1
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Marcus EA, Sachs G, Scott DR. Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization. Helicobacter 2018; 23:e12490. [PMID: 29696729 PMCID: PMC5980792 DOI: 10.1111/hel.12490] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The pathogen Helicobacter pylori encounters many stressors as it transits to and infects the gastric epithelium. Gastric acidity is the predominate stressor encountered by the bacterium during initial infection and establishment of persistent infection. H. pylori initiates a rapid response to acid to maintain intracellular pH and proton motive force appropriate for a neutralophile. However, acid sensing by H. pylori may also serve as a transcriptional trigger to increase the levels of other pathogenic factors needed to subvert host defenses such as acid acclimation, antioxidants, flagellar synthesis and assembly, and CagA secretion. MATERIALS AND METHODS Helicobacter pylori were acid challenged at pH 3.0, 4.5, 6.0 vs nonacidic pH for 4 hours in the presence of urea, followed by RNA-seq analysis and qPCR. Cytoplasmic pH was monitored under the same conditions. RESULTS About 250 genes were induced, and an equal number were repressed at acidic pHs. Genes encoding for antioxidant proteins, flagellar structural proteins, particularly class 2 genes, T4SS/Cag-PAI, Fo F1 -ATPase, and proteins involved in acid acclimation were highly expressed at acidic pH. Cytoplasmic pH decreased from 7.8 at pHout of 8.0 to 6.0 at pHout of 3.0. CONCLUSIONS These results suggest that increasing extracellular or intracellular acidity or both are detected by the bacterium and serve as a signal to initiate increased production of protective and pathogenic factors needed to counter host defenses for persistent infection. These changes are dependent on degree of acidity and time of acid exposure, triggering a coordinated response to the environment required for colonization.
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Affiliation(s)
- Elizabeth A. Marcus
- Department of Pediatrics, David Geffen School of Medicine at UCLA,VA GLAHS, Los Angeles, CA
| | - George Sachs
- Department Medicine, David Geffen School of Medicine at UCLA,Department Physiology, David Geffen School of Medicine at UCLA,VA GLAHS, Los Angeles, CA
| | - David R. Scott
- Department Physiology, David Geffen School of Medicine at UCLA,VA GLAHS, Los Angeles, CA,Corresponding author: David R. Scott, Department of Physiology, DGSOM at UCLA, VA GLAHS, Bldg 113, Rm 324, 11301 Wilshire Blvd, Los Angeles, CA 90073, , phone: 310-478-3711 x42046; Fax: 310-312-9478
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2
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Kóbori TO, Uzumaki T, Kis M, Kovács L, Domonkos I, Itoh S, Krynická V, Kuppusamy SG, Zakar T, Dean J, Szilák L, Komenda J, Gombos Z, Ughy B. Phosphatidylglycerol is implicated in divisome formation and metabolic processes of cyanobacteria. JOURNAL OF PLANT PHYSIOLOGY 2018; 223:96-104. [PMID: 29558689 DOI: 10.1016/j.jplph.2018.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 06/08/2023]
Abstract
Phosphatidylglycerol is an essential phospholipid for photosynthesis and other cellular processes. We investigated the role of phosphatidylglycerol in cell division and metabolism in a phophatidylglycerol-auxotrophic strain of Synechococcus PCC7942. Here we show that phosphatidylglycerol is essential for the photosynthetic electron transfer and for the oligomerisation of the photosynthetic complexes, notably, we revealed that this lipid is important for non-linear electron transport. Furthermore, we demonstrate that phosphatidylglycerol starvation elevated the expressions of proteins of nitrogen and carbon metabolism. Moreover, we show that phosphatidylglycerol-deficient cells changed the morphology, became elongated, the FtsZ ring did not assemble correctly, and subsequently the division was hindered. However, supplementation with phosphatidylglycerol restored the ring-like structure at the mid-cell region and the normal cell size, demonstrating the phosphatidylglycerol is needed for normal septum formation. Taken together, central roles of phosphatidylglycerol were revealed; it is implicated in the photosynthetic activity, the metabolism and the fission of bacteria.
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Affiliation(s)
- Tímea O Kóbori
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary; Doctoral School of Biology, University of Szeged, H-6726 Szeged, Hungary
| | - Tatsuya Uzumaki
- Center for Gene Research, Nagoya University, Furocyo, Chikusa, Nagoya 464-8607, Japan
| | - Mihály Kis
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - László Kovács
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - Ildikó Domonkos
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - Shigeru Itoh
- Center for Gene Research, Nagoya University, Furocyo, Chikusa, Nagoya 464-8607, Japan
| | - Vendula Krynická
- Institute of Microbiology, Center Algatech, Czech Academy of Sciences, Opatovický mlýn, 37981 Třeboň, Czech Republic
| | - Saravanan G Kuppusamy
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - Tomas Zakar
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - Jason Dean
- Institute of Microbiology, Center Algatech, Czech Academy of Sciences, Opatovický mlýn, 37981 Třeboň, Czech Republic
| | - László Szilák
- Institute of Biology, Savaria Campus, Eötvös Lorand University, Szombathely, H-9700, Hungary
| | - Josef Komenda
- Institute of Microbiology, Center Algatech, Czech Academy of Sciences, Opatovický mlýn, 37981 Třeboň, Czech Republic
| | - Zoltán Gombos
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - Bettina Ughy
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary.
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3
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Mizuuchi K, Vecchiarelli AG. Mechanistic insights of the Min oscillator via cell-free reconstitution and imaging. Phys Biol 2018; 15:031001. [PMID: 29188788 DOI: 10.1088/1478-3975/aa9e5e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The MinD and MinE proteins of Escherichia coli self-organize into a standing-wave oscillator on the membrane to help align division at mid-cell. When unleashed from cellular confines, MinD and MinE form a spectrum of patterns on artificial bilayers-static amoebas, traveling waves, traveling mushrooms, and bursts with standing-wave dynamics. We recently focused our cell-free studies on bursts because their dynamics recapitulate many features of Min oscillation observed in vivo. The data unveiled a patterning mechanism largely governed by MinE regulation of MinD interaction with membrane. We proposed that the MinD to MinE ratio on the membrane acts as a toggle switch between MinE-stimulated recruitment and release of MinD from the membrane. In this review, we summarize cell-free data on the Min system and expand upon a molecular mechanism that provides a biochemical explanation as to how these two 'simple' proteins can form the remarkable spectrum of patterns.
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Affiliation(s)
- Kiyoshi Mizuuchi
- Laboratory of Molecular Biology, National Institute of Diabetes, and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States of America
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4
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Walsh JC, Angstmann CN, Duggin IG, Curmi PMG. Non-linear Min protein interactions generate harmonics that signal mid-cell division in Escherichia coli. PLoS One 2017; 12:e0185947. [PMID: 29040283 PMCID: PMC5645087 DOI: 10.1371/journal.pone.0185947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/21/2017] [Indexed: 11/18/2022] Open
Abstract
The Min protein system creates a dynamic spatial pattern in Escherichia coli cells where the proteins MinD and MinE oscillate from pole to pole. MinD positions MinC, an inhibitor of FtsZ ring formation, contributing to the mid-cell localization of cell division. In this paper, Fourier analysis is used to decompose experimental and model MinD spatial distributions into time-dependent harmonic components. In both experiment and model, the second harmonic component is responsible for producing a mid-cell minimum in MinD concentration. The features of this harmonic are robust in both experiment and model. Fourier analysis reveals a close correspondence between the time-dependent behaviour of the harmonic components in the experimental data and model. Given this, each molecular species in the model was analysed individually. This analysis revealed that membrane-bound MinD dimer shows the mid-cell minimum with the highest contrast when averaged over time, carrying the strongest signal for positioning the cell division ring. This concurs with previous data showing that the MinD dimer binds to MinC inhibiting FtsZ ring formation. These results show that non-linear interactions of Min proteins are essential for producing the mid-cell positioning signal via the generation of second-order harmonic components in the time-dependent spatial protein distribution.
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Affiliation(s)
- James C. Walsh
- School of Physics, University of New South Wales, Sydney, NSW, Australia
- The Ithree Institute, University of Technology Sydney, Sydney, NSW, Australia
| | | | - Iain G. Duggin
- The Ithree Institute, University of Technology Sydney, Sydney, NSW, Australia
| | - Paul M. G. Curmi
- School of Physics, University of New South Wales, Sydney, NSW, Australia
- * E-mail:
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5
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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.
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6
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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.
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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
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7
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C. Walsh J, N. Angstmann C, V. McGann A, I. Henry B, G. Duggin I, M. G. Curmi P. Patterning of the MinD cell division protein in cells of arbitrary shape can be predicted using a heuristic dispersion relation. AIMS BIOPHYSICS 2016. [DOI: 10.3934/biophy.2016.1.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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8
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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.
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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
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9
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Walsh JC, Angstmann CN, Duggin IG, Curmi PMG. Molecular Interactions of the Min Protein System Reproduce Spatiotemporal Patterning in Growing and Dividing Escherichia coli Cells. PLoS One 2015; 10:e0128148. [PMID: 26018614 PMCID: PMC4446092 DOI: 10.1371/journal.pone.0128148] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/22/2015] [Indexed: 11/24/2022] Open
Abstract
Oscillations of the Min protein system are involved in the correct midcell placement of the divisome during Escherichia coli cell division. Based on molecular interactions of the Min system, we formulated a mathematical model that reproduces Min patterning during cell growth and division. Specifically, the increase in the residence time of MinD attached to the membrane as its own concentration increases, is accounted for by dimerisation of membrane-bound MinD and its interaction with MinE. Simulation of this system generates unparalleled correlation between the waveshape of experimental and theoretical MinD distributions, suggesting that the dominant interactions of the physical system have been successfully incorporated into the model. For cells where MinD is fully-labelled with GFP, the model reproduces the stationary localization of MinD-GFP for short cells, followed by oscillations from pole to pole in larger cells, and the transition to the symmetric distribution during cell filamentation. Cells containing a secondary, GFP-labelled MinD display a contrasting pattern. The model is able to account for these differences, including temporary midcell localization just prior to division, by increasing the rate constant controlling MinD ATPase and heterotetramer dissociation. For both experimental conditions, the model can explain how cell division results in an equal distribution of MinD and MinE in the two daughter cells, and accounts for the temperature dependence of the period of Min oscillations. Thus, we show that while other interactions may be present, they are not needed to reproduce the main characteristics of the Min system in vivo.
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Affiliation(s)
- James C. Walsh
- School of Physics, University of New South Wales, Sydney NSW 2052, Australia
- The ithree institute, University of Technology, Sydney NSW 2007, Australia
| | | | - Iain G. Duggin
- The ithree institute, University of Technology, Sydney NSW 2007, Australia
| | - Paul M. G. Curmi
- School of Physics, University of New South Wales, Sydney NSW 2052, Australia
- * E-mail:
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10
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Kretschmer S, Schwille P. Toward Spatially Regulated Division of Protocells: Insights into the E. coli Min System from in Vitro Studies. Life (Basel) 2014; 4:915-28. [PMID: 25513760 PMCID: PMC4284474 DOI: 10.3390/life4040915] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 11/25/2014] [Accepted: 12/03/2014] [Indexed: 11/16/2022] Open
Abstract
For reconstruction of controlled cell division in a minimal cell model, or protocell, a positioning mechanism that spatially regulates division is indispensable. In Escherichia coli, the Min proteins oscillate from pole to pole to determine the division site by inhibition of the primary divisome protein FtsZ anywhere but in the cell middle. Remarkably, when reconstituted under defined conditions in vitro, the Min proteins self-organize into spatiotemporal patterns in the presence of a lipid membrane and ATP. We review recent progress made in studying the Min system in vitro, particularly focusing on the effects of various physicochemical parameters and boundary conditions on pattern formation. Furthermore, we discuss implications and challenges for utilizing the Min system for division site placement in protocells.
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Affiliation(s)
- Simon Kretschmer
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany.
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany.
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11
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Ghasriani H, Goto NK. Regulation of symmetric bacterial cell division by MinE. Commun Integr Biol 2014. [DOI: 10.4161/cib.14162] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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12
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Zheng M, Chiang YL, Lee HL, Kong LR, Hsu STD, Hwang IS, Rothfield LI, Shih YL. Self-assembly of MinE on the membrane underlies formation of the MinE ring to sustain function of the Escherichia coli Min system. J Biol Chem 2014; 289:21252-66. [PMID: 24914211 DOI: 10.1074/jbc.m114.571976] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pole-to-pole oscillation of the Min proteins in Escherichia coli results in the inhibition of aberrant polar division, thus facilitating placement of the division septum at the midcell. MinE of the Min system forms a ring-like structure that plays a critical role in triggering the oscillation cycle. However, the mechanism underlying the formation of the MinE ring remains unclear. This study demonstrates that MinE self-assembles into fibrillar structures on the supported lipid bilayer. The MinD-interacting domain of MinE shows amyloidogenic properties, providing a possible mechanism for self-assembly of MinE. Supporting the idea, mutations in residues Ile-24 and Ile-25 of the MinD-interacting domain affect fibril formation, membrane binding ability of MinE and MinD, and subcellular localization of three Min proteins. Additional mutations in residues Ile-72 and Ile-74 suggest a role of the C-terminal domain of MinE in regulating the folding propensity of the MinD-interacting domain for different molecular interactions. The study suggests a self-assembly mechanism that may underlie the ring-like structure formed by MinE-GFP observed in vivo.
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Affiliation(s)
- Min Zheng
- From the Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Ya-Ling Chiang
- Department of Material Science and Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Road, Hsinchu 013, Taiwan
| | - Hsiao-Lin Lee
- From the Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Lih-Ren Kong
- From the Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Shang-Te Danny Hsu
- From the Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Ing-Shouh Hwang
- Department of Material Science and Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Road, Hsinchu 013, Taiwan, Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Taipei 115, Taiwan, and
| | - Lawrence I Rothfield
- Department of Structural, Microbial, and Molecular Biology, University of Connecticut Health Center, Farmington, Connecticut 06032
| | - Yu-Ling Shih
- From the Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan,
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13
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Shih YL, Zheng M. Spatial control of the cell division site by the Min system in Escherichia coli. Environ Microbiol 2013; 15:3229-39. [PMID: 23574354 DOI: 10.1111/1462-2920.12119] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/05/2013] [Accepted: 03/10/2013] [Indexed: 11/28/2022]
Abstract
The Min system of Escherichia coli is involved in mediating placement of the cell division site at the midcell; this is accomplished through partitioning of the cell division inhibitor MinC to the cell poles to block aberrant polar division. The partitioning of MinC is achieved through its interaction with MinDE, which alternates its cellular distribution periodically between opposite cell poles throughout the cell cycle. This dynamic oscillation is the result of intricate molecular interactions occurring between the three Min proteins on the membrane in a spatiotemporal manner. In this minireview, we discuss recent developments in understanding the molecular mechanisms of the E. coli Min system from cellular, biochemical and biophysical perspectives. In addition, we propose a model that involves the balancing of different molecular interactions at different stages of the oscillation cycle.
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Affiliation(s)
- Yu-Ling Shih
- Institute of Biological Chemistry, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, 1 Sec. 4 Roosevelt Road, Taipei, 106, Taiwan
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14
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Unusual biophysics of intrinsically disordered proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:932-51. [PMID: 23269364 DOI: 10.1016/j.bbapap.2012.12.008] [Citation(s) in RCA: 413] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 11/21/2012] [Accepted: 12/12/2012] [Indexed: 02/08/2023]
Abstract
Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where IDPs possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of IDPs are covered. In addition to the peculiar sequence characteristics of IDPs these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. IDPs are also characterized by the "turned-out" response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some IDPs is associated with the awaking of the dormant disorder. It is possible that IDPs represent the "edge of chaos" systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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15
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Martos A, Jiménez M, Rivas G, Schwille P. Towards a bottom-up reconstitution of bacterial cell division. Trends Cell Biol 2012; 22:634-43. [DOI: 10.1016/j.tcb.2012.09.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 09/05/2012] [Accepted: 09/07/2012] [Indexed: 10/27/2022]
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16
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Abstract
One of the most fundamental features of biological systems is probably their ability to self-organize in space and time on different scales. Despite many elaborate theoretical models of how molecular self-organization can come about, only a few experimental systems of biological origin have so far been rigorously described, due mostly to their inherent complexity. The most promising strategy of modern biophysics is thus to identify minimal biological systems showing self-organized emergent behavior. One of the best-understood examples of protein self-organization, which has recently been successfully reconstituted in vitro, is represented by the oscillations of the Min proteins in Escherichia coli. In this review, we summarize the current understanding of the mechanism of Min protein self-organization in vivo and in vitro. We discuss the potential of the Min oscillations to sense the geometry of the cell and suggest that spontaneous protein waves could be a general means of intracellular organization. We hypothesize that cooperative membrane binding and unbinding, e.g., as an energy-dependent switch, may act as an important regulatory mechanism for protein oscillations and pattern formation in the cell.
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Affiliation(s)
- Martin Loose
- Biophysics, BIOTEC, Dresden University of Technology, Dresden, Germany.
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17
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Park KT, Wu W, Battaile KP, Lovell S, Holyoak T, Lutkenhaus J. The Min oscillator uses MinD-dependent conformational changes in MinE to spatially regulate cytokinesis. Cell 2011; 146:396-407. [PMID: 21816275 PMCID: PMC3155264 DOI: 10.1016/j.cell.2011.06.042] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 05/23/2011] [Accepted: 06/24/2011] [Indexed: 10/17/2022]
Abstract
In E. coli, MinD recruits MinE to the membrane, leading to a coupled oscillation required for spatial regulation of the cytokinetic Z ring. How these proteins interact, however, is not clear because the MinD-binding regions of MinE are sequestered within a six-stranded β sheet and masked by N-terminal helices. minE mutations that restore interaction between some MinD and MinE mutants were isolated. These mutations alter the MinE structure leading to release of the MinD-binding regions and the N-terminal helices that bind the membrane. Crystallization of MinD-MinE complexes revealed a four-stranded β sheet MinE dimer with the released β strands (MinD-binding regions) converted to α helices bound to MinD dimers. These results identify the MinD-dependent conformational changes in MinE that convert it from a latent to an active form and lead to a model of how MinE persists at the MinD-membrane surface.
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Affiliation(s)
- Kyung-Tae Park
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City KS 66160
| | - Wei Wu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City KS 66160
| | - Kevin P. Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, Sector 17, APS Argonne National Laboratory 9700 S. Cass Avenue, Bldg. 435A, Argonne, IL 60439 USA
| | - Scott Lovell
- Structural Biology Center, University of Kansas, 2121 Simons Drive, Lawrence, KS 66047
| | - Todd Holyoak
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City KS 66160
| | - Joe Lutkenhaus
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City KS 66160
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Ghasriani H, Goto NK. Regulation of symmetric bacterial cell division by MinE: What is the role of conformational dynamics? Commun Integr Biol 2011; 4:101-3. [PMID: 21509194 DOI: 10.4161/cib.4.1.14162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 11/09/2010] [Indexed: 11/19/2022] Open
Abstract
Symmetric cell division in Gram-negative bacteria requires the concerted action of three Min proteins that together ensure exclusive formation of the cell division septum at the mid-point of the cell. We have recently described the structure and dynamic properties of MinE, the protein responsible for directing the cell division inhibitor complex formed by the MinC and MinD proteins away from the middle of the cell. An unexpected feature of this structure was the location of MinD-binding residues at buried, non-accessible sites in the dimeric interface. Here we elaborate on the potential role of conformational changes that might be involved to allow access to these residues, along with the interesting questions raised by these features of the MinE structure.
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19
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Shih YL, Huang KF, Lai HM, Liao JH, Lee CS, Chang CM, Mak HM, Hsieh CW, Lin CC. The N-terminal amphipathic helix of the topological specificity factor MinE is associated with shaping membrane curvature. PLoS One 2011; 6:e21425. [PMID: 21738659 PMCID: PMC3124506 DOI: 10.1371/journal.pone.0021425] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 06/01/2011] [Indexed: 02/01/2023] Open
Abstract
Pole-to-pole oscillations of the Min proteins in Escherichia coli are required for the proper placement of the division septum. Direct interaction of MinE with the cell membrane is critical for the dynamic behavior of the Min system. In vitro, this MinE-membrane interaction led to membrane deformation; however, the underlying mechanism remained unclear. Here we report that MinE-induced membrane deformation involves the formation of an amphipathic helix of MinE2–9, which, together with the adjacent basic residues, function as membrane anchors. Biochemical evidence suggested that the membrane association induces formation of the helix, with the helical face, consisting of A2, L3, and F6, inserted into the membrane. Insertion of this helix into the cell membrane can influence local membrane curvature and lead to drastic changes in membrane topology. Accordingly, MinE showed characteristic features of protein-induced membrane tubulation and lipid clustering in in vitro reconstituted systems. In conclusion, MinE shares common protein signatures with a group of membrane trafficking proteins in eukaryotic cells. These MinE signatures appear to affect membrane curvature.
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Affiliation(s)
- Yu-Ling Shih
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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20
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Wu W, Park KT, Holyoak T, Lutkenhaus J. Determination of the structure of the MinD-ATP complex reveals the orientation of MinD on the membrane and the relative location of the binding sites for MinE and MinC. Mol Microbiol 2011; 79:1515-28. [PMID: 21231967 DOI: 10.1111/j.1365-2958.2010.07536.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The three Min proteins spatially regulate Z ring positioning in Escherichia coli and are dynamically associated with the membrane. MinD binds to vesicles in the presence of ATP and can recruit MinC or MinE. Biochemical and genetic evidence indicate the binding sites for these two proteins on MinD overlap. Here we solved the structure of a hydrolytic-deficient mutant of MinD truncated for the C-terminal amphipathic helix involved in binding to the membrane. The structure solved in the presence of ATP is a dimer and reveals the face of MinD abutting the membrane. Using a combination of random and extensive site-directed mutagenesis additional residues important for MinE and MinC binding were identified. The location of these residues on the MinD structure confirms that the binding sites overlap and reveals that the binding sites are at the dimer interface and exposed to the cytosol. The location of the binding sites at the dimer interface offers a simple explanation for the ATP dependence of MinC and MinE binding to MinD.
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Affiliation(s)
- Wei Wu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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21
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Appropriation of the MinD protein-interaction motif by the dimeric interface of the bacterial cell division regulator MinE. Proc Natl Acad Sci U S A 2010; 107:18416-21. [PMID: 20937912 DOI: 10.1073/pnas.1007141107] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MinE is required for the dynamic oscillation of Min proteins that restricts formation of the cytokinetic septum to the midpoint of the cell in gram negative bacteria. Critical for this oscillation is MinD-binding by MinE to stimulate MinD ATP hydrolysis, a function that had been assigned to the first ∼30 residues in MinE. Previous models based on the structure of an autonomously folded dimeric C-terminal fragment suggested that the N-terminal domain is freely accessible for interactions with MinD. We report here the solution NMR structure of the full-length MinE dimer from Neisseria gonorrhoeae, with two parts of the N-terminal domain forming an integral part of the dimerization interface. Unexpectedly, solvent accessibility is highly restricted for residues that were previously hypothesized to directly interact with MinD. To delineate the true MinD-binding region, in vitro assays for MinE-stimulated MinD activity were performed. The relative MinD-binding affinities obtained for full-length and N-terminal peptides from MinE demonstrated that residues that are buried in the dimeric interface nonetheless participate in direct interactions with MinD. According to results from NMR spin relaxation experiments, access to these buried residues may be facilitated by the presence of conformational exchange. We suggest that this concealment of MinD-binding residues by the MinE dimeric interface provides a mechanism for prevention of nonspecific interactions, particularly with the lipid membrane, to allow the free diffusion of MinE that is critical for Min protein oscillation.
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