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Molecular Mechanisms and Applications of N-Acyl Homoserine Lactone-Mediated Quorum Sensing in Bacteria. Molecules 2022; 27:molecules27217584. [PMID: 36364411 PMCID: PMC9654057 DOI: 10.3390/molecules27217584] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial biodiversity includes biotic and abiotic components that support all life forms by adapting to environmental conditions. Climate change, pollution, human activity, and natural calamities affect microbial biodiversity. Microbes have diverse growth conditions, physiology, and metabolism. Bacteria use signaling systems such as quorum sensing (QS) to regulate cellular interactions via small chemical signaling molecules which also help with adaptation under undesirable survival conditions. Proteobacteria use acyl-homoserine lactone (AHL) molecules as autoinducers to sense population density and modulate gene expression. The LuxI-type enzymes synthesize AHL molecules, while the LuxR-type proteins (AHL transcriptional regulators) bind to AHLs to regulate QS-dependent gene expression. Diverse AHLs have been identified, and the diversity extends to AHL synthases and AHL receptors. This review comprehensively explains the molecular diversity of AHL signaling components of Pseudomonas aeruginosa, Chromobacterium violaceum, Agrobacterium tumefaciens, and Escherichia coli. The regulatory mechanism of AHL signaling is also highlighted in this review, which adds to the current understanding of AHL signaling in Gram-negative bacteria. We summarize molecular diversity among well-studied QS systems and recent advances in the role of QS proteins in bacterial cellular signaling pathways. This review describes AHL-dependent QS details in bacteria that can be employed to understand their features, improve environmental adaptation, and develop broad biomolecule-based biotechnological applications.
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2
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Pacheco T, Gomes AÉI, Siqueira NMG, Assoni L, Darrieux M, Venter H, Ferraz LFC. SdiA, a Quorum-Sensing Regulator, Suppresses Fimbriae Expression, Biofilm Formation, and Quorum-Sensing Signaling Molecules Production in Klebsiella pneumoniae. Front Microbiol 2021; 12:597735. [PMID: 34234747 PMCID: PMC8255378 DOI: 10.3389/fmicb.2021.597735] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/26/2021] [Indexed: 12/24/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative pathogen that has become a worldwide concern due to the emergence of multidrug-resistant isolates responsible for various invasive infectious diseases. Biofilm formation constitutes a major virulence factor for K. pneumoniae and relies on the expression of fimbrial adhesins and aggregation of bacterial cells on biotic or abiotic surfaces in a coordinated manner. During biofilm aggregation, bacterial cells communicate with each other through inter- or intra-species interactions mediated by signallng molecules, called autoinducers, in a mechanism known as quorum sensing (QS). In most Gram-negative bacteria, intra-species communication typically involves the LuxI/LuxR system: LuxI synthase produces N-acyl homoserine lactones (AHLs) as autoinducers and the LuxR transcription factor is their cognate receptor. However, K. pneumoniae does not produce AHL but encodes SdiA, an orphan LuxR-type receptor that responds to exogenous AHL molecules produced by other bacterial species. While SdiA regulates several cellular processes and the expression of virulence factors in many pathogens, the role of this regulator in K. pneumoniae remains unknown. In this study, we describe the characterization of sdiA mutant strain of K. pneumoniae. The sdiA mutant strain has increased biofilm formation, which correlates with the increased expression of type 1 fimbriae, thus revealing a repressive role of SdiA in fimbriae expression and bacterial cell adherence and aggregation. On the other hand, SdiA acts as a transcriptional activator of cell division machinery assembly in the septum, since cells lacking SdiA regulator exhibited a filamentary shape rather than the typical rod shape. We also show that K. pneumoniae cells lacking SdiA regulator present constant production of QS autoinducers at maximum levels, suggesting a putative role for SdiA in the regulation of AI-2 production. Taken together, our results demonstrate that SdiA regulates cell division and the expression of virulence factors such as fimbriae expression, biofilm formation, and production of QS autoinducers in K. pneumoniae.
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Affiliation(s)
- Thaisy Pacheco
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Ana Érika Inácio Gomes
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | | | - Lucas Assoni
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Michelle Darrieux
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Lúcio Fábio Caldas Ferraz
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
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Ziegler M, Zieringer J, Takors R. Transcriptional profiling of the stringent response mutant strain E. coli SR reveals enhanced robustness to large-scale conditions. Microb Biotechnol 2021; 14:993-1010. [PMID: 33369128 PMCID: PMC8085953 DOI: 10.1111/1751-7915.13738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/05/2022] Open
Abstract
In large-scale fed-batch production processes, microbes are exposed to heterogeneous substrate availability caused by long mixing times. Escherichia coli, the most common industrial host for recombinant protein production, reacts by recurring accumulation of the alarmone ppGpp and energetically wasteful transcriptional strategies. Here, we compare the regulatory responses of the stringent response mutant strain E. coli SR and its parent strain E. coli MG1655 to repeated nutrient starvation in a two-compartment scale-down reactor. Our data show that E. coli SR can withstand these stress conditions without a ppGpp-mediated stress response maintaining fully functional ammonium uptake and biomass formation. Furthermore, E. coli SR exhibited a substantially reduced short-term transcriptional response compared to E. coli MG1655 (less than half as many differentially expressed genes). E. coli SR proceeded adaptation via more general SOS response pathways by initiating negative regulation of transcription, translation and cell division. Our results show that locally induced stress responses propagating through the bioreactor do not result in cyclical induction and repression of genes in E. coli SR, but in a reduced and coordinated response, which makes it potentially suitable for large-scale production processes.
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Affiliation(s)
- Martin Ziegler
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Julia Zieringer
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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Geisinger E, Mortman NJ, Vargas-Cuebas G, Tai AK, Isberg RR. A global regulatory system links virulence and antibiotic resistance to envelope homeostasis in Acinetobacter baumannii. PLoS Pathog 2018; 14:e1007030. [PMID: 29795704 PMCID: PMC5967708 DOI: 10.1371/journal.ppat.1007030] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/16/2018] [Indexed: 11/19/2022] Open
Abstract
The nosocomial pathogen Acinetobacter baumannii is a significant threat due to its ability to cause infections refractory to a broad range of antibiotic treatments. We show here that a highly conserved sensory-transduction system, BfmRS, mediates the coordinate development of both enhanced virulence and resistance in this microorganism. Hyperactive alleles of BfmRS conferred increased protection from serum complement killing and allowed lethal systemic disease in mice. BfmRS also augmented resistance and tolerance against an expansive set of antibiotics, including dramatic protection from β-lactam toxicity. Through transcriptome profiling, we showed that BfmRS governs these phenotypes through global transcriptional regulation of a post-exponential-phase-like program of gene expression, a key feature of which is modulation of envelope biogenesis and defense pathways. BfmRS activity defended against cell-wall lesions through both β-lactamase-dependent and -independent mechanisms, with the latter being connected to control of lytic transglycosylase production and proper coordination of morphogenesis and division. In addition, hypersensitivity of bfmRS knockouts could be suppressed by unlinked mutations restoring a short, rod cell morphology, indicating that regulation of drug resistance, pathogenicity, and envelope morphogenesis are intimately linked by this central regulatory system in A. baumannii. This work demonstrates that BfmRS controls a global regulatory network coupling cellular physiology to the ability to cause invasive, drug-resistant infections. Infections with the hospital-acquired bacterium Acinetobacter baumannii are highly difficult to treat. The pathogen has evolved multiple lines of defense against antimicrobial stress, including a barrier-forming cell envelope as well as control systems that respond to antimicrobial stresses by enhancing antibiotic resistance and virulence. Here, we uncovered the role of a key stress-response system, BfmRS, in controlling the transition of A. baumannii to a state of heightened resistance and virulence. We show that BfmRS enhances pathogenicity in mammalian hosts, and augments the ability to grow in the presence of diverse antibiotics and tolerate transient, high-level antibiotic exposures. Connected to these effects is the ability of BfmRS to globally reprogram gene expression and control multiple pathways that build, protect, and shape the cell envelope. Moreover, we determined that resistance-enhancing mutations bypassing the need for BfmRS also modulate envelope- and morphology-associated pathways, further linking control of physiology with resistance in A. baumannii. This work uncovers a global control circuit that shifts cellular physiology in ways that promote hospital-associated disease, and points to inhibition of this circuit as a potential strategy for disarming the pathogen.
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Affiliation(s)
- Edward Geisinger
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Nadav J. Mortman
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Germán Vargas-Cuebas
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Albert K. Tai
- Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Ralph R. Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
- * E-mail:
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5
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Cho J, Carr AN, Whitworth L, Johnson B, Wilson KS. MazEF toxin-antitoxin proteins alter Escherichia coli cell morphology and infrastructure during persister formation and regrowth. Microbiology (Reading) 2017; 163:308-321. [DOI: 10.1099/mic.0.000436] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Junho Cho
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Anita Nicole Carr
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Lisa Whitworth
- Microscopy Laboratory, Oklahoma State University, Stillwater, OK 74078, USA
| | - Brent Johnson
- Microscopy Laboratory, Oklahoma State University, Stillwater, OK 74078, USA
| | - Kevin Scott Wilson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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Hudson AO, Harkness TCM, Savka MA. Functional Complementation Analysis (FCA): A Laboratory Exercise Designed and Implemented to Supplement the Teaching of Biochemical Pathways. J Vis Exp 2016:53850. [PMID: 27403640 PMCID: PMC4993271 DOI: 10.3791/53850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
Functional complementation assay (FCA) is an in vivo assay that is widely used to elucidate the function/role of genes/enzymes. This technique is very common in biochemistry, genetics and many other disciplines. A comprehensive overview of the technique to supplement the teaching of biochemical pathways pertaining to amino acids, peptidoglycan and the bacterial stringent response is reported in this manuscript. Two cDNAs from the model plant organism Arabidopsis thaliana that are involved in the metabolism of lysine (L,L-diaminopimelate aminotransferase (dapL) and tyrosine aminotransferase (tyrB) involved in the metabolism of tyrosine and phenylalanine are highlighted. In addition, the bacterial peptidoglycan anabolic pathway is highlighted through the analysis of the UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-meso-2,6-diaminopimelate ligase (murE) gene from the bacterium Verrucomicrobium spinosum involved in the cross-linking of peptidoglycan. The bacterial stringent response is also reported through the analysis of the rsh (relA/spoT homolog) bifunctional gene responsible for a hyper-mucoid phenotype in the bacterium Novosphingobium sp. Four examples of FCA are presented. The video will focus on three of them, namely lysine, peptidoglycan and the stringent response.
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Affiliation(s)
- André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology;
| | - Taylor C M Harkness
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology
| | - Michael A Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology
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Inactivation of Cell Division Protein FtsZ by SulA Makes Lon Indispensable for the Viability of a ppGpp0 Strain of Escherichia coli. J Bacteriol 2015; 198:688-700. [PMID: 26644431 DOI: 10.1128/jb.00693-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/27/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The modified nucleotides (p)ppGpp play an important role in bacterial physiology. While the accumulation of the nucleotides is vital for adaptation to various kinds of stress, changes in the basal level modulates growth rate and vice versa. Studying the phenotypes unique to the strain lacking (p)ppGpp (ppGpp(0)) under overtly unstressed growth conditions may be useful to understand functions regulated by basal levels of (p)ppGpp and its physiological significance. In this study, we show that the ppGpp(0) strain, unlike the wild type, requires the Lon protease for cell division and viability in LB. Our results indicate the decrease in FtsZ concentration in the ppGpp(0) strain makes cell division vulnerable to SulA inhibition. We did not find evidence for SOS induction contributing to the cell division defect in the ppGpp(0) Δlon strain. Based on the results, we propose that basal levels of (p)ppGpp are required to sustain normal cell division in Escherichia coli during growth in rich medium and that the basal SulA level set by Lon protease is important for insulating cell division against a decrease in FtsZ concentration and conditions that can increase the susceptibility of FtsZ to SulA. IMPORTANCE The physiology of the stringent response has been the subject of investigation for more than 4 decades, with the majority of the work carried out using the bacterial model organism Escherichia coli. These studies have revealed that the accumulation of (p)ppGpp, the effector of the stringent response, is associated with growth retardation and changes in gene expression that vary with the intracellular concentration of (p)ppGpp. By studying a synthetic lethal phenotype, we have uncovered a function modulated by the basal levels of (p)ppGpp and studied its physiological significance. Our results show that (p)ppGpp and Lon protease contribute to the robustness of the cell division machinery in E. coli during growth in rich medium.
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Yamaguchi T, Iida KI, Shiota S, Nakayama H, Yoshida SI. Filament formation of Salmonella Paratyphi A accompanied by FtsZ assembly impairment and low level ppGpp. Can J Microbiol 2015; 61:955-64. [PMID: 26549184 DOI: 10.1139/cjm-2015-0415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Previously, we reported that Salmonella enterica serovar Paratyphi A strain S602 grew into multinuclear, nonseptate, and nonlethal filaments on agar plates containing nitrogenous salts. Strain S602 was more sensitive to osmotic and oxidative stress than the reference strain 3P243 of nonfilamentous Salmonella Paratyphi A. Strain S602 had an amber mutation (C154T) in rpoS. The revertant of this mutant, SR603, was repressed to form filaments under conditions with abundant nitrogenous salts. However, 3PR244, an rpoS mutant of 3P243 (C154T), did not form filaments, which implies that the rpoS mutation is not the sole cause of filamentation in strain S602. Next, we examined whether the level of guanosine 5'-diphosphate 3'-diphosphate (ppGpp) in S602 strain is involved in filament formation. The intracellular ppGpp level in filamentous cells was lower than that in nonfilamentous cells. Furthermore, cells belonging to strain RE606, a derivative of S602 where the intracellular concentration of ppGpp was increased by overexpression of the relA gene, exhibited normal Z-ring formation and cell division. In the S602 strain, the decrease in the ppGpp level induced by the presence of nitrogenous salt and the rpoS mutation led to the inhibition of Z-ring formation and the subsequent filamentation of cells.
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Affiliation(s)
- Takayoshi Yamaguchi
- a Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ken-Ichiro Iida
- a Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Susumu Shiota
- b Department of Oral Health, Growth, and Development, Division of Oral Infectious Diseases and Immunology, Faculty of Dental Science, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hiroaki Nakayama
- a Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shin-Ichi Yoshida
- a Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
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9
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A comprehensive proteomic analysis of totarol induced alterations in Bacillus subtilis by multipronged quantitative proteomics. J Proteomics 2015; 114:247-62. [DOI: 10.1016/j.jprot.2014.10.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/28/2014] [Accepted: 10/20/2014] [Indexed: 12/25/2022]
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10
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The hierarchy quorum sensing network in Pseudomonas aeruginosa. Protein Cell 2014; 6:26-41. [PMID: 25249263 PMCID: PMC4286720 DOI: 10.1007/s13238-014-0100-x] [Citation(s) in RCA: 739] [Impact Index Per Article: 73.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 08/28/2014] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa causes severe and persistent infections in immune compromised individuals and cystic fibrosis sufferers. The infection is hard to eradicate as P. aeruginosa has developed strong resistance to most conventional antibiotics. The problem is further compounded by the ability of the pathogen to form biofilm matrix, which provides bacterial cells a protected environment withstanding various stresses including antibiotics. Quorum sensing (QS), a cell density-based intercellular communication system, which plays a key role in regulation of the bacterial virulence and biofilm formation, could be a promising target for developing new strategies against P. aeruginosa infection. The QS network of P. aeruginosa is organized in a multi-layered hierarchy consisting of at least four interconnected signaling mechanisms. Evidence is accumulating that the QS regulatory network not only responds to bacterial population changes but also could react to environmental stress cues. This plasticity should be taken into consideration during exploration and development of anti-QS therapeutics.
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11
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Chen L, Xu Q, Tu J, Ge Y, Liu J, Liang FT. Increasing RpoS expression causes cell death in Borrelia burgdorferi. PLoS One 2013; 8:e83276. [PMID: 24358270 PMCID: PMC3865164 DOI: 10.1371/journal.pone.0083276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/11/2013] [Indexed: 01/25/2023] Open
Abstract
RpoS, one of the two alternative σ factors in Borrelia burgdorferi, is tightly controlled by multiple regulators and, in turn, determines expression of many critical virulence factors. Here we show that increasing RpoS expression causes cell death. The immediate effect of increasing RpoS expression was to promote bacterial division and as a consequence result in a rapid increase in cell number before causing bacterial death. No DNA fragmentation or degradation was observed during this induced cell death. Cryo-electron microscopy showed induced cells first formed blebs, which were eventually released from dying cells. Apparently blebbing initiated cell disintegration leading to cell death. These findings led us to hypothesize that increasing RpoS expression triggers intracellular programs and/or pathways that cause spirochete death. The potential biological significance of induced cell death may help B. burgdorferi regulate its population to maintain its life cycle in nature.
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Affiliation(s)
- Linxu Chen
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Qilong Xu
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jiagang Tu
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, Taxes, United States of America
| | - Yihe Ge
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, Taxes, United States of America
| | - Fang Ting Liang
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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12
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Häkkinen A, Ribeiro AS. Evolving kinetics of gene expression in stochastic environments. Comput Biol Chem 2012; 37:11-6. [PMID: 22410387 DOI: 10.1016/j.compbiolchem.2012.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 01/18/2012] [Accepted: 02/14/2012] [Indexed: 10/28/2022]
Abstract
Recent studies have shown that the in vivo dynamics of RNA numbers in bacteria is regulated, to a great extent, by the kinetics of rate limiting steps in transcription. Strong evidence suggests that the kinetics of these steps is sequence dependent. We investigate the selective advantages of rate limiting steps of differing kinetics. For that, we model the kinetics of expression of a gene responsible for promoting cell division at the expense of resources in the environment in individual cells of a population. We model mutations that affect the kinetics of the rate limiting steps and selective pressure in various environmental conditions. Depletion of resources leads to cell death. We find that small changes in the evolutionary constraints can favor widely different noise levels in RNA and protein numbers. Increasing the cost in nutrients for division favors noisier expression. The results provide a better understanding of why different genes differ in the kinetics of production of RNA and proteins.
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Affiliation(s)
- Antti Häkkinen
- Laboratory of Biosystem Dynamics, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, Finland.
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13
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Bergmiller T, Peña-Miller R, Boehm A, Ackermann M. Single-cell time-lapse analysis of depletion of the universally conserved essential protein YgjD. BMC Microbiol 2011; 11:118. [PMID: 21619589 PMCID: PMC3115834 DOI: 10.1186/1471-2180-11-118] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 05/27/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The essential Escherichia coli gene ygjD belongs to a universally conserved group of genes whose function has been the focus of a number of recent studies. Here, we put ygjD under control of an inducible promoter, and used time-lapse microscopy and single cell analysis to investigate the phenotypic consequences of the depletion of YgjD protein from growing cells. RESULTS We show that loss of YgjD leads to a marked decrease in cell size and termination of cell division. The transition towards smaller size occurs in a controlled manner: cell elongation and cell division remain coupled, but cell size at division decreases. We also find evidence that depletion of YgjD leads to the synthesis of the intracellular signaling molecule (p)ppGpp, inducing a cellular reaction resembling the stringent response. Concomitant deletion of the relA and spoT genes - leading to a strain that is uncapable of synthesizing (p)ppGpp - abrogates the decrease in cell size, but does not prevent termination of cell division upon YgjD depletion. CONCLUSIONS Depletion of YgjD protein from growing cells leads to a decrease in cell size that is contingent on (p)ppGpp, and to a termination of cell division. The combination of single-cell timelapse microscopy and statistical analysis can give detailed insights into the phenotypic consequences of the loss of essential genes, and can thus serve as a new tool to study the function of essential genes.
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Affiliation(s)
- Tobias Bergmiller
- Department of Environmental Sciences, ETH Zurich, Switzerland, and Department of Environmental Microbiology, Eawag, Switzerland.
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14
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Gan HM, Buckley L, Szegedi E, Hudson AO, Savka MA. Identification of an rsh gene from a Novosphingobium sp. necessary for quorum-sensing signal accumulation. J Bacteriol 2009; 191:2551-60. [PMID: 19201802 PMCID: PMC2668395 DOI: 10.1128/jb.01692-08] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 01/29/2009] [Indexed: 11/20/2022] Open
Abstract
The stringent response is a mechanism by which bacteria adapt to environmental stresses and nutritional deficiencies through the synthesis and hydrolysis of (p)ppGpp by RelA/SpoT enzymes. Alphaproteobacteria and plants contain a single Rsh enzyme (named for RelA/SpoT homolog) that is bifunctional. Here we report the identification of a new species of bacteria belonging to the genus Novosphingobium and characterization of an rsh mutation in this plant tumor-associated isolate. Isolate Rr 2-17, from a grapevine crown gall tumor, is a member of the Novosphingobium genus that produces the N-acyl-homoserine lactone (AHL) quorum-sensing (QS) signals. A Tn5 mutant, Hx 699, deficient in AHL production was found to have an insertion in an rsh gene. The Rsh protein showed significant percent sequence identity to Rsh proteins of alphaproteobacteria. The Novosphingobium sp. rsh gene (rsh(Nsp)) complemented the multiple amino acid requirements of the Escherichia coli relA spoT double mutant by restoring the growth on selection media. Besides QS signal production, the rsh mutation also affects soluble polysaccharide production and cell aggregation. Genetic complementation of the Hx 699 mutant with the rsh(Nsp) gene restored these phenotypes. This is the first discovery of a functional rsh gene in a member of the Novosphingobium genus.
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MESH Headings
- Acyl-Butyrolactones/metabolism
- Amino Acid Sequence
- Bacterial Adhesion
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- DNA Transposable Elements
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Escherichia coli/genetics
- Genes, rRNA
- Genetic Complementation Test
- Molecular Sequence Data
- Mutagenesis, Insertional
- Phylogeny
- Polysaccharides, Bacterial/metabolism
- Quorum Sensing
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Sphingomonadaceae/classification
- Sphingomonadaceae/genetics
- Sphingomonadaceae/isolation & purification
- Sphingomonadaceae/physiology
- Vitis/microbiology
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Affiliation(s)
- Han Ming Gan
- Department of Biological Sciences, Rochester Institute of Technology, 85 Lomb Memorial Dr., A350 Gosnell Bldg., Rochester, NY 14534, USA.
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15
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Malik A, Jenzsch M, Lübbert A, Rudolph R, Söhling B. Periplasmic production of native human proinsulin as a fusion to E. coli ecotin. Protein Expr Purif 2007; 55:100-11. [PMID: 17509894 DOI: 10.1016/j.pep.2007.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Revised: 04/02/2007] [Accepted: 04/03/2007] [Indexed: 10/23/2022]
Abstract
Native proinsulin belongs to the class of the difficult-to-express proteins in Escherichia coli. Problems mainly arise due to its small size, a high proteolytic decay, and the necessity to form a native disulfide pattern. In the present study, human proinsulin was produced in the periplasm of E. coli as a fusion to ecotin, which is a small periplasmic protein of 16 kDa encoded by the host, containing one disulfide bond. The fusion protein was secreted to the periplasm and native proinsulin was determined by ELISA. Cultivation parameters were studied in parallel batch mode fermentations using E. coli BL21(DE3)Gold as a host. After improvement of fed-batch high density fermentation conditions, 153 mg fusion protein corresponding to 51.5mg native proinsulin was obtained per L. Proteins were extracted from the periplasm by osmotic shock treatment. The fusion protein was purified in one step by ecotin affinity chromatography on immobilized trypsinogen. After thrombin cleavage of the fusion protein, the products were separated by Ni-NTA chromatography. Proinsulin was quantified by ELISA and characterized by mass spectrometry. To evaluate the influence of periplasmic proteases, the amount of ecotin-proinsulin was determined in E. coli BL21(DE3)Gold and in a periplasmic protease deficient strain, E. coli SF120.
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Affiliation(s)
- Ajamaluddin Malik
- Institute for Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str 3, D-06120 Halle (Saale), Germany
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16
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Abstract
The process of cell division has been intensively studied at the molecular level for decades but some basic questions remain unanswered. The mechanisms of cell division are probably best characterized in the rod-shaped bacteria Escherichia coli and Bacillus subtilis. Many of the key players are known, but detailed descriptions of the molecular mechanisms which determine where, how and when cells form the division septum are lacking. Different models have been proposed to account for the high precision with which the septum is constructed at the midcell and these models have been evaluated and refined against new data emerging from the fast improving methodologies of cell biology. This review summarizes important advances in our understanding of how the cell positions the division septum, whether it be vegetative or asymmetric. It also describes how the asymmetric septum forms and how this septation event is linked to chromosome segregation and subsequent asymmetric gene expression during spore formation in B. subtilis.
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Affiliation(s)
- Imrich Barák
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia.
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17
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Reddy M. Role of FtsEX in cell division of Escherichia coli: viability of ftsEX mutants is dependent on functional SufI or high osmotic strength. J Bacteriol 2006; 189:98-108. [PMID: 17071757 PMCID: PMC1797223 DOI: 10.1128/jb.01347-06] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, at least 12 proteins, FtsZ, ZipA, FtsA, FtsE/X, FtsK, FtsQ, FtsL, FtsB, FtsW, FtsI, FtsN, and AmiC, are known to localize to the septal ring in an interdependent and sequential pathway to coordinate the septum formation at the midcell. The FtsEX complex is the latest recruit of this pathway, and unlike other division proteins, it is shown to be essential only on low-salt media. In this study, it is shown that ftsEX null mutations are not only salt remedial but also osmoremedial, which suggests that FtsEX may not be involved in salt transport as previously thought. Increased coexpression of cell division proteins FtsQ-FtsA-FtsZ or FtsN alone restored the growth defects of ftsEX mutants. ftsEX deletion exacerbated the defects of most of the mutants affected in Z ring localization and septal assembly; however, the ftsZ84 allele was a weak suppressor of ftsEX. The viability of ftsEX mutants in high-osmolarity conditions was shown to be dependent on the presence of a periplasmic protein, SufI, a substrate of twin-arginine translocase. In addition, SufI in multiple copies could substitute for the functions of FtsEX. Taken together, these results suggest that FtsE and FtsX are absolutely required for the process of cell division in conditions of low osmotic strength for the stability of the septal ring assembly and that, during high-osmolarity conditions, the FtsEX and SufI functions are redundant for this essential process.
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Affiliation(s)
- Manjula Reddy
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
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18
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Nagahama H, Sakamoto Y, Matsumoto K, Hara H. RcsA-dependent and -independent growth defects caused by the activated Rcs phosphorelay system in the Escherichia coli pgsA null mutant. J GEN APPL MICROBIOL 2006; 52:91-8. [PMID: 16778352 DOI: 10.2323/jgam.52.91] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In the Escherichia coli pgsA null mutant, which lacks the major acidic phospholipids, the Rcs phosphorelay signal transduction system is activated, causing thermosensitive growth. The mutant grows poorly at 37 degrees C and lyses at 42 degrees C. We showed that the poor growth at 37 degrees C was corrected by disruption of the rcsA gene, which codes for a coregulator protein that interacts with the RcsB response regulator of the phosphorelay system. However, mutant cells still lysed when incubated at 42 degrees C even in the absence of RcsA. We conclude that the activated Rcs phosphorelay in the pgsA null mutant has both RcsA-dependent and -independent growth inhibitory effects. Since the Rcs system has been shown to positively regulate the essential cell division genes ftsA and ftsZ independently of RcsA, we measured cellular levels of the FtsZ protein, but found that the growth defect of the mutant at 42 degrees C did not involve a change in the level of this protein.
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Affiliation(s)
- Hideki Nagahama
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Japan
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19
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Abstract
Cellular metabolism constantly generates by-products that are wasteful or even harmful. Such compounds are excreted from the cell or are removed through hydrolysis to normal cellular metabolites by various 'house-cleaning' enzymes. Some of the most important contaminants are non-canonical nucleoside triphosphates (NTPs) whose incorporation into the nascent DNA leads to increased mutagenesis and DNA damage. Enzymes intercepting abnormal NTPs from incorporation by DNA polymerases work in parallel with DNA repair enzymes that remove lesions produced by modified nucleotides. House-cleaning NTP pyrophosphatases targeting non-canonical NTPs belong to at least four structural superfamilies: MutT-related (Nudix) hydrolases, dUTPase, ITPase (Maf/HAM1) and all-alpha NTP pyrophosphatases (MazG). These enzymes have high affinity (Km's in the micromolar range) for their natural substrates (8-oxo-dGTP, dUTP, dITP, 2-oxo-dATP), which allows them to select these substrates from a mixture containing a approximately 1000-fold excess of canonical NTPs. To date, many house-cleaning NTPases have been identified only on the basis of their side activity towards canonical NTPs and NDP derivatives. Integration of growing structural and biochemical data on these superfamilies suggests that their new family members cleanse the nucleotide pool of the products of oxidative damage and inappropriate methylation. House-cleaning enzymes, such as 6-phosphogluconolactonase, are also part of normal intermediary metabolism. Genomic data suggest that house-cleaning systems are more abundant than previously thought and include numerous analogous enzymes with overlapping functions. We discuss the structural diversity of these enzymes, their phylogenetic distribution, substrate specificity and the problem of identifying their true substrates.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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20
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Yoshida T, Maki M, Okamoto H, Hiroishi S. Coordination of DNA replication and cell division in CyanobacteriaMicrocystis aeruginosa. FEMS Microbiol Lett 2005; 251:149-54. [PMID: 16112821 DOI: 10.1016/j.femsle.2005.07.041] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 07/22/2005] [Accepted: 07/27/2005] [Indexed: 11/25/2022] Open
Abstract
Little is known about the cyanobacterial cell cycle. When either nalidixic acid or hydroxyurea was added to a synchronized culture of Microcystis aeruginosa to block DNA replication, cell division did not occur. Furthermore, transcription of the essential cell division gene, ftsZ was repressed. After DNA replication, ftsZ transcription, as well as cell division, was not affected by hydroxyl urea, suggesting that the DNA replication and cell division of M. aeruginosa are coordinated and that this coordination is partly controlled by ftsZ transcription depending on DNA replication.
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Affiliation(s)
- Takashi Yoshida
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui 917-0003, Japan.
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21
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Mergulhão FJM, Taipa MA, Cabral JMS, Monteiro GA. Evaluation of bottlenecks in proinsulin secretion by Escherichia coli. J Biotechnol 2004; 109:31-43. [PMID: 15063612 DOI: 10.1016/j.jbiotec.2003.10.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2002] [Revised: 09/08/2003] [Accepted: 10/14/2003] [Indexed: 10/26/2022]
Abstract
This work evaluates three potential bottlenecks in recombinant human proinsulin secretion by Escherichia coli: protein stability, secretion capacity and the effect of molecular size on secretion efficiency. A maximum secretion level of 7.2 mg g(-1) dry cell weight was obtained in the periplasm of E. coli JM109(DE3) host cells. This value probably represents an upper limit in the transport capacity of E. coli cells secreting ZZ-proinsulin and similar proteins with the protein A signal peptide. A selective deletion study was performed in the fusion partner and no effect of the molecular size (17-24 kDa) was detected on secretion efficiency. The protective effect against proteolysis provided by the ZZ domain was thoroughly demonstrated in the periplasm of E. coli and it was also shown that a single Z domain is able to provide the same protection level without compromising the downstream processing. The use of this shorter fusion partner enables a 1.6-fold increase in the recovery of the target protein after cleavage of the affinity handle.
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Affiliation(s)
- F J M Mergulhão
- Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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22
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Romberg L, Levin PA. Assembly dynamics of the bacterial cell division protein FTSZ: poised at the edge of stability. Annu Rev Microbiol 2004; 57:125-54. [PMID: 14527275 PMCID: PMC5517307 DOI: 10.1146/annurev.micro.57.012903.074300] [Citation(s) in RCA: 207] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
FtsZ is a prokaryotic tubulin homolog that assembles into a ring at the future site of cell division. The resulting "Z ring" forms the framework for the division apparatus, and its assembly is regulated throughout the bacterial cell cycle. A highly dynamic structure, the Z ring exhibits continual subunit turnover and the ability to rapidly assemble, disassemble, and, under certain circumstances, relocalize. These in vivo properties are ultimately due to FtsZ's capacity for guanosine triphosphate (GTP)-dependent, reversible polymerization. FtsZ polymer stability appears to be fine-tuned such that subtle changes in its assembly kinetics result in large changes in the Z ring structure. Thus, regulatory proteins that modulate FtsZ's assembly dynamics can cause the ring to rapidly remodel in response to developmental and environmental cues.
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Affiliation(s)
- Laura Romberg
- Institute for Cellular and Chemical Biology, Harvard Medical School, SGM 604, 250 Longwood Avenue, Boston, Massachusetts 02115, USA.
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23
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Abstract
FtsZ is an essential cell division protein conserved throughout the bacteria and archaea. In response to an unknown cell cycle signal, FtsZ polymerizes into a ring that establishes the future division site. We conducted a series of experiments examining the link between growth rate, medial FtsZ ring formation, and the intracellular concentration of FtsZ in the gram-positive bacterium Bacillus subtilis. We found that, although the frequency of cells with FtsZ rings varies as much as threefold in a growth rate-dependent manner, the average intracellular concentration of FtsZ remains constant irrespective of doubling time. Additionally, expressing ftsZ solely from a constitutive promoter, thereby eliminating normal transcriptional control, did not alter the growth rate regulation of medial FtsZ ring formation. Finally, our data indicate that overexpressing FtsZ does not dramatically increase the frequency of cells with medial FtsZ rings, suggesting that the mechanisms governing ring formation are refractile to increases in FtsZ concentration. These results support a model in which the timing of FtsZ assembly is governed primarily through cell cycle-dependent changes in FtsZ polymerization kinetics and not simply via oscillations in the intracellular concentration of FtsZ. Importantly, this model can be extended to the gram-negative bacterium Escherichia coli. Our data show that, like those in B. subtilis, average FtsZ levels in E. coli are constant irrespective of doubling time.
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Affiliation(s)
- Richard B Weart
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
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24
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Addinall SG, Holland B. The tubulin ancestor, FtsZ, draughtsman, designer and driving force for bacterial cytokinesis. J Mol Biol 2002; 318:219-36. [PMID: 12051832 DOI: 10.1016/s0022-2836(02)00024-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We discuss in this review the regulation of synthesis and action of FtsZ, its structure in relation to tubulin and microtubules, and the mechanism of polymerization and disassembly (contraction) of FtsZ rings from a specific nucleation site (NS) at mid cell. These topics are considered in the light of recent immunocytological studies, high resolution structures of some division proteins and results indicating how bacteria may measure their mid cell point.
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Affiliation(s)
- Stephen G Addinall
- School of Biological Sciences, University Manchester, 2.205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
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25
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van Delden C, Comte R, Bally AM. Stringent response activates quorum sensing and modulates cell density-dependent gene expression in Pseudomonas aeruginosa. J Bacteriol 2001; 183:5376-84. [PMID: 11514523 PMCID: PMC95422 DOI: 10.1128/jb.183.18.5376-5384.2001] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During nutrient starvation, Escherichia coli elicits a stringent response involving the ribosome-associated protein RelA. Activation of RelA results in a global change in the cellular metabolism including enhanced expression of the stationary-phase sigma factor RpoS. In the human pathogen Pseudomonas aeruginosa, a complex quorum-sensing circuitry, linked to RpoS expression, is required for cell density-dependent production of many secreted virulence factors, including LasB elastase. Quorum sensing relies on the activation of specific transcriptional regulators (LasR and RhlR) by their corresponding autoinducers (3-oxo-C(12)-homoserine lactone [HSL] and C(4)-HSL), which function as intercellular signals. We found that overexpression of relA activated the expression of rpoS in P. aeruginosa and led to premature, cell density-independent LasB elastase production. We therefore investigated the effects of the stringent response on quorum sensing. Both lasR and rhlR gene expression and autoinducer synthesis were prematurely activated during the stringent response induced by overexpression of relA. Premature expression of lasR and rhlR was also observed when relA was overexpressed in a PAO1 rpoS mutant. The stringent response induced by the amino acid analogue serine hydroxamate (SHX) also led to premature production of the 3-oxo-C(12)-HSL autoinducer. This response to SHX was absent in a PAO1 relA mutant. These findings suggest that the stringent response can activate the two quorum-sensing systems of P. aeruginosa independently of cell density.
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Affiliation(s)
- C van Delden
- Department of Genetics and Microbiology, University of Geneva Medical School, CH-1211 Geneva 4, Switzerland
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26
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Wei Y, Lee JM, Smulski DR, LaRossa RA. Global impact of sdiA amplification revealed by comprehensive gene expression profiling of Escherichia coli. J Bacteriol 2001; 183:2265-72. [PMID: 11244066 PMCID: PMC95133 DOI: 10.1128/jb.183.7.2265-2272.2001] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli the amplification of sdiA, a positive activator of ftsQAZ, genes that are essential for septation, results in mitomycin C resistance. To help us understand this resistance phenotype, genes whose expression was altered by increased sdiA dosage were identified using a DNA microarray-based, comprehensive transcript profiling method. The expression of 62 genes was reduced by more than threefold; of these, 41 are involved in motility and chemotaxis. Moreover, the expression of 75 genes, 36 of which had been previously characterized, was elevated at least threefold. As expected, increased sdiA dosage led to significantly elevated sdiA and 'ddlB-ftsQAZ-lpxC operon expression. Transcription of two genes, uvrY and uvrC, located downstream of sdiA and oriented in the same direction, was elevated about 10-fold, although the intervening gene, yecF, of opposite polarity was unaffected by increased sdiA dosage. Three genes (mioC and gidAB) flanking the replication origin, oriC, were transcribed more often when sdiA dosage was high, as were 12 genes within 1 min of a terminus of replication, terB. Transcription of the acrABDEF genes, mapping in three widely spaced loci, was elevated significantly, while several genes involved in DNA repair and replication (e.g., nei, recN, mioC, and mcrC) were moderately elevated in expression. Such global analysis provides a link between septation and the response to DNA-damaging agents.
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Affiliation(s)
- Y Wei
- Central Research and Development, DuPont Company, Wilmington, Delaware 19880-0173, USA
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27
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Holtzendorff J, Partensky F, Jacquet S, Bruyant F, Marie D, Garczarek L, Mary I, Vaulot D, Hess WR. Diel expression of cell cycle-related genes in synchronized cultures of Prochlorococcus sp. strain PCC 9511. J Bacteriol 2001; 183:915-20. [PMID: 11208789 PMCID: PMC94958 DOI: 10.1128/jb.183.3.915-920.2001] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cell cycle of the chlorophyll b-possessing marine cyanobacterium Prochlorococcus is highly synchronized under natural conditions. To understand the underlying molecular mechanisms we cloned and sequenced dnaA and ftsZ, two key cell cycle-associated genes, and studied their expression. An axenic culture of Prochlorococcus sp. strain PCC 9511 was grown in a turbidostat with a 12 h-12 h light-dark cycle for 2 weeks. During the light periods, a dynamic light regimen was used in order to simulate the natural conditions found in the upper layers of the world's oceans. This treatment resulted in strong cell cycle synchronization that was monitored by flow cytometry. The steady-state mRNA levels of dnaA and ftsZ were monitored at 4-h intervals during four consecutive division cycles. Both genes exhibited clear diel expression patterns with mRNA maxima during the replication (S) phase. Western blot experiments indicated that the peak of FtsZ concentration occurred at night, i.e., at the time of cell division. Thus, the transcript accumulation of genes involved in replication and division is coordinated in Prochlorococcus sp. strain PCC 9511 and might be crucial for determining the timing of DNA replication and cell division.
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Affiliation(s)
- J Holtzendorff
- Institute of Biology/Genetics, Humboldt-University, D-10115 Berlin, Germany
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28
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Barker MM, Gaal T, Josaitis CA, Gourse RL. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J Mol Biol 2001; 305:673-88. [PMID: 11162084 DOI: 10.1006/jmbi.2000.4327] [Citation(s) in RCA: 269] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To determine the role of ppGpp in both negative and positive regulation of transcription initiation during exponential growth in Escherichia coli, we examined transcription in vivo and in vitro from the growth-rate-dependent rRNA promoter rrnB P1 and from the inversely growth-rate-dependent amino acid biosynthesis/transport promoters PargI, PhisG, PlysC, PpheA, PthrABC, and PlivJ. rrnB P1 promoter activity was slightly higher at all growth-rates in strains unable to synthesize ppGpp (deltarelAdeltaspoT) than in wild-type strains. Consistent with this observation and with the large decrease in rRNA transcription during the stringent response (when ppGpp levels are much higher), ppGpp inhibited transcription from rrnB P1 in vitro. In contrast, amino acid promoter activity was considerably lower in deltarelAdeltaspoT strains than in wild-type strains, but ppGpp had no effect on amino acid promoter activity in vitro. Detailed kinetic analysis in vitro indicated that open complexes at amino acid promoters formed much more slowly and were much longer-lived than rrnB P1 open complexes. ppGpp did not increase the rates of association with, or escape from, amino acid promoters in vitro, consistent with its failure to stimulate transcription directly. In contrast, ppGpp decreased the half-lives of open complexes at all promoters, whether the half-life was seconds (rrnB P1) or hours (amino acid promoters). The results described here and in the accompanying paper indicate that ppGpp directly inhibits transcription, but only from promoters like rrnB P1 that make short-lived open complexes. The results indicate that stimulation of amino acid promoters occurs indirectly. The accompanying paper evaluates potential models for positive control of amino acid promoters by ppGpp that might explain the requirement of ppGpp for amino acid prototrophy.
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Affiliation(s)
- M M Barker
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, 53706, USA
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29
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Vinella D, Cashel M, D'Ari R. Selected amplification of the cell division genes ftsQ-ftsA-ftsZ in Escherichia coli. Genetics 2000; 156:1483-92. [PMID: 11102351 PMCID: PMC1461353 DOI: 10.1093/genetics/156.4.1483] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rapidly growing Escherichia coli is unable to divide in the presence of the antibiotic mecillinam, whose direct target is penicillin-binding protein 2 (PBP2), responsible for the elongation of the cylindrical portion of the cell wall. Division can be restored in the absence of PBP2 activity by increasing the concentration of the cell division proteins FtsQ, FtsA, and FtsZ. We tried to identify regulators of the ftsQ-ftsA-ftsZ operon among mecillinam-resistant mutants, which include strains overexpressing these genes. By insertional mutagenesis with mini-Tn10 elements, we selected for insertions that conferred mecillinam resistance. Among 15 such mutants, 7 suppressed the thermosensitivity of the ftsZ84(Ts) mutant, strongly suggesting that they had increased FtsZ activity. In all 7 cases, however, the mutants resulted from a duplication of the ftsQAZ region. These duplications seemed to result from multiple events, suggesting that no simple insertional inactivation can result in a mutant with sufficiently amplified ftsQAZ expression to confer mecillinam resistance. The structure of the duplications suggests a general method for constructing directed duplications of precise sequences.
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Affiliation(s)
- D Vinella
- Institut Jacques Monod (CNRS, Université Paris 7, Université Paris 6), 75251 Paris Cedex 05, France.
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30
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Abstract
Perhaps the biggest single task facing a bacterial cell is to divide into daughter cells that contain the normal complement of chromosomes. Recent technical and conceptual breakthroughs in bacterial cell biology, combined with the flood of genome sequence information and the excellent genetic tools in several model systems, have shed new light on the mechanism of prokaryotic cell division. There is good evidence that in most species, a molecular machine, organized by the tubulin-like FtsZ protein, assembles at the site of division and orchestrates the splitting of the cell. The determinants that target the machine to the right place at the right time are beginning to be understood in the model systems, but it is still a mystery how the machine actually generates the constrictive force necessary for cytokinesis. Moreover, although some cell division determinants such as FtsZ are present in a broad spectrum of prokaryotic species, the lack of FtsZ in some species and different profiles of cell division proteins in different families suggests that there are diverse mechanisms for regulating cell division.
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Affiliation(s)
- W Margolin
- Department of Microbiology and Molecular Genetics, University of Texas-Houston Medical School, 6431 Fannin, Houston, Texas 77030, USA.
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31
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Abstract
Duplication of the Escherichia coli bacterial cell culminates in the formation of a division septum that splits the progenitor cell into two identical daughter cells. Invagination of the cell envelope is brought about by the co-ordinated interplay of a family of septation-specific proteins that act locally at mid-cell at a specific time in the cell cycle. The majority of the genes known to be required for septum formation are found within the large mra cluster located at 2 min on the E. coli genetic map (nucleotides 89552-107474). Examination of the controls exerted on the mra operon shows that E. coli uses an extraordinary range of strategies to co-ordinate the expression of the cell division genes with respect to each other and to the cell cycle.
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Affiliation(s)
- S J Dewar
- Department of Biological Sciences, Heriot Watt University, EH14 4AS, Edinburgh, UK.
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32
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Ghuysen JM, Goffin C. Lack of cell wall peptidoglycan versus penicillin sensitivity: new insights into the chlamydial anomaly. Antimicrob Agents Chemother 1999; 43:2339-44. [PMID: 10508003 PMCID: PMC89479 DOI: 10.1128/aac.43.10.2339] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- J M Ghuysen
- Centre d'Ingénierie des Protéines, Institut de Chimie, B6, Université de Liège, B-4000 Sart Tilman (Liège), Belgium.
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33
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Dassain M, Leroy A, Colosetti L, Carolé S, Bouché JP. A new essential gene of the 'minimal genome' affecting cell division. Biochimie 1999; 81:889-95. [PMID: 10572302 DOI: 10.1016/s0300-9084(99)00207-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complete sequencing of bacterial genomes has offered new opportunities for the identification of essential genes involved in the control and progression of the cell cycle. For this purpose, we have disrupted ten E. coli genes belonging to the so-called 'minimal genome'. One of these genes, yihA, was necessary for normal cell division. The yihA gene possesses characteristic GTPase motifs and its homologues are present in eukaryotes, archaea and most prokaryotes. Depletion of YihA protein led to a severe reduction in growth rate and to extensive filamentation, with a block beyond the stage of nucleoid segregation. Filamentation was correlated with reduced FtsZ levels and could be specifically suppressed by overexpression of ftsQI, ftsA and ftsZ, and to some extent by ftsZ alone. We hypothesize that YihA, like the Era GTPase, may participate in a checkpoint mechanism that ensures a correct coordination of cell cycle events.
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Affiliation(s)
- M Dassain
- Laboratoire de Microbiologie et de Génétique Cellulaire du CNRS, 118, route de Narbonne, 31062 Toulouse, France
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34
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Abstract
The presence of intricate global cell regulation mechanisms may be one reason for the exceptional environmental and evolutionary success of microbes. Promoters, the cis-acting signals, are responsive to several stimuli related to growth, stress and substrate specificity. Their response is mediated by a wide variety of trans-acting regulators that sense the environment and the physiological state of the cell and adjust the transcription of specific genes. One of the main transcriptional regulation webs operates in the transition from affluent to barren conditions, with sigmaS being the chief actor in a company of players that stage a competition for the sparsely available RNA polymerase molecules. In this role, sigmaS may be assisted by several factors, including nucleoid-related proteins and metabolites. In addition, the levels of sigmaS itself are regulated by mechanisms that include inactivation and degradation. Several transcription factors, belonging to different regulatory pathways, may operate in the same promoter. In such a case, the final transcriptional output depends both on the interplay of effectors and on the properties of the recruitment of the effector-RNA polymerase complex to the promoter. RNA polymerase itself is also capable of establishing selective interactions with activators and specific promoter regions through the carboxy-terminal domain of its alpha subunit (alphaCTD). Transcriptional regulation controls pervade such crucial events in the life of bacterial cells as Escherichia coli cell division, Bacillus subtilis sporulation and Caulobacter crescentus differentiation. These examples suggest that bacteria have been particularly inventive in adapting gene expression regulation to survive under a diversity of environments and have done so by exploiting the malleable molecular mechanisms involved in transcription, developing complexities that may match those found in eukaryotic cells.
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Affiliation(s)
- M Vicente
- Centro Nacional de Biotecnología CSIC, Campus de Cantoblanco, 28049 Madrid, Spain.
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