapse
|
116
|
Abstract
In bacteria and archaea, the most widespread cell division system is based on the tubulin homologue FtsZ protein, whose filaments form the cytokinetic Z-ring. FtsZ filaments are tethered to the membrane by anchors such as FtsA and SepF and are regulated by accessory proteins. One such set of proteins is responsible for Z-ring's spatiotemporal regulation, essential for the production of two equal-sized daughter cells. Here, we describe how our still partial understanding of the FtsZ-based cell division process has been progressed by visualising near-atomic structures of Z-rings and complexes that control Z-ring positioning in cells, most notably the MinCDE and Noc systems that act by negatively regulating FtsZ filaments. We summarise available data and how they inform mechanistic models for the cell division process.
Collapse
|
117
|
Abstract
Cytokinesis in E. coli is organized by a cytoskeletal element designated the Z ring. The Z ring is formed at midcell by the coalescence of FtsZ filaments tethered to the membrane by interaction of FtsZ's conserved C-terminal peptide (CCTP) with two membrane-associated proteins, FtsA and ZipA. Although interaction between an FtsZ monomer and either of these proteins is of low affinity, high affinity is achieved through avidity - polymerization linked CCTPs interacting with the membrane tethers. The placement of the Z ring at midcell is ensured by antagonists of FtsZ polymerization that are positioned within the cell and target FtsZ filaments through the CCTP. The placement of the ring is reinforced by a protein network that extends from the terminus (Ter) region of the chromosome to the Z ring. Once the Z ring is established, additional proteins are recruited through interaction with FtsA, to form the divisome. The assembled divisome is then activated by FtsN to carry out septal peptidoglycan synthesis, with a dynamic Z ring serving as a guide for septum formation. As the septum forms, the cell wall is split by spatially regulated hydrolases and the outer membrane invaginates in step with the aid of a transenvelope complex to yield progeny cells.
Collapse
Affiliation(s)
- Joe Lutkenhaus
- University of Kansas Medical Center, Kansas City, KS, USA.
| | - Shishen Du
- University of Kansas Medical Center, Kansas City, KS, USA
| |
Collapse
|
118
|
Schumacher MA. Bacterial Nucleoid Occlusion: Multiple Mechanisms for Preventing Chromosome Bisection During Cell Division. Subcell Biochem 2017; 84:267-298. [PMID: 28500529 DOI: 10.1007/978-3-319-53047-5_9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In most bacteria cell division is driven by the prokaryotic tubulin homolog, FtsZ, which forms the cytokinetic Z ring. Cell survival demands both the spatial and temporal accuracy of this process to ensure that equal progeny are produced with intact genomes. While mechanisms preventing septum formation at the cell poles have been known for decades, the means by which the bacterial nucleoid is spared from bisection during cell division, called nucleoid exclusion (NO), have only recently been deduced. The NO theory was originally posited decades ago based on the key observation that the cell division machinery appeared to be inhibited from forming near the bacterial nucleoid. However, what might drive the NO process was unclear. Within the last 10 years specific proteins have been identified as important mediators of NO. Arguably the best studied NO mechanisms are those employed by the Escherichia coli SlmA and Bacillus subtilis Noc proteins. Both proteins bind specific DNA sequences within selected chromosomal regions to act as timing devices. However, Noc and SlmA contain completely different structural folds and utilize distinct NO mechanisms. Recent studies have identified additional processes and factors that participate in preventing nucleoid septation during cell division. These combined data show multiple levels of redundancy as well as a striking diversity of mechanisms have evolved to protect cells against catastrophic bisection of the nucleoid. Here we discuss these recent findings with particular emphasis on what is known about the molecular underpinnings of specific NO machinery and processes.
Collapse
Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, 243 Nanaline H. Duke, Durham, NC, 27710, USA.
| |
Collapse
|
119
|
Li XT, Jun Y, Erickstad MJ, Brown SD, Parks A, Court DL, Jun S. tCRISPRi: tunable and reversible, one-step control of gene expression. Sci Rep 2016; 6:39076. [PMID: 27996021 PMCID: PMC5171832 DOI: 10.1038/srep39076] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/17/2016] [Indexed: 02/06/2023] Open
Abstract
The ability to control the level of gene expression is a major quest in biology. A widely used approach employs deletion of a nonessential gene of interest (knockout), or multi-step recombineering to move a gene of interest under a repressible promoter (knockdown). However, these genetic methods are laborious, and limited for quantitative study. Here, we report a tunable CRISPR-cas system, "tCRISPRi", for precise and continuous titration of gene expression by more than 30-fold. Our tCRISPRi system employs various previous advancements into a single strain: (1) We constructed a new strain containing a tunable arabinose operon promoter PBAD to quantitatively control the expression of CRISPR-(d)Cas protein over two orders of magnitude in a plasmid-free system. (2) tCRISPRi is reversible, and gene expression is repressed under knockdown conditions. (3) tCRISPRi shows significantly less than 10% leaky expression. (4) Most important from a practical perspective, construction of tCRISPRi to target a new gene requires only one-step of oligo recombineering. Our results show that tCRISPRi, in combination with recombineering, provides a simple and easy-to-implement tool for gene expression control, and is ideally suited for construction of both individual strains and high-throughput tunable knockdown libraries.
Collapse
Affiliation(s)
- Xin-tian Li
- Section of Molecular Biology, Division of Biological Sciences and Department of Physics, UC San Diego, La Jolla, CA 92093, USA
| | - Yonggun Jun
- Section of Molecular Biology, Division of Biological Sciences and Department of Physics, UC San Diego, La Jolla, CA 92093, USA
| | - Michael J. Erickstad
- Section of Molecular Biology, Division of Biological Sciences and Department of Physics, UC San Diego, La Jolla, CA 92093, USA
| | - Steven D. Brown
- Section of Molecular Biology, Division of Biological Sciences and Department of Physics, UC San Diego, La Jolla, CA 92093, USA
| | - Adam Parks
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
| | - Donald L. Court
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
| | - Suckjoon Jun
- Section of Molecular Biology, Division of Biological Sciences and Department of Physics, UC San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
120
|
Cass JA, Stylianidou S, Kuwada NJ, Traxler B, Wiggins PA. Probing bacterial cell biology using image cytometry. Mol Microbiol 2016; 103:818-828. [PMID: 27935200 DOI: 10.1111/mmi.13591] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2016] [Indexed: 01/01/2023]
Abstract
Advances in automated fluorescence microscopy have made snapshot and time-lapse imaging of bacterial cells commonplace, yet fundamental challenges remain in analysis. The vast quantity of data collected in high-throughput experiments requires a fast and reliable automated method to analyze fluorescence intensity and localization, cell morphology and proliferation as well as other descriptors. Inspired by effective yet tractable methods of population-level analysis using flow cytometry, we have developed a framework and tools for facilitating analogous analyses in image cytometry. These tools can both visualize and gate (generate subpopulations) more than 70 cell descriptors, including cell size, age and fluorescence. The method is well suited to multi-well imaging, analysis of bacterial cultures with high cell density (thousands of cells per frame) and complete cell cycle imaging. We give a brief description of the analysis of four distinct applications to emphasize the broad applicability of the tool.
Collapse
Affiliation(s)
- Julie A Cass
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Stella Stylianidou
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Nathan J Kuwada
- Department of Physics, Central Washington University, Ellensburg, WA, 98926, USA
| | - Beth Traxler
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Paul A Wiggins
- Department of Physics, University of Washington, Seattle, WA, 98195, USA.,Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.,Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| |
Collapse
|
121
|
HubP, a Polar Landmark Protein, Regulates Flagellar Number by Assisting in the Proper Polar Localization of FlhG in Vibrio alginolyticus. J Bacteriol 2016; 198:3091-3098. [PMID: 27573015 DOI: 10.1128/jb.00462-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/22/2016] [Indexed: 01/06/2023] Open
Abstract
The marine bacterium Vibrio alginolyticus has a single polar flagellum, the number of which is regulated positively by FlhF and negatively by FlhG. FlhF is intrinsically localized at the cell pole, whereas FlhG is localized there through putative interactions with the polar landmark protein HubP. Here we focused on the role of HubP in the regulation of flagellar number in V. alginolyticus Deletion of hubP increased the flagellar number and completely disrupted the polar localization of FlhG. It was thought that the flagellar number is determined primarily by the absolute amount of FlhF localized at the cell pole. Here we found that deletion of hubP increased the flagellar number although it did not increase the polar amount of FlhF. We also found that FlhG overproduction did not reduce the polar localization of FlhF. These results show that the absolute amount of FlhF is not always the determinant of flagellar number. We speculate that cytoplasmic FlhG works as a quantitative regulator, controlling the amount of FlhF localized at the pole, and HubP-anchored polar FlhG works as a qualitative regulator, directly inhibiting the activity of polar FlhF. This regulation by FlhF, FlhG, and HubP might contribute to achieving optimal flagellar biogenesis at the cell pole in V. alginolyticus IMPORTANCE: For regulation of the flagellar number in marine Vibrio, two proteins, FlhF and FlhG, work as positive and negative regulators, respectively. In this study, we found that the polar landmark protein HubP is involved in the regulation of flagellar biogenesis. Deletion of hubP increased the number of flagella without increasing the amount of pole-localizing FlhF, indicating that the number of flagella is not determined solely by the absolute amount of pole-localizing FlhF, which is inconsistent with the previous model. We propose that cytoplasmic FlhG and HubP-anchored polar FlhG negatively regulate flagellar formation through two independent schemes.
Collapse
|
122
|
Monterroso B, Zorrilla S, Sobrinos-Sanguino M, Keating CD, Rivas G. Microenvironments created by liquid-liquid phase transition control the dynamic distribution of bacterial division FtsZ protein. Sci Rep 2016; 6:35140. [PMID: 27725777 PMCID: PMC5057132 DOI: 10.1038/srep35140] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 09/21/2016] [Indexed: 11/09/2022] Open
Abstract
The influence of membrane-free microcompartments resulting from crowding-induced liquid/liquid phase separation (LLPS) on the dynamic spatial organization of FtsZ, the main component of the bacterial division machinery, has been studied using several LLPS systems. The GTP-dependent assembly cycle of FtsZ is thought to be crucial for the formation of the septal ring, which is highly regulated in time and space. We found that FtsZ accumulates in one of the phases and/or at the interface, depending on the system composition and on the oligomerization state of the protein. These results were observed both in bulk LLPS and in lipid-stabilized, phase-separated aqueous microdroplets. The visualization of the droplets revealed that both the location and structural arrangement of FtsZ filaments is determined by the nature of the LLPS. Relocation upon depolymerization of the dynamic filaments suggests the protein may shift among microenvironments in response to changes in its association state. The existence of these dynamic compartments driven by phase transitions can alter the local composition and reactivity of FtsZ during its life cycle acting as a nonspecific modulating factor of cell function.
Collapse
Affiliation(s)
- Begoña Monterroso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain
| | - Silvia Zorrilla
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain
| | - Marta Sobrinos-Sanguino
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain
| | - Christine D Keating
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain
| |
Collapse
|
123
|
Kojima S. Studies on the mechanism of bacterial flagellar rotation and the flagellar number regulation. Nihon Saikingaku Zasshi 2016; 71:185-97. [PMID: 27581279 DOI: 10.3412/jsb.71.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Many motile bacteria have the motility organ, the flagellum. It rotates by the rotary motor driven by the ion-motive force and is embedded in the cell surface at the base of each flagellar filament. Many researchers have been studying its rotary mechanism for years, but most of the energy conversion processes have been remained in mystery. We focused on the flagellar stator, which works at the core process of energy conversion, and found that the periplasmic region of the stator changes its conformation to be activated only when the stator units are incorporated into the motor and anchored at the cell wall. Meanwhile, the physiologically important supramolecular complex is localized in the cell at the right place and the right time with a proper amount. How the cell achieves such a proper localization is the fundamental question for life science, and we undertake this problem by analyzing the mechanism for biogenesis of a single polar flagellum of Vibrio alginolyticus. Here I describe the molecular mechanism of how the flagellum is generated at the specific place with a proper number, and also how the flagellar stator is incorporated into the motor to complete the functional motor assembly, based on our studies.
Collapse
Affiliation(s)
- Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University
| |
Collapse
|
124
|
An intracellular compass spatially coordinates cell cycle modules in Caulobacter crescentus. Curr Opin Microbiol 2016; 33:131-139. [PMID: 27517351 DOI: 10.1016/j.mib.2016.06.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/24/2016] [Indexed: 12/27/2022]
Abstract
Cellular functions in Bacteria, such as chromosome segregation and cytokinesis, result from cascades of molecular events operating largely as self-contained modules. Regulated timing of these cellular modules stems from global genetic circuits that allow precise temporal activation with respect to cell cycle progression and cell differentiation. Critically, many of these functions occur at defined locations within the cell, and therefore regulators of each module must communicate to remain coordinated in space. In this perspective, we highlight recent discoveries in Caulobacter crescentus asymmetric cell division to illuminate diverse mechanisms by which a cellular compass, composed of scaffolding and signaling proteins, directs cell cycle modules to their exact cellular addresses.
Collapse
|
125
|
Maurya GK, Modi K, Misra HS. Divisome and segrosome components of Deinococcus radiodurans interact through cell division regulatory proteins. Microbiology (Reading) 2016; 162:1321-1334. [DOI: 10.1099/mic.0.000330] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ganesh K. Maurya
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute (DAE-Deemed University), Mumbai- 400094, India
| | - Kruti Modi
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Hari S. Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute (DAE-Deemed University), Mumbai- 400094, India
| |
Collapse
|
126
|
A mechanistic stochastic framework for regulating bacterial cell division. Sci Rep 2016; 6:30229. [PMID: 27456660 PMCID: PMC4960620 DOI: 10.1038/srep30229] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/29/2016] [Indexed: 12/20/2022] Open
Abstract
How exponentially growing cells maintain size homeostasis is an important fundamental problem. Recent single-cell studies in prokaryotes have uncovered the adder principle, where cells add a fixed size (volume) from birth to division, irrespective of their size at birth. To mechanistically explain the adder principle, we consider a timekeeper protein that begins to get stochastically expressed after cell birth at a rate proportional to the volume. Cell-division time is formulated as the first-passage time for protein copy numbers to hit a fixed threshold. Consistent with data, the model predicts that the noise in division timing increases with size at birth. Intriguingly, our results show that the distribution of the volume added between successive cell-division events is independent of the newborn cell size. This was dramatically seen in experimental studies, where histograms of the added volume corresponding to different newborn sizes collapsed on top of each other. The model provides further insights consistent with experimental observations: the distribution of the added volume when scaled by its mean becomes invariant of the growth rate. In summary, our simple yet elegant model explains key experimental findings and suggests a mechanism for regulating both the mean and fluctuations in cell-division timing for controlling size.
Collapse
|
127
|
Grzybowski BA, Huck WTS. The nanotechnology of life-inspired systems. NATURE NANOTECHNOLOGY 2016; 11:585-92. [PMID: 27380745 DOI: 10.1038/nnano.2016.116] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 05/27/2016] [Indexed: 05/19/2023]
Abstract
For some decades now, nanotechnology has been touted as the 'next big thing' with potential impact comparable to the steam, electricity or Internet revolutions - but has it lived up to these expectations? While advances in top-down nanolithography, now reaching 10-nm resolution, have resulted in devices that are rapidly approaching mass production, attempts to produce nanoscale devices using bottom-up approaches have met with only limited success. We have been inundated with nanoparticles of almost any shape, material and composition, but their societal impact has been far from revolutionary, with growing concerns over their toxicity. Despite nebulous hopes that making hierarchical nanomaterials will lead to new, emergent properties, no breakthrough applications seem imminent. In this Perspective, we argue that the time is ripe to look beyond individual nano-objects and their static assemblies, and instead focus on systems comprising different types of 'nanoparts' interacting and/or communicating with one another to perform desired functions. Such systems are interesting for a variety of reasons: they can act autonomously without external electrical or optical connections, can be dynamic and reconfigurable, and can act as 'nanomachines' by directing the flow of mass, energy or information . In thinking how this systems nanoscience approach could be implemented to design useful - as opposed to toy-model - nanosystems, our choice of applications and our nanoengineering should be inspired by living matter.
Collapse
Affiliation(s)
- Bartosz A Grzybowski
- IBS Center for Soft and Living Matter and the Department of Chemistry, UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan 689-798, Republic of Korea
| | - Wilhelm T S Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| |
Collapse
|
128
|
Cell division licensing in the multi-chromosomal Vibrio cholerae bacterium. Nat Microbiol 2016; 1:16094. [PMID: 27562255 DOI: 10.1038/nmicrobiol.2016.94] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/20/2016] [Indexed: 12/20/2022]
Abstract
Cell division must be coordinated with chromosome replication and segregation to ensure the faithful transmission of genetic information during proliferation. In most bacteria, assembly of the division apparatus, the divisome, starts with the polymerization of a tubulin homologue, FtsZ, into a ring-like structure at mid-cell, the Z-ring(1). It typically occurs at half of the cell cycle when most of the replication and segregation cycle of the unique chromosome they generally harbour is achieved(2). The chromosome itself participates in the regulation of cell division, at least in part because it serves as a scaffold to position FtsZ polymerization antagonists(3). However, about 10% of bacteria have more than one chromosome(4), which raises questions about the way they license cell division(3). For instance, the genome of Vibrio cholerae, the agent of cholera, is divided between a 3 Mbp replicon that originates from the chromosome of its mono-chromosomal ancestor, Chr1, and a 1 Mbp plasmid-derived replicon, Chr2 (ref. 5). Here, we show that Chr2 harbours binding motifs for an inhibitor of Z-ring formation, which helps accurately position the V. cholerae divisome at mid-cell and postpones its assembly to the very end of the cell cycle.
Collapse
|
129
|
Lambertz C, Martos A, Henkel A, Neiser A, Kliesch TT, Janshoff A, Schwille P, Sönnichsen C. Single Particle Plasmon Sensors as Label-Free Technique To Monitor MinDE Protein Wave Propagation on Membranes. NANO LETTERS 2016; 16:3540-4. [PMID: 27172130 DOI: 10.1021/acs.nanolett.6b00507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We use individual gold nanorods as pointlike detectors for the intrinsic dynamics of an oscillating biological system. We chose the pattern forming MinDE protein system from Escherichia coli (E. coli), a prominent example for self-organized chemical oscillations of membrane-associated proteins that are involved in the bacterial cell division process. Similar to surface plasmon resonance (SPR), the gold nanorods report changes in their protein surface coverage without the need for fluorescence labeling, a technique we refer to as NanoSPR. Comparing the dynamics for fluorescence labeled and unlabeled proteins, we find a reduction of the oscillation period by about 20%. The absence of photobleaching allows us to investigate Min proteins attaching and detaching from lipid coated gold nanorods with an unprecedented bandwidth of 100 ms time resolution and 1 h observation time. The long observation reveals small changes of the oscillation period over time. Averaging many cycles yields the precise wave profile that exhibits the four phases suggested in previous reports. Unexpected from previous fluorescence-based studies, we found an immobile static protein layer not dissociating during the oscillation cycle. Hence, NanoSPR is an attractive label-free real-time technique for the local investigation of molecular dynamics with high observation bandwidth. It gives access to systems, which cannot be fluorescently labeled, and resolves local dynamics that would average out over the sensor area used in conventional SPR.
Collapse
Affiliation(s)
- Christina Lambertz
- Institute of Physical Chemistry, University of Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Ariadna Martos
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry , Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Andreas Henkel
- Institute of Physical Chemistry, University of Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Andreas Neiser
- Institute of Physical Chemistry, University of Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Torben-Tobias Kliesch
- Institute of Physical Chemistry, University of Goettingen , Tammannstrasse 6, D-37077 Goettingen, Germany
| | - Andreas Janshoff
- Institute of Physical Chemistry, University of Goettingen , Tammannstrasse 6, D-37077 Goettingen, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry , Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Carsten Sönnichsen
- Institute of Physical Chemistry, University of Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| |
Collapse
|
130
|
Abstract
Filamenting temperature-sensitive mutant Z (FtsZ), an essential cell division protein in bacteria, has recently emerged as an important and exploitable antibacterial target. Cytokinesis in bacteria is regulated by the assembly dynamics of this protein, which is ubiquitously present in eubacteria. The perturbation of FtsZ assembly has been found to have a deleterious effect on the cytokinetic machinery and, in turn, upon cell survival. FtsZ is highly conserved among prokaryotes, offering the possibility of broad-spectrum antibacterial agents, while its limited sequence homology with tubulin (an essential protein in eukaryotic mitosis) offers the possibility of selective toxicity. This review aims to summarize current knowledge regarding the mechanism of action of FtsZ, and to highlight existing attempts toward the development of clinically useful inhibitors.
Collapse
|
131
|
Kloosterman TG, Lenarcic R, Willis CR, Roberts DM, Hamoen LW, Errington J, Wu LJ. Complex polar machinery required for proper chromosome segregation in vegetative and sporulating cells of Bacillus subtilis. Mol Microbiol 2016; 101:333-50. [PMID: 27059541 PMCID: PMC4949633 DOI: 10.1111/mmi.13393] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 01/16/2023]
Abstract
Chromosome segregation is an essential process of cell multiplication. In prokaryotes, segregation starts with the newly replicated sister origins of replication, oriCs, which move apart to defined positions in the cell. We have developed a genetic screen to identify mutants defective in placement of oriC during spore development in the Gram‐positive bacterium Bacillus subtilis. In addition to the previously identified proteins Soj and DivIVA, our screen identified several new factors involved in polar recruitment of oriC: a reported regulator of competence ComN, and the regulators of division site selection MinD and MinJ. Previous work implicated Soj as an important regulator of oriC positioning in the cell. Our results suggest a model in which the DivIVA‐interacting proteins ComN and MinJ recruit MinD to the cell pole, and that these proteins work upstream of Soj to enable oriC placement. We show that these proteins form a polar complex, which acts in parallel with but distinct from the sporulation‐specific RacA pathway of oriC placement, and also functions during vegetative growth. Our study further shows that MinD has two distinct cell cycle roles, in cell division and chromosome segregation, and highlights that cell probably use multiple parallel mechanisms to ensure accurate chromosome segregation.
Collapse
Affiliation(s)
- Tomas G Kloosterman
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK.,Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Rok Lenarcic
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK.,Lek Pharmaceuticals d.d., Menges, Slovenia
| | - Clare R Willis
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - David M Roberts
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Leendert W Hamoen
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK.,Department of Cell Biology & Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Ling J Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
132
|
Laddomada F, Miyachiro MM, Dessen A. Structural Insights into Protein-Protein Interactions Involved in Bacterial Cell Wall Biogenesis. Antibiotics (Basel) 2016; 5:antibiotics5020014. [PMID: 27136593 PMCID: PMC4929429 DOI: 10.3390/antibiotics5020014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 03/15/2016] [Accepted: 04/09/2016] [Indexed: 12/30/2022] Open
Abstract
The bacterial cell wall is essential for survival, and proteins that participate in its biosynthesis have been the targets of antibiotic development efforts for decades. The biosynthesis of its main component, the peptidoglycan, involves the coordinated action of proteins that are involved in multi-member complexes which are essential for cell division (the “divisome”) and/or cell wall elongation (the “elongasome”), in the case of rod-shaped cells. Our knowledge regarding these interactions has greatly benefitted from the visualization of different aspects of the bacterial cell wall and its cytoskeleton by cryoelectron microscopy and tomography, as well as genetic and biochemical screens that have complemented information from high resolution crystal structures of protein complexes involved in divisome or elongasome formation. This review summarizes structural and functional aspects of protein complexes involved in the cytoplasmic and membrane-related steps of peptidoglycan biosynthesis, with a particular focus on protein-protein interactions whereby disruption could lead to the development of novel antibacterial strategies.
Collapse
Affiliation(s)
- Federica Laddomada
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Grenoble F-38044, France.
- Centre National de la Recherche Scientifique (CNRS), IBS, Grenoble F-38044, France.
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), IBS, Grenoble F-38044, France.
| | - Mayara M Miyachiro
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo 13083-100, Brazil.
| | - Andréa Dessen
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Grenoble F-38044, France.
- Centre National de la Recherche Scientifique (CNRS), IBS, Grenoble F-38044, France.
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), IBS, Grenoble F-38044, France.
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo 13083-100, Brazil.
| |
Collapse
|
133
|
Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ. Proc Natl Acad Sci U S A 2016; 113:4988-93. [PMID: 27091999 DOI: 10.1073/pnas.1602327113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cell division in most prokaryotes is mediated by FtsZ, which polymerizes to create the cytokinetic Z ring. Multiple FtsZ-binding proteins regulate FtsZ polymerization to ensure the proper spatiotemporal formation of the Z ring at the division site. The DNA-binding protein SlmA binds to FtsZ and prevents Z-ring formation through the nucleoid in a process called "nucleoid occlusion" (NO). As do most FtsZ-accessory proteins, SlmA interacts with the conserved C-terminal domain (CTD) that is connected to the FtsZ core by a long, flexible linker. However, SlmA is distinct from other regulatory factors in that it must be DNA-bound to interact with the FtsZ CTD. Few structures of FtsZ regulator-CTD complexes are available, but all reveal the CTD bound as a helix. To deduce the molecular basis for the unique SlmA-DNA-FtsZ CTD regulatory interaction and provide insight into FtsZ-regulator protein complex formation, we determined structures of Escherichia coli, Vibrio cholera, and Klebsiella pneumonia SlmA-DNA-FtsZ CTD ternary complexes. Strikingly, the FtsZ CTD does not interact with SlmA as a helix but binds as an extended conformation in a narrow, surface-exposed pocket formed only in the DNA-bound state of SlmA and located at the junction between the DNA-binding and C-terminal dimer domains. Binding studies are consistent with the structure and underscore key interactions in complex formation. Combined, these data reveal the molecular basis for the SlmA-DNA-FtsZ interaction with implications for SlmA's NO function and underscore the ability of the FtsZ CTD to adopt a wide range of conformations, explaining its ability to bind diverse regulatory proteins.
Collapse
|
134
|
|
135
|
Hurley KA, Santos TMA, Nepomuceno GM, Huynh V, Shaw JT, Weibel DB. Targeting the Bacterial Division Protein FtsZ. J Med Chem 2016; 59:6975-98. [DOI: 10.1021/acs.jmedchem.5b01098] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katherine A. Hurley
- Department of Pharmaceutical Sciences, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Thiago M. A. Santos
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Gabriella M. Nepomuceno
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Valerie Huynh
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Jared T. Shaw
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Douglas B. Weibel
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Biomedical Engineering, University of Wisconsin—Madison, 1550 Engineering Drive, Madison, Wisconsin 53706, United States
| |
Collapse
|
136
|
Adder and a coarse-grained approach to cell size homeostasis in bacteria. Curr Opin Cell Biol 2016; 38:38-44. [PMID: 26901290 DOI: 10.1016/j.ceb.2016.02.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/14/2016] [Accepted: 02/03/2016] [Indexed: 12/29/2022]
Abstract
Cell size control and homeostasis is a long-standing subject in biology. Recent experimental work provides extensive evidence for a simple, quantitative size homeostasis principle coined adder (as opposed to sizer or timer). The adder principle provides unexpected insights into how bacteria maintain their size without employing a feedback mechanism. We review the genesis of adder and recent cell size homeostasis study on evolutionarily divergent bacterial organisms and beyond. We propose new coarse-grained approaches to understand the underlying mechanisms of cell size control at the whole cell level.
Collapse
|
137
|
Membrane-bound MinDE complex acts as a toggle switch that drives Min oscillation coupled to cytoplasmic depletion of MinD. Proc Natl Acad Sci U S A 2016; 113:E1479-88. [PMID: 26884160 DOI: 10.1073/pnas.1600644113] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Escherichia coli Min system self-organizes into a cell-pole to cell-pole oscillator on the membrane to prevent divisions at the cell poles. Reconstituting the Min system on a lipid bilayer has contributed to elucidating the oscillatory mechanism. However, previous in vitro patterns were attained with protein densities on the bilayer far in excess of those in vivo and failed to recapitulate the standing wave oscillations observed in vivo. Here we studied Min protein patterning at limiting MinD concentrations reflecting the in vivo conditions. We identified "burst" patterns--radially expanding and imploding binding zones of MinD, accompanied by a peripheral ring of MinE. Bursts share several features with the in vivo dynamics of the Min system including standing wave oscillations. Our data support a patterning mechanism whereby the MinD-to-MinE ratio on the membrane acts as a toggle switch: recruiting and stabilizing MinD on the membrane when the ratio is high and releasing MinD from the membrane when the ratio is low. Coupling this toggle switch behavior with MinD depletion from the cytoplasm drives a self-organized standing wave oscillator.
Collapse
|
138
|
Mandakovic D, Trigo C, Andrade D, Riquelme B, Gómez-Lillo G, Soto-Liebe K, Díez B, Vásquez M. CyDiv, a Conserved and Novel Filamentous Cyanobacterial Cell Division Protein Involved in Septum Localization. Front Microbiol 2016; 7:94. [PMID: 26903973 PMCID: PMC4748335 DOI: 10.3389/fmicb.2016.00094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/18/2016] [Indexed: 11/13/2022] Open
Abstract
Cell division in bacteria has been studied mostly in Escherichia coli and Bacillus subtilis, model organisms for Gram-negative and Gram-positive bacteria, respectively. However, cell division in filamentous cyanobacteria is poorly understood. Here, we identified a novel protein, named CyDiv (Cyanobacterial Division), encoded by the all2320 gene in Anabaena sp. PCC 7120. We show that CyDiv plays a key role during cell division. CyDiv has been previously described only as an exclusive and conserved hypothetical protein in filamentous cyanobacteria. Using polyclonal antibodies against CyDiv, we showed that it localizes at different positions depending on cell division timing: poles, septum, in both daughter cells, but also in only one of the daughter cells. The partial deletion of CyDiv gene generates partial defects in cell division, including severe membrane instability and anomalous septum localization during late division. The inability to complete knock out CyDiv strains suggests that it is an essential gene. In silico structural protein analyses and our experimental results suggest that CyDiv is an FtsB/DivIC-like protein, and could therefore, be part of an essential late divisome complex in Anabaena sp. PCC 7120.
Collapse
Affiliation(s)
- Dinka Mandakovic
- Fondap Center for Genome Regulation, Universidad de ChileSantiago, Chile; Laboratorio de Ecología Microbiana y Toxicología Ambiental, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Carla Trigo
- Laboratorio de Ecología Microbiana y Toxicología Ambiental, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile Santiago, Chile
| | - Derly Andrade
- Laboratorio de Ecología Microbiana y Toxicología Ambiental, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile Santiago, Chile
| | - Brenda Riquelme
- Laboratorio de Ecología Microbiana y Toxicología Ambiental, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile Santiago, Chile
| | - Gabriela Gómez-Lillo
- Laboratorio de Ecología Microbiana y Toxicología Ambiental, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile Santiago, Chile
| | - Katia Soto-Liebe
- Laboratorio de Ecología Microbiana y Toxicología Ambiental, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile Santiago, Chile
| | - Beatriz Díez
- Laboratorio de Ecología Microbiana de Sistemas Extremos, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile Santiago, Chile
| | - Mónica Vásquez
- Laboratorio de Ecología Microbiana y Toxicología Ambiental, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile Santiago, Chile
| |
Collapse
|
139
|
Nishida Y, Takeuchi H, Morimoto N, Umeda A, Kadota Y, Kira M, Okazaki A, Matsumura Y, Sugiura T. Intrinsic characteristics of Min proteins on the cell division of Helicobacter pylori. FEMS Microbiol Lett 2016; 363:fnw025. [PMID: 26862143 DOI: 10.1093/femsle/fnw025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2016] [Indexed: 01/24/2023] Open
Abstract
Helicobacter pylori divides in the human stomach resulting in persistent infections and causing various disorders. Bacterial cell division is precisely coordinated by many molecules, including FtsZ and Min proteins. However, the role of Min proteins in H. pylori division is poorly understood. We investigated the functional characteristics of Min proteins in wild-type HPK5 and five HPK5-derivative mutants using morphological and genetic approaches. All mutants showed a filamentous shape. However, the bacterial cell growth and viability of three single-gene mutants (minC, minD, minE) were similar to that of the wild-type. The coccoid form number was lowest in the minE-disruptant, indicating that MinE contributes to the coccoid form conversion during the stationary phase. Immunofluorescence microscopic observations showed that FtsZ was dispersedly distributed throughout the bacterial cell irrespective of nucleoid position in only minD-disruptants, indicating that MinD is involved in the nucleoid occlusion system. A chase assay demonstrated that MinC loss suppressed FtsZ-degradation, indicating that FtsZ degrades in a MinC-dependent manner. Molecular interactions between FtsZ and Min proteins were confirmed by immunoprecipitation (IP)-western blotting (WB), suggesting the functional cooperation of these molecules during bacterial cell division. This study describes the intrinsic characteristics of Min proteins and provides new insights into H. pylori cell division.
Collapse
Affiliation(s)
- Yoshie Nishida
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kohasu, Oko-cho, Nankoku-city, Kochi 783-8505, Japan
| | - Hiroaki Takeuchi
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kohasu, Oko-cho, Nankoku-city, Kochi 783-8505, Japan
| | - Norihito Morimoto
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kohasu, Oko-cho, Nankoku-city, Kochi 783-8505, Japan
| | - Akiko Umeda
- Department of Clinical Laboratory Medicine, Yamaguchi University, 1-1-1 MinamiKogushi, Ube-city, Yamaguchi 755-8505, Japan
| | - Yoshu Kadota
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kohasu, Oko-cho, Nankoku-city, Kochi 783-8505, Japan
| | - Mizuki Kira
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kohasu, Oko-cho, Nankoku-city, Kochi 783-8505, Japan
| | - Ami Okazaki
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kohasu, Oko-cho, Nankoku-city, Kochi 783-8505, Japan
| | - Yoshihisa Matsumura
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kohasu, Oko-cho, Nankoku-city, Kochi 783-8505, Japan
| | - Tetsuro Sugiura
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kohasu, Oko-cho, Nankoku-city, Kochi 783-8505, Japan
| |
Collapse
|
140
|
Vedyaykin AD, Vishnyakov IE, Polinovskaya VS, Khodorkovskii MA, Sabantsev AV. New insights into FtsZ rearrangements during the cell division of Escherichia coli from single-molecule localization microscopy of fixed cells. Microbiologyopen 2016; 5:378-86. [PMID: 26840800 PMCID: PMC4905991 DOI: 10.1002/mbo3.336] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/02/2015] [Accepted: 12/17/2015] [Indexed: 11/06/2022] Open
Abstract
FtsZ - a prokaryotic tubulin homolog - is one of the central components of bacterial division machinery. At the early stage of cytokinesis FtsZ forms the so-called Z-ring at mid-cell that guides septum formation. Many approaches were used to resolve the structure of the Z-ring, however, researchers are still far from consensus on this question. We utilized single-molecule localization microscopy (SMLM) in combination with immunofluorescence staining to visualize FtsZ in Esherichia coli fixed cells that were grown under slow and fast growth conditions. This approach allowed us to obtain images of FtsZ structures at different stages of cell division and accurately measure Z-ring dimensions. Analysis of these images demonstrated that Z-ring thickness increases during constriction, starting at about 70 nm at the beginning of division and increasing by approximately 25% half-way through constriction.
Collapse
Affiliation(s)
- Alexey D Vedyaykin
- Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya str. 29, Saint Petersburg, 195251, Russia
| | - Innokentii E Vishnyakov
- Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya str. 29, Saint Petersburg, 195251, Russia.,Institute of Cytology, Russian Academy of Sciences, Tikhoretsky av. 4, Saint Petersburg, 194064, Russia
| | - Vasilisa S Polinovskaya
- Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya str. 29, Saint Petersburg, 195251, Russia
| | - Mikhail A Khodorkovskii
- Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya str. 29, Saint Petersburg, 195251, Russia
| | - Anton V Sabantsev
- Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya str. 29, Saint Petersburg, 195251, Russia
| |
Collapse
|
141
|
Abstract
Protein patterns are known to adapt to cell shape and serve as spatial templates that choreograph downstream processes like cell polarity or cell division. However, how can pattern-forming proteins sense and respond to the geometry of a cell, and what mechanistic principles underlie pattern formation? Current models invoke mechanisms based on dynamic instabilities arising from nonlinear interactions between proteins but neglect the influence of the spatial geometry itself. Here, we show that patterns can emerge as a direct result of adaptation to cell geometry, in the absence of dynamical instability. We present a generic reaction module that allows protein densities robustly to adapt to the symmetry of the spatial geometry. The key component is an NTPase protein that cycles between nucleotide-dependent membrane-bound and cytosolic states. For elongated cells, we find that the protein dynamics generically leads to a bipolar pattern, which vanishes as the geometry becomes spherically symmetrical. We show that such a reaction module facilitates universal adaptation to cell geometry by sensing the local ratio of membrane area to cytosolic volume. This sensing mechanism is controlled by the membrane affinities of the different states. We apply the theory to explain AtMinD bipolar patterns in [Formula: see text] EcMinDE Escherichia coli. Due to its generic nature, the mechanism could also serve as a hitherto-unrecognized spatial template in many other bacterial systems. Moreover, the robustness of the mechanism enables self-organized optimization of protein patterns by evolutionary processes. Finally, the proposed module can be used to establish geometry-sensitive protein gradients in synthetic biological systems.
Collapse
|
142
|
Ha NR, Lee SC, Hyun JW, Yoon MY. Development of inhibitory ssDNA aptamers for the FtsZ cell division protein from citrus canker phytopathogen. Process Biochem 2016. [DOI: 10.1016/j.procbio.2015.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
143
|
A 1 MDa protein complex containing critical components of the Escherichia coli divisome. Sci Rep 2015; 5:18190. [PMID: 26643979 PMCID: PMC4672292 DOI: 10.1038/srep18190] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/13/2015] [Indexed: 11/09/2022] Open
Abstract
Cell division in bacteria is an essential process that is carried out at mid-cell by a group of cell division proteins referred to as the divisome. In Escherichia coli, over two dozen cell division proteins have been identified of which ten are essential. These division proteins localize sequentially and interdependently to the division site, after which constriction eventually produces two daughter cells. Various genetic and biochemical techniques have identified many interactions amongst cell division proteins, however the existence of the divisome as a large multi-protein complex has never been shown. Here, we identify a 1 MDa protein complex by native page that contains seven essential cell division proteins (FtsZ, ZipA, FtsK, FtsQ, FtsB, FtsL, and FtsN). The 1 MDa complex is present in rapidly dividing cells, but absent when cultures enter the stationary growth phase. Slight overexpression of the ftsQ D237N mutation that blocks cell division prevents formation of this 1 MDa complex. In cells depleted of FtsN, the 1 MDa complex is not assembled. Combined, our findings indicate that a large protein complex containing many different cell division proteins indeed exists. We note that this complex is very fragile and sensitive to the expression of tagged versions of FtsQ.
Collapse
|
144
|
Ullal P, McDonald NA, Chen JS, Lo Presti L, Roberts-Galbraith RH, Gould KL, Martin SG. The DYRK-family kinase Pom1 phosphorylates the F-BAR protein Cdc15 to prevent division at cell poles. J Cell Biol 2015; 211:653-68. [PMID: 26553932 PMCID: PMC4639868 DOI: 10.1083/jcb.201504073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 10/01/2015] [Indexed: 12/14/2022] Open
Abstract
Division site positioning is critical for both symmetric and asymmetric cell divisions. In many organisms, positive and negative signals cooperate to position the contractile actin ring for cytokinesis. In rod-shaped fission yeast Schizosaccharomyces pombe cells, division at midcell is achieved through positive Mid1/anillin-dependent signaling emanating from the central nucleus and negative signals from the dual-specificity tyrosine phosphorylation-regulated kinase family kinase Pom1 at the cell poles. In this study, we show that Pom1 directly phosphorylates the F-BAR protein Cdc15, a central component of the cytokinetic ring. Pom1-dependent phosphorylation blocks Cdc15 binding to paxillin Pxl1 and C2 domain protein Fic1 and enhances Cdc15 dynamics. This promotes ring sliding from cell poles, which prevents septum assembly at the ends of cells with a displaced nucleus or lacking Mid1. Pom1 also slows down ring constriction. These results indicate that a strong negative signal from the Pom1 kinase at cell poles converts Cdc15 to its closed state, destabilizes the actomyosin ring, and thus promotes medial septation.
Collapse
Affiliation(s)
- Pranav Ullal
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Nathan A McDonald
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Libera Lo Presti
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Rachel H Roberts-Galbraith
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Kathleen L Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Sophie G Martin
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| |
Collapse
|
145
|
Gulbronson CJ, Ribardo DA, Balaban M, Knauer C, Bange G, Hendrixson DR. FlhG employs diverse intrinsic domains and influences FlhF GTPase activity to numerically regulate polar flagellar biogenesis in Campylobacter jejuni. Mol Microbiol 2015; 99:291-306. [PMID: 26411371 DOI: 10.1111/mmi.13231] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 11/30/2022]
Abstract
Flagellation in polar flagellates is one of the rare biosynthetic processes known to be numerically regulated in bacteria. Polar flagellates must spatially and numerically regulate flagellar biogenesis to create flagellation patterns for each species that are ideal for motility. FlhG ATPases numerically regulate polar flagellar biogenesis, yet FlhG orthologs are diverse in motif composition. We discovered that Campylobacter jejuni FlhG is at the center of a multipartite mechanism that likely influences a flagellar biosynthetic step to control flagellar number for amphitrichous flagellation, rather than suppressing activators of flagellar gene transcription as in Vibrio and Pseudomonas species. Unlike other FlhG orthologs, the FlhG ATPase domain was not required to regulate flagellar number in C. jejuni. Instead, two regions of C. jejuni FlhG that are absent or significantly altered in FlhG orthologs are involved in numerical regulation of flagellar biogenesis. Additionally, we found that C. jejuni FlhG influences FlhF GTPase activity, which may mechanistically contribute to flagellar number regulation. Our work suggests that FlhG ATPases divergently evolved in each polarly flagellated species to employ different intrinsic domains and extrinsic effectors to ultimately mediate a common output - precise numerical control of polar flagellar biogenesis required to create species-specific flagellation patterns optimal for motility.
Collapse
Affiliation(s)
- Connor J Gulbronson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Deborah A Ribardo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Murat Balaban
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Carina Knauer
- LOEWE Center for Synthetic Microbiology (Synmikro) and Department of Chemistry, Philipps University Marburg, 35403, Marburg, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology (Synmikro) and Department of Chemistry, Philipps University Marburg, 35403, Marburg, Germany
| | - David R Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| |
Collapse
|
146
|
Schulte JB, Zeto RW, Roundy D. Theoretical Prediction of Disrupted Min Oscillation in Flattened Escherichia coli. PLoS One 2015; 10:e0139813. [PMID: 26457805 PMCID: PMC4601790 DOI: 10.1371/journal.pone.0139813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 09/16/2015] [Indexed: 11/18/2022] Open
Abstract
The dynamics of the Min-protein system help Escherichia coli regulate the process of cell division by identifying the center of the cell. While this system exhibits robust bipolar oscillations in wild-type cell shapes, recent experiments have shown that when the cells are mechanically deformed into wide, flattened out, irregular shapes, the spatial regularity of these oscillations breaks down. We employ widely used stochastic and deterministic models of the Min system to simulate cells with flattened shapes. The deterministic model predicts strong bipolar oscillations, in contradiction with the experimentally observed behavior, while the stochastic model, which is based on the same reaction-diffusion equations, predicts more spatially irregular oscillations. We further report simulations of flattened but more symmetric shapes, which suggest that the flattening and lateral expansion may contribute as much to the irregular oscillation behavior as the asymmetry of the cell shapes.
Collapse
Affiliation(s)
- Jeff B. Schulte
- Dept. of Physics, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Rene W. Zeto
- Dept. of Physics, Oregon State University, Corvallis, Oregon, United States of America
| | - David Roundy
- Dept. of Physics, Oregon State University, Corvallis, Oregon, United States of America
| |
Collapse
|
147
|
Park KT, Du S, Lutkenhaus J. MinC/MinD copolymers are not required for Min function. Mol Microbiol 2015; 98:895-909. [PMID: 26268537 DOI: 10.1111/mmi.13164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2015] [Indexed: 11/27/2022]
Abstract
In Escherichia coli, precise placement of the cytokinetic Z ring at midcell requires the concerted action of the three Min proteins. MinD activates MinC, an inhibitor of FtsZ, at least in part, by recruiting it to the membrane and targeting it to the Z ring, while MinE stimulates the MinD ATPase inducing an oscillation that directs MinC/MinD activity away from midcell. Recently, MinC and MinD were shown to form copolymers of alternating dimers of MinC and MinD, and it was suggested that these copolymers are the active form of MinC/MinD. Here, we use MinD mutants defective in binding MinC to generate heterodimers with wild-type MinD that are unable to form MinC/MinD copolymers. Similarly, MinC mutants defective in binding to MinD were used to generate heterodimers with wild-type MinC that are unable to form copolymers. Such heterodimers are active and in the case of MinC were shown to mediate spatial regulation of the Z ring demonstrating that MinC/MinD copolymer formation is not required. Our results are consistent with a model in which a membrane anchored MinC/MinD complex is targeted to the Z ring through the conserved carboxy tail of FtsZ leading to breakage of FtsZ filaments.
Collapse
Affiliation(s)
- Kyung-Tae Park
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Shishen Du
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Joe Lutkenhaus
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| |
Collapse
|
148
|
Haselwandter CA, Kardar M, Triller A, da Silveira RA. Self-assembly and plasticity of synaptic domains through a reaction-diffusion mechanism. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:032705. [PMID: 26465496 DOI: 10.1103/physreve.92.032705] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 06/05/2023]
Abstract
Signal transmission across chemical synapses relies crucially on neurotransmitter receptor molecules, concentrated in postsynaptic membrane domains along with scaffold and other postsynaptic molecules. The strength of the transmitted signal depends on the number of receptor molecules in postsynaptic domains, and activity-induced variation in the receptor number is one of the mechanisms of postsynaptic plasticity. Recent experiments have demonstrated that the reaction and diffusion properties of receptors and scaffolds at the membrane, alone, yield spontaneous formation of receptor-scaffold domains of the stable characteristic size observed in neurons. On the basis of these experiments we develop a model describing synaptic receptor domains in terms of the underlying reaction-diffusion processes. Our model predicts that the spontaneous formation of receptor-scaffold domains of the stable characteristic size observed in experiments depends on a few key reactions between receptors and scaffolds. Furthermore, our model suggests novel mechanisms for the alignment of pre- and postsynaptic domains and for short-term postsynaptic plasticity in receptor number. We predict that synaptic receptor domains localize in membrane regions with an increased receptor diffusion coefficient or a decreased scaffold diffusion coefficient. Similarly, we find that activity-dependent increases or decreases in receptor or scaffold diffusion yield a transient increase in the number of receptor molecules concentrated in postsynaptic domains. Thus, the proposed reaction-diffusion model puts forth a coherent set of biophysical mechanisms for the formation, stability, and plasticity of molecular domains on the postsynaptic membrane.
Collapse
Affiliation(s)
- Christoph A Haselwandter
- Departments of Physics & Astronomy and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Antoine Triller
- IBENS, Institute of Biology at Ecole Normale Supérieure, Inserm U1024, CNRS UMR5197, 46 rue d'Ulm, 75005 Paris, France
| | - Rava Azeredo da Silveira
- Department of Physics, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France
- Laboratoire de Physique Statistique, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, Université Denis Diderot, France
| |
Collapse
|
149
|
Tu Y, Zhang Z, Li D, Li H, Dong J, Wang T. Potato virus Y HC-Pro Reduces the ATPase Activity of NtMinD, Which Results in Enlarged Chloroplasts in HC-Pro Transgenic Tobacco. PLoS One 2015; 10:e0136210. [PMID: 26309250 PMCID: PMC4550256 DOI: 10.1371/journal.pone.0136210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 07/30/2015] [Indexed: 11/18/2022] Open
Abstract
Potato virus Y (PVY) is an important plant virus and causes great losses every year. Viral infection often leads to abnormal chloroplasts. The first step of chloroplast division is the formation of FtsZ ring (Z-ring), and the placement of Z-ring is coordinated by the Min system in both bacteria and plants. In our lab, the helper-component proteinase (HC-Pro) of PVY was previously found to interact with the chloroplast division protein NtMinD through a yeast two-hybrid screening assay and a bimolecular fluorescence complementation (BiFC) assay in vivo. Here, we further investigated the biological significance of the NtMinD/HC-Pro interaction. We purified the NtMinD and HC-Pro proteins using a prokaryotic protein purification system and tested the effect of HC-Pro on the ATPase activity of NtMinD in vitro. We found that the ATPase activity of NtMinD was reduced in the presence of HC-Pro. In addition, another important chloroplast division related protein, NtMinE, was cloned from the cDNA of Nicotiana tabacum. And the NtMinD/NtMinE interaction site was mapped to the C-terminus of NtMinD, which overlaps the NtMinD/HC-Pro interaction site. Yeast three-hybrid assay demonstrated that HC-Pro competes with NtMinE for binding to NtMinD. HC-Pro was previously reported to accumulate in the chloroplasts of PVY-infected tobacco and we confirmed this result in our present work. The NtMinD/NtMinE interaction is very important in the regulation of chloroplast division. To demonstrate the influence of HC-Pro on chloroplast division, we generated HC-Pro transgenic tobacco with a transit peptide to retarget HC-Pro to the chloroplasts. The HC-Pro transgenic plants showed enlarged chloroplasts. Our present study demonstrated that the interaction between HC-Pro and NtMinD interfered with the function of NtMinD in chloroplast division, which results in enlarged chloroplasts in HC-Pro transgenic tobacco. The HC-Pro/NtMinD interaction may cause the formation of abnormal chloroplasts in PVY-infected plants.
Collapse
Affiliation(s)
- Yayi Tu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Zhenqian Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Daofeng Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Heng Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| |
Collapse
|
150
|
Abstract
It is now well established that prokaryotic cells assemble diverse proteins into dynamic cytoskeletal filaments that perform essential cellular functions. Although most of the filaments assemble on their own to form higher order structures, growing evidence suggests that there are a number of prokaryotic proteins that polymerise only in the presence of a matrix such as DNA, lipid membrane or even another filament. Matrix-assisted filament systems are frequently nucleotide dependent and cytomotive but rarely considered as part of the bacterial cytoskeleton. Here, we categorise this family of filament-forming systems as collaborative filaments and introduce a simple nomenclature. Collaborative filaments are frequent in both eukaryotes and prokaryotes and are involved in vital cellular processes including chromosome segregation, DNA repair and maintenance, gene silencing and cytokinesis to mention a few. In this review, we highlight common principles underlying collaborative filaments and correlate these with known functions.
Collapse
Affiliation(s)
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, UK
| |
Collapse
|