1
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Homma M, Mizuno A, Hao Y, Kojima S. Functional analysis of the N-terminal region of Vibrio FlhG, a MinD-type ATPase in flagellar number control. J Biochem 2022; 172:99-107. [DOI: 10.1093/jb/mvac047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/17/2022] [Indexed: 11/12/2022] Open
Abstract
Summary
GTPase FlhF and ATPase FlhG are two key factors involved in regulating the flagellum number in Vibrio alginolyticus. FlhG is a paralog of the Escherichia coli cell division regulator MinD and has a longer N-terminal region than MinD with a conserved DQAxxLR motif. The deletion of this N-terminal region or a Q9A mutation in the DQAxxLR motif prevents FlhG from activating the GTPase activity of FlhF in vitro and causes a multi-flagellation phenotype. The mutant FlhG proteins, especially the N-terminally deleted variant, was remarkably reduced compared to that of the wild-type protein in vivo. When the mutant FlhG was expressed at the same level as the wild-type FlhG, the number of flagella was restored to the wild-type level. Once synthesized in Vibrio cells, the N-terminal region mutation in FlhG seems not to affect the protein stability. We speculated that the flhG translation efficiency is decreased by N-terminal mutation. Our results suggest that the N-terminal region of FlhG controls the number of flagella by adjusting the FlhF activity and the amount of FlhG in vivo. We speculate that the regulation by FlhG, achieved through transcription by the master regulator FlaK, is affected by the mutations, resulting in reduced flagellar formation by FlhF.
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Affiliation(s)
- Michio Homma
- Graduate School of Science Division of Biological Science, , Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Akira Mizuno
- Graduate School of Science Division of Biological Science, , Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yuxi Hao
- Graduate School of Science Division of Biological Science, , Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Seiji Kojima
- Graduate School of Science Division of Biological Science, , Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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2
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Levin PA, Janakiraman A. Localization, Assembly, and Activation of the Escherichia coli Cell Division Machinery. EcoSal Plus 2021; 9:eESP00222021. [PMID: 34910577 PMCID: PMC8919703 DOI: 10.1128/ecosalplus.esp-0022-2021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/14/2021] [Indexed: 01/01/2023]
Abstract
Decades of research, much of it in Escherichia coli, have yielded a wealth of insight into bacterial cell division. Here, we provide an overview of the E. coli division machinery with an emphasis on recent findings. We begin with a short historical perspective into the discovery of FtsZ, the tubulin homolog that is essential for division in bacteria and archaea. We then discuss assembly of the divisome, an FtsZ-dependent multiprotein platform, at the midcell septal site. Not simply a scaffold, the dynamic properties of polymeric FtsZ ensure the efficient and uniform synthesis of septal peptidoglycan. Next, we describe the remodeling of the cell wall, invagination of the cell envelope, and disassembly of the division apparatus culminating in scission of the mother cell into two daughter cells. We conclude this review by highlighting some of the open questions in the cell division field, emphasizing that much remains to be discovered, even in an organism as extensively studied as E. coli.
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Affiliation(s)
- Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Anuradha Janakiraman
- Department of Biology, The City College of New York, New York, New York, USA
- Programs in Biology and Biochemistry, The Graduate Center of the City University of New York, New York, New York, USA
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3
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Heermann T, Ramm B, Glaser S, Schwille P. Local Self-Enhancement of MinD Membrane Binding in Min Protein Pattern Formation. J Mol Biol 2020; 432:3191-3204. [PMID: 32199984 DOI: 10.1016/j.jmb.2020.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/07/2020] [Accepted: 03/09/2020] [Indexed: 01/06/2023]
Abstract
The proteins MinD, MinE and MinC are constitutive for the spatiotemporal organization of cell division in Escherichia coli, in particular, for positioning the division machinery at mid-cell. To achieve this function, the ATPase MinD and the ATPase-activating protein MinE undergo coordinated pole-to-pole oscillations and have thus become a paradigm for protein pattern formation in biology. The exact molecular mechanisms enabling MinDE self-organization, and particularly the role of cooperativity in the membrane binding of MinD, thought to be a key requirement, have remained poorly understood. However, for bottom-up synthetic biology aiming at a de novo design of key cellular features, elucidating these mechanisms is of great relevance. By combining in vitro reconstitution with rationally guided mutagenesis of MinD, we found that when bound to membranes, MinD displays new interfaces for multimerization, which are distinct from the canonical MinD dimerization site. We propose that these additional transient interactions contribute to the local self-enhancement of MinD at the membrane, while their relative lability maintains the structural plasticity required for MinDE wave propagation. This could represent a powerful structural regulation feature not reported so far for self-organizing proteins.
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Affiliation(s)
- Tamara Heermann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany
| | - Beatrice Ramm
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany
| | - Samson Glaser
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany.
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4
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Ramm B, Heermann T, Schwille P. The E. coli MinCDE system in the regulation of protein patterns and gradients. Cell Mol Life Sci 2019; 76:4245-4273. [PMID: 31317204 PMCID: PMC6803595 DOI: 10.1007/s00018-019-03218-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022]
Abstract
Molecular self-organziation, also regarded as pattern formation, is crucial for the correct distribution of cellular content. The processes leading to spatiotemporal patterns often involve a multitude of molecules interacting in complex networks, so that only very few cellular pattern-forming systems can be regarded as well understood. Due to its compositional simplicity, the Escherichia coli MinCDE system has, thus, become a paradigm for protein pattern formation. This biological reaction diffusion system spatiotemporally positions the division machinery in E. coli and is closely related to ParA-type ATPases involved in most aspects of spatiotemporal organization in bacteria. The ATPase MinD and the ATPase-activating protein MinE self-organize on the membrane as a reaction matrix. In vivo, these two proteins typically oscillate from pole-to-pole, while in vitro they can form a variety of distinct patterns. MinC is a passenger protein supposedly operating as a downstream cue of the system, coupling it to the division machinery. The MinCDE system has helped to extract not only the principles underlying intracellular patterns, but also how they are shaped by cellular boundaries. Moreover, it serves as a model to investigate how patterns can confer information through specific and non-specific interactions with other molecules. Here, we review how the three Min proteins self-organize to form patterns, their response to geometric boundaries, and how these patterns can in turn induce patterns of other molecules, focusing primarily on experimental approaches and developments.
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Affiliation(s)
- Beatrice Ramm
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Tamara Heermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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5
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Maclean AE, Kimonis VE, Balk J. Pathogenic mutations in NUBPL affect complex I activity and cold tolerance in the yeast model Yarrowia lipolytica. Hum Mol Genet 2019; 27:3697-3709. [PMID: 29982452 PMCID: PMC6196649 DOI: 10.1093/hmg/ddy247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/22/2018] [Indexed: 11/26/2022] Open
Abstract
Complex I deficiency is a common cause of mitochondrial disease, resulting from mutations in genes encoding structural subunits, assembly factors or defects in mitochondrial gene expression. Advances in genetic diagnostics and sequencing have led to identification of several variants in NUBPL (nucleotide binding protein-like), encoding an assembly factor of complex I, which are potentially pathogenic. To help assign pathogenicity and learn more about the function of NUBPL, amino acid substitutions were recreated in the homologous Ind1 protein of the yeast model Yarrowia lipolytica. Leu102Pro destabilized the Ind1 protein, leading to a null-mutant phenotype. Asp103Tyr, Leu191Phe and Gly285Cys affected complex I assembly to varying degrees, whereas Gly136Asp substitution in Ind1 did not impact on complex I levels nor dNADH:ubiquinone activity. Blue-native polyacrylamide gel electrophoresis and immunolabelling of the structural subunits NUBM and NUCM revealed that all Ind1 variants accumulated a Q module intermediate of complex I. In the Ind1 Asp103Tyr variant, the matrix arm intermediate was virtually absent, indicating a dominant effect. Dysfunction of Ind1, but not absence of complex I, rendered Y. lipolytica sensitive to cold. The Ind1 Gly285Cys variant was able to support complex I assembly at 28°C, but not at 10°C. Our results indicate that Ind1 is required for progression of assembly from the Q module to the full matrix arm. Cold sensitivity could be developed as a phenotype assay to demonstrate pathogenicity of NUBPL mutations and other complex I defects.
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Affiliation(s)
- Andrew E Maclean
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK.,School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Virginia E Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, USA.,Children's Hospital of Orange County, Orange, CA, USA
| | - Janneke Balk
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK.,School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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6
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Grossman JD, Gay KA, Camire EJ, Walden WE, Perlstein DL. Coupling Nucleotide Binding and Hydrolysis to Iron-Sulfur Cluster Acquisition and Transfer Revealed through Genetic Dissection of the Nbp35 ATPase Site. Biochemistry 2019; 58:2017-2027. [PMID: 30865432 DOI: 10.1021/acs.biochem.8b00737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cytosolic iron-sulfur cluster assembly (CIA) scaffold, comprising Nbp35 and Cfd1 in yeast, assembles iron-sulfur (FeS) clusters destined for cytosolic and nuclear enzymes. ATP hydrolysis by the CIA scaffold plays an essential but poorly understood role in cluster biogenesis. Here we find that mutation of conserved residues in the four motifs comprising the ATPase site of Nbp35 diminished the scaffold's ability to both assemble and transfer its FeS cluster in vivo. The mutants fall into four phenotypic classes that can be understood by how each set of mutations affects ATP binding and hydrolysis. In vitro studies additionally revealed that occupancy of the bridging FeS cluster binding site decreases the scaffold's affinity for the nucleotide. On the basis of our findings, we propose that nucleotide binding and hydrolysis by the CIA scaffold drive a series of protein conformational changes that regulate association with other proteins in the pathway and with its newly formed FeS cluster. Our results provide insight into how the ATPase and cluster scaffolding activities are allosterically integrated.
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Affiliation(s)
- John D Grossman
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Kelly A Gay
- Department of Microbiology and Immunology , University of Illinois at Chicago , Chicago , Illinois 60612 , United States
| | - Eric J Camire
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - William E Walden
- Department of Microbiology and Immunology , University of Illinois at Chicago , Chicago , Illinois 60612 , United States
| | - Deborah L Perlstein
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
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7
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MacCready JS, Schossau J, Osteryoung KW, Ducat DC. Robust Min-system oscillation in the presence of internal photosynthetic membranes in cyanobacteria. Mol Microbiol 2016; 103:483-503. [PMID: 27891682 DOI: 10.1111/mmi.13571] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2016] [Indexed: 11/29/2022]
Abstract
The oscillatory Min system of Escherichia coli defines the cell division plane by regulating the site of FtsZ-ring formation and represents one of the best-understood examples of emergent protein self-organization in nature. The oscillatory patterns of the Min-system proteins MinC, MinD and MinE (MinCDE) are strongly dependent on the geometry of membranes they bind. Complex internal membranes within cyanobacteria could disrupt this self-organization by sterically occluding or sequestering MinCDE from the plasma membrane. Here, it was shown that the Min system in the cyanobacterium Synechococcus elongatus PCC 7942 oscillates from pole-to-pole despite the potential spatial constraints imposed by their extensive thylakoid network. Moreover, reaction-diffusion simulations predict robust oscillations in modeled cyanobacterial cells provided that thylakoid network permeability is maintained to facilitate diffusion, and suggest that Min proteins require preferential affinity for the plasma membrane over thylakoids to correctly position the FtsZ ring. Interestingly, in addition to oscillating, MinC exhibits a midcell localization dependent on MinD and the DivIVA-like protein Cdv3, indicating that two distinct pools of MinC are coordinated in S. elongatus. Our results provide the first direct evidence for Min oscillation outside of E. coli and have broader implications for Min-system function in bacteria and organelles with internal membrane systems.
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Affiliation(s)
- Joshua S MacCready
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Jory Schossau
- Department of Computer Science, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Daniel C Ducat
- Department of Biochemistry, MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
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8
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Camire EJ, Grossman JD, Thole GJ, Fleischman NM, Perlstein DL. The Yeast Nbp35-Cfd1 Cytosolic Iron-Sulfur Cluster Scaffold Is an ATPase. J Biol Chem 2015. [PMID: 26195633 DOI: 10.1074/jbc.m115.667022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nbp35 and Cfd1 are prototypical members of the MRP/Nbp35 class of iron-sulfur (FeS) cluster scaffolds that function to assemble nascent FeS clusters for transfer to FeS-requiring enzymes. Both proteins contain a conserved NTPase domain that genetic studies have demonstrated is essential for their cluster assembly activity inside the cell. It was recently reported that these proteins possess no or very low nucleotide hydrolysis activity in vitro, and thus the role of the NTPase domain in cluster biogenesis has remained uncertain. We have reexamined the NTPase activity of Nbp35, Cfd1, and their complex. Using in vitro assays and site-directed mutagenesis, we demonstrate that the Nbp35 homodimer and the Nbp35-Cfd1 heterodimer are ATPases, whereas the Cfd1 homodimer exhibited no or very low ATPase activity. We ruled out the possibility that the observed ATP hydrolysis activity might result from a contaminating ATPase by showing that mutation of key active site residues reduced activity to background levels. Finally, we demonstrate that the fluorescent ATP analog 2'/3'-O-(N'-methylanthraniloyl)-ATP (mantATP) binds stoichiometrically to Nbp35 with a KD = 15.6 μM and that an Nbp35 mutant deficient in ATP hydrolysis activity also displays an increased KD for mantATP. Together, our results demonstrate that the cytosolic iron-sulfur cluster assembly scaffold is an ATPase and pave the way for interrogating the role of nucleotide hydrolysis in cluster biogenesis by this large family of cluster scaffolding proteins found across all domains of life.
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Affiliation(s)
- Eric J Camire
- From the Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | - John D Grossman
- From the Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | - Grace J Thole
- From the Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | | | - Deborah L Perlstein
- From the Department of Chemistry, Boston University, Boston, Massachusetts 02215
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9
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MinCD cell division proteins form alternating copolymeric cytomotive filaments. Nat Commun 2014; 5:5341. [PMID: 25500731 PMCID: PMC4338524 DOI: 10.1038/ncomms6341] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/20/2014] [Indexed: 11/28/2022] Open
Abstract
During bacterial cell division, filaments of the tubulin-like protein FtsZ assemble at midcell to form the cytokinetic Z-ring. Its positioning is regulated by the oscillation of MinCDE proteins. MinC is activated by MinD through an unknown mechanism and prevents Z-ring assembly anywhere but midcell. Here, using X-ray crystallography, electron microscopy and in vivo analyses we show that MinD activates MinC by forming a new class of alternating copolymeric filaments that show similarity to eukaryotic septin filaments A non-polymerising mutation in MinD causes aberrant cell division in E. coli. MinCD copolymers bind to membrane, interact with FtsZ, and are disassembled by MinE. Imaging a functional msfGFP-MinC fusion protein in MinE deleted cells reveals filamentous structures. EM imaging of our reconstitution of the MinCD-FtsZ interaction on liposome surfaces reveals a plausible mechanism for regulation of FtsZ ring assembly by MinCD copolymers.
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10
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Basak I, Møller SG. Emerging facets of plastid division regulation. PLANTA 2013; 237:389-98. [PMID: 22965912 DOI: 10.1007/s00425-012-1743-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 08/19/2012] [Indexed: 05/08/2023]
Abstract
Plastids are complex organelles that are integrated into the plant host cell where they differentiate and divide in tune with plant differentiation and development. In line with their prokaryotic origin, plastid division involves both evolutionary conserved proteins and proteins of eukaryotic origin where the host has acquired control over the process. The plastid division apparatus is spatially separated between the stromal and the cytosolic space but where clear coordination mechanisms exist between the two machineries. Our knowledge of the plastid division process has increased dramatically during the past decade and recent findings have not only shed light on plastid division enzymology and the formation of plastid division complexes but also on the integration of the division process into a multicellular context. This review summarises our current knowledge of plastid division with an emphasis on biochemical features, the functional assembly of protein complexes and regulatory features of the overall process.
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Affiliation(s)
- Indranil Basak
- Department of Biological Sciences, St John's University, 8000 Utopia Parkway, NY 11439, USA
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11
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Perez-Cheeks BA, Planet PJ, Sarkar IN, Clock SA, Xu Q, Figurski DH. The product of tadZ, a new member of the parA/minD superfamily, localizes to a pole in Aggregatibacter actinomycetemcomitans. Mol Microbiol 2012; 83:694-711. [PMID: 22239271 DOI: 10.1111/j.1365-2958.2011.07955.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Aggregatibacter actinomycetemcomitans establishes a tenacious biofilm that is important for periodontal disease. The tad locus encodes the components for the secretion and biogenesis of Flp pili, which are necessary for the biofilm to form. TadZ is required, but its function has been elusive. We show that tadZ genes belong to the parA/minD superfamily of genes and that TadZ from A. actinomycetemcomitans (AaTadZ) forms a polar focus in the cell independent of any other tad locus protein. Mutations indicate that regions in AaTadZ are required for polar localization and biofilm formation. We show that AaTadZ dimerizes and that all TadZ proteins are predicted to have a Walker-like A box. However, they all lack the conserved lysine at position 6 (K6) present in the canonical Walker-like A box. When the alanine residue (A6) in the atypical Walker-like A box of AaTadZ was converted to lysine, the mutant protein remained able to dimerize and localize, but it was unable to allow the formation of a biofilm. Another essential biofilm protein, the ATPase (AaTadA), also localizes to a pole. However, its correct localization depends on the presence of AaTadZ. We suggest that the TadZ proteins mediate polar localization of the Tad secretion apparatus.
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Affiliation(s)
- Brenda A Perez-Cheeks
- Department of Microbiology & Immunology, College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
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12
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Okuno T, Ohgita T, Sasa T, Nonaka A, Funasaki N, Kogure K. Fluorescence polarization analysis for revealing molecular mechanism of nucleotide-dependent phospholipid membrane binding of MinD adenosine 5'-triphosphate, adenosine triphosphatase. Biol Pharm Bull 2011; 33:1746-50. [PMID: 20930386 DOI: 10.1248/bpb.33.1746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Membrane binding of Walker type adenosine 5'-triphosphate, adenosine triphosphatase (ATPase), MinD, is a key step in regulating the site of cell division in Escherichia coli. Two lysine residues (K11, K16) in the Walker A motif of MinD have been suggested to be essential for both membrane binding and ATPase activity, but the relationship between the membrane binding of MinD and its ATPase activity is still unclear. To reveal the role of K11 and K16 in MinD membrane interaction and ATP-binding, we compared the functionality of wild-type MinD (WT) and two MinD mutants that lack ATPase activity, where alanine was substituted for lysine at positions 11 and 16 (K11A, K16A), using liposomes and fluorescent-labeled ATP. The ATP dissociation constant (K(d)) of wild-type MinD was 4.9 µM. Unexpectedly, the K(d) values of the two lysine mutants were almost the same as that of wild type, indicating that ATP can bind to MinD mutants, even though these mutants showed no ATPase activity and membrane binding ability. Our results presumed that K11 and K16 residues might play an important role in dimmer formation of MinD, but not ATP binding step, for recruiting to membrane.
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Affiliation(s)
- Takashi Okuno
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Japan.
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13
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Arjunan SNV, Tomita M. A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation. SYSTEMS AND SYNTHETIC BIOLOGY 2009; 4:35-53. [PMID: 20012222 PMCID: PMC2816228 DOI: 10.1007/s11693-009-9047-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 10/06/2009] [Accepted: 10/08/2009] [Indexed: 11/25/2022]
Abstract
Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization patterns of molecules in fluorescence microscopy images with simulation, we devised a visualization method that mimics the microphotography process by showing the trajectory of simulated molecules averaged according to the camera exposure time. In the rod-shaped bacterium Escherichia coli, the division site is suppressed at the cell poles by periodic pole-to-pole oscillations of the Min proteins (MinC, MinD and MinE) arising from carefully orchestrated RD in both cytoplasm and membrane compartments. Using Spatiocyte we could model and reproduce the in vivo MinDE localization dynamics by accounting for the previously reported properties of MinE. Our results suggest that the MinE ring, which is essential in preventing polar septation, is largely composed of MinE that is transiently attached to the membrane independently after recruited by MinD. Overall, Spatiocyte allows simulation and visualization of complex spatial and reaction-diffusion mediated cellular processes in volumes and surfaces. As we showed, it can potentially provide mechanistic insights otherwise difficult to obtain experimentally.
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Affiliation(s)
- Satya Nanda Vel Arjunan
- Institute for Advanced Biosciences, Keio University, Baba-cho 14-1, Tsuruoka, 997-0035 Yamagata Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-8520 Kanagawa Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Baba-cho 14-1, Tsuruoka, 997-0035 Yamagata Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-8520 Kanagawa Japan
- Department of Environment and Information, Keio University, Fujisawa, 252-8520 Kanagawa Japan
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14
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Adams S, Maple J, Møller SG. Functional conservation of the MIN plastid division homologues of Chlamydomonas reinhardtii. PLANTA 2008; 227:1199-1211. [PMID: 18270733 DOI: 10.1007/s00425-008-0692-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Accepted: 01/18/2008] [Indexed: 05/25/2023]
Abstract
Chloroplasts arise by binary fission from pre-existing plastids, thus division plays a key role in the development of these essential photosynthetic organelles. To ensure that actively dividing tissues accumulate large numbers of chloroplasts prior to cell division, chloroplast division and the cell cycle must be intimately linked. However, little is known about the regulation of the plastid division machinery during cell division and these questions are difficult to address in higher plants. For this purpose we have studied the unicellular green alga Chlamydomonas reinhardtii for its potential as a new system for chloroplast division research. Here we show the functional conservation of key components of the higher plant chloroplast machinery in Chlamydomonas. The highly conserved Chlamydomonas MinD homologue, CrMinD1, retains crucial protein-protein interactions, sub-cellular localisation and the ability to affect both higher plant plastid division and bacterial cell division. Furthermore, using the coupling of chloroplast and cell division in Chlamydomonas we have established that transcript levels of chloroplast division homologues significantly increase during cell division, with levels falling as division reaches completion.
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Affiliation(s)
- Sally Adams
- Department of Biology, University of Leicester, Leicester, LE1 7RH, UK
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15
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Dajkovic A, Lan G, Sun SX, Wirtz D, Lutkenhaus J. MinC Spatially Controls Bacterial Cytokinesis by Antagonizing the Scaffolding Function of FtsZ. Curr Biol 2008; 18:235-44. [DOI: 10.1016/j.cub.2008.01.042] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 12/21/2007] [Accepted: 01/04/2008] [Indexed: 10/22/2022]
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Abstract
BACKGROUND The continuity of chloroplasts is maintained by division of pre-existing chloroplasts. Chloroplasts originated as bacterial endosymbionts; however, the majority of bacterial division factors are absent from chloroplasts and the eukaryotic host has added several new components. For example, the ftsZ gene has been duplicated and modified, and the Min system has retained MinE and MinD but lost MinC, acquiring at least one new component ARC3. Further, the mechanism has evolved to include two members of the dynamin protein family, ARC5 and FZL, and plastid-dividing (PD) rings were most probably added by the eukaryotic host. SCOPE Deciphering how the division of plastids is coordinated and controlled by nuclear-encoded factors is key to our understanding of this important biological process. Through a number of molecular-genetic and biochemical approaches, it is evident that FtsZ initiates plastid division where the coordinated action of MinD and MinE ensures correct FtsZ (Z)-ring placement. Although the classical FtsZ antagonist MinC does not exist in plants, ARC3 may fulfil this role. Together with other prokaryotic-derived proteins such as ARC6 and GC1 and key eukaryotic-derived proteins such as ARC5 and FZL, these proteins make up a sophisticated division machinery. The regulation of plastid division in a cellular context is largely unknown; however, recent microarray data shed light on this. Here the current understanding of the mechanism of chloroplast division in higher plants is reviewed with an emphasis on how recent findings are beginning to shape our understanding of the function and evolution of the components. CONCLUSIONS Extrapolation from the mechanism of bacterial cell division provides valuable clues as to how the chloroplast division process is achieved in plant cells. However, it is becoming increasingly clear that the highly regulated mechanism of plastid division within the host cell has led to the evolution of features unique to the plastid division process.
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Abstract
Division site placement in Escherichia coli involves interactions of the MinD protein with MinC and MinE and with other MinD molecules to form membrane-associated polymeric structures. In this work, as part of a study of these interactions, we established that heterologous membrane-associated proteins such as MinD can be targeted to the yeast nuclear membrane, dependent only on the presence of a membrane-binding domain and a nuclear targeting sequence. Targeting to the nuclear membrane was equally effective using the intrinsic MinD membrane-targeting domain or the completely unrelated membrane-targeting domain of cytochrome b(5). The chimeric proteins differing in their membrane-targeting sequences were then used to establish the roles of membrane association and specificity of the membrane anchor in MinD interactions, using the yeast two-hybrid system. The chimeric proteins were also used to show that the membrane association of MinD and MinE in E. coli cells had no specificity for the membrane anchor, whereas formation of MinDE polar zones and MinE rings required the presence of the native MinD membrane-targeting sequence.
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Affiliation(s)
- Aziz Taghbalout
- Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, Farmington, CT 06032, USA.
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18
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Eng NF, Szeto J, Acharya S, Tessier D, Dillon JAR. The C-terminus of MinE from Neisseria gonorrhoeae acts as a topological specificity factor by modulating MinD activity in bacterial cell division. Res Microbiol 2005; 157:333-44. [PMID: 16376524 DOI: 10.1016/j.resmic.2005.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Revised: 07/27/2005] [Accepted: 09/19/2005] [Indexed: 11/30/2022]
Abstract
MinE regulates the proper placement of the cytokinetic FtsZ ring at midcell by inducing the pole-to-pole movement of MinCD complexes. While the N-terminus of MinE has been implicated in MinD binding, a clear functional role of the C-terminus has not been elucidated. We previously determined that MinE from Neisseria gonorrhoeae (Ng) was functional in Escherichia coli (Ec). Thus, using E. coli as a model organism, gonococcal MinE (MinE(Ng)) function was examined by generating amino acid substitutions of highly conserved MinE(Ng) residues and by testing the ability of the mutant proteins to interact with gonococcal MinD (MinD(Ng)), to induce a minicell phenotype upon overexpression, to initiate MinD(Ng) oscillation, and to stimulate MinD(Ng) ATPase activity. N-terminal MinE(Ng) mutants were unable to bind to MinD(Ng); thus, they did not induce a minicell phenotype, promote MinD(Ng) oscillation or stimulate MinD(Ng) ATPase activity. While C-terminal MinE(Ng) mutants exhibited reduced abilities to bind to MinD(Ng), we show that differences in MinD(Ng) binding to the C-terminus of MinE(Ng) alter the ability of MinE(Ng) to properly stimulate MinD(Ng) activity. We present four major findings from our studies of MinE(Ng): both the N- and C-termini of MinE(Ng) interact with MinD(Ng); interaction between MinD(Ng) and MinE(Ng) is required for the recruitment of MinD(Ng) to the coiled array; oscillation of MinD(Ng) does not require ATPase stimulation; and, the extent of MinD(Ng) ATPase stimulation depends on the binding strength between MinD(Ng) and the C-terminus of MinE(Ng.).
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Affiliation(s)
- Nelson F Eng
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
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19
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Pichoff S, Lutkenhaus J. Tethering the Z ring to the membrane through a conserved membrane targeting sequence in FtsA. Mol Microbiol 2005; 55:1722-34. [PMID: 15752196 DOI: 10.1111/j.1365-2958.2005.04522.x] [Citation(s) in RCA: 324] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cytokinetic Z ring is required for bacterial cell division. It consists of polymers of FtsZ, the bacterial ancestor of eukaryotic tubulin, linked to the cytoplasmic membrane. Formation of a Z ring in Escherichia coli occurs as long as one of two proteins, ZipA or FtsA, is present. Both of these proteins bind FtsZ suggesting that they might function to tether FtsZ filaments to the membrane. Although ZipA has a transmembrane domain and therefore can function as a membrane anchor, interaction of FtsA with the membrane has not been explored. In this study we demonstrate that FtsA, which is structurally related to eukaryotic actin, has a conserved C-terminal amphipathic helix that is essential for FtsA function. It is required to target FtsA to the membrane and subsequently to the Z ring. As FtsA is much more widely conserved in bacteria than ZipA, it is likely that FtsA serves as the principal membrane anchor for the Z ring.
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Affiliation(s)
- Sebastien Pichoff
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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20
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Aldridge C, Møller SG. The plastid division protein AtMinD1 is a Ca2+-ATPase stimulated by AtMinE1. J Biol Chem 2005; 280:31673-8. [PMID: 16014621 DOI: 10.1074/jbc.m505126200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteria and plastids divide symmetrically through binary fission by accurately placing the division site at midpoint, a process initiated by FtsZ polymerization, which forms a Z-ring. In Escherichia coli precise Z-ring placement at midcell depends on controlled oscillatory behavior of MinD and MinE: In the presence of ATP MinD interacts with the FtsZ inhibitor MinC and migrates to the membrane where the MinD-MinC complex recruits MinE, followed by MinD-mediated ATP hydrolysis and membrane release. Although correct Z-ring placement during Arabidopsis plastid division depends on the precise localization of the bacterial homologs AtMinD1 and AtMinE1, the underlying mechanism of this process remains unknown. Here we have shown that AtMinD1 is a Ca2+-dependent ATPase and through mutation analysis demonstrated the physiological importance of this activity where loss of ATP hydrolysis results in protein mislocalization within plastids. The observed mislocalization is not due to disrupted AtMinD1 dimerization, however; the active site AtMinD1(K72A) mutant is unable to interact with the topological specificity factor AtMinE1. We have shown that AtMinE1, but not E. coli MinE, stimulates AtMinD1-mediated ATP hydrolysis, but in contrast to prokaryotes stimulation occurs in the absence of membrane lipids. Although AtMinD1 appears highly evolutionarily conserved, we found that important biochemical and cell biological properties have diverged. We propose that correct intraplastidic AtMinD1 localization is dependent on AtMinE1-stimulated, Ca2+-dependent AtMinD1 ATP hydrolysis, ultimately ensuring precise Z-ring placement and symmetric plastid division.
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Affiliation(s)
- Cassie Aldridge
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
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21
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Zhou H, Lutkenhaus J. MinC mutants deficient in MinD- and DicB-mediated cell division inhibition due to loss of interaction with MinD, DicB, or a septal component. J Bacteriol 2005; 187:2846-57. [PMID: 15805531 PMCID: PMC1070367 DOI: 10.1128/jb.187.8.2846-2857.2005] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The min locus encodes a negative regulatory system that limits formation of the cytokinetic Z ring to midcell by preventing its formation near the poles. Of the three Min proteins, MinC is the inhibitor and prevents Z-ring formation by interacting directly with FtsZ. MinD activates MinC by recruiting it to the membrane and conferring a higher affinity on the MinCD complex for a septal component. MinE regulates the cellular location of MinCD by inducing MinD, and thereby MinC, to oscillate between the poles of the cell, resulting in a time-averaged concentration of MinCD on the membrane that is lowest at midcell. MinC can also be activated by the prophage-encoded protein DicB, which targets MinC to the septum without recruiting it first to the membrane. Previous studies have shown that the C-terminal domain of MinC is responsible for the interaction with MinD, DicB, and the septal component. In the present study, we isolated mutations in the C-terminal domain of MinC that affected its interaction with MinD, DicB, and the septal component. Among the mutations isolated, R133A and S134A are specifically deficient in the interaction with MinD, E156A is primarily affected in the interaction with DicB, and R172A is primarily deficient in the interaction with the septum. These mutations differentiate the interactions of MinC with its partners and further support the model of MinCD- and MinC-DicB-mediated cell division inhibition.
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Affiliation(s)
- Huaijin Zhou
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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22
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Szeto J, Eng NF, Acharya S, Rigden MD, Dillon JAR. A conserved polar region in the cell division site determinant MinD is required for responding to MinE-induced oscillation but not for localization within coiled arrays. Res Microbiol 2005; 156:17-29. [PMID: 15636744 DOI: 10.1016/j.resmic.2004.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Accepted: 07/20/2004] [Indexed: 10/26/2022]
Abstract
A region in the cell division site determinant MinD required for stimulation by MinE and which determines MinD topological specificity along coil-like structures has been identified. Structural modeling of dimeric MinD and sequence alignment of 24 MinD proteins revealed a conserved polar region in Gram-negative bacterial MinD proteins, corresponding to residues 92-94 of Neisseria gonorrhoeae MinD (MinD(Ng)). Using MinD(Ng) as a paradigm for MinD functionality in Gram-negative organisms, mutation of these conserved residues did not abrogate MinD(Ng) self-association, nor its interaction with MinE(Ng) and the cell division inhibitor MinC. Although the MinD(Ng) mutant dimerized in the presence of ATP, its ATPase activity was not stimulated by MinE(Ng), unlike wild-type MinD(Ng). GFP fusions to either MinD(Ng) or to Escherichia coli MinD bearing simultaneous or individual mutations to residues 92-94 localized within coiled arrays along the E. coli inner cell periphery, similar to wild-type GFP-MinD. However, unlike wild-type GFP-fusions, the mutant proteins were distributed uniformly throughout the array, despite the presence of MinE, which normally imparts topological specificity to MinD by inducing the latter to oscillate from pole-to-pole and away from midcell. Hence, despite localizing along the inner cell periphery as a polymeric structure, the mutant MinD proteins in this study have lost the ability to be efficiently stimulated by MinE(Ng), resulting in a loss of distinct pole-to-pole oscillation.
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Affiliation(s)
- Jason Szeto
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
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Zhou H, Schulze R, Cox S, Saez C, Hu Z, Lutkenhaus J. Analysis of MinD mutations reveals residues required for MinE stimulation of the MinD ATPase and residues required for MinC interaction. J Bacteriol 2005; 187:629-38. [PMID: 15629934 PMCID: PMC543533 DOI: 10.1128/jb.187.2.629-638.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The MinD ATPase is critical to the oscillation of the Min proteins, which limits formation of the Z ring to midcell. In the presence of ATP, MinD binds to the membrane and recruits MinC, forming a complex that can destabilize the cytokinetic Z ring. MinE, which is also recruited to the membrane by MinD, displaces MinC and stimulates the MinD ATPase, resulting in the oscillation of the Min proteins. In this study we have investigated the role of lysine 11, present in the deviant Walker A motif of MinD, and the three residues in helix 7 (E146, S148, and D152) that interact electrostatically with lysine 11. Lysine 11 is required for interaction of MinD with the membrane, MinC, MinE, and itself. In contrast, the three residues in helix 7 that interact with lysine 11 are not required for binding to the membrane or activation of MinC. They are also not required for MinE binding; however, they are required for MinE to stimulate the MinD ATPase. Interestingly, the D152A mutant self-interacts, binds to the membrane, and recruits MinC and MinE in the presence of ADP as well as ATP. This mutant provides evidence that dimerization of MinD is sufficient for MinD to bind the membrane and recruit its partners.
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Affiliation(s)
- Huaijin Zhou
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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