651
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Johnston RJ, Desplan C. Stochastic mechanisms of cell fate specification that yield random or robust outcomes. Annu Rev Cell Dev Biol 2010; 26:689-719. [PMID: 20590453 DOI: 10.1146/annurev-cellbio-100109-104113] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although cell fate specification is tightly controlled to yield highly reproducible results and avoid extreme variation, developmental programs often incorporate stochastic mechanisms to diversify cell types. Stochastic specification phenomena are observed in a wide range of species and an assorted set of developmental contexts. In bacteria, stochastic mechanisms are utilized to generate transient subpopulations capable of surviving adverse environmental conditions. In vertebrate, insect, and worm nervous systems, stochastic fate choices are used to increase the repertoire of sensory and motor neuron subtypes. Random fate choices are also integrated into developmental programs controlling organogenesis. Although stochastic decisions can be maintained to produce a mosaic of fates within a population of cells, they can also be compensated for or directed to yield robust and reproducible outcomes.
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652
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Abstract
Recent discoveries suggest that cells of a clonal population often display multiple metabolic phenotypes at the same time. Motivated by the success of mass spectrometry (MS) in the investigation of population-level metabolomics, the analytical community has initiated efforts towards MS-based single cell metabolomics to investigate metabolic phenomena that are buried under the population average. Here, we review the current approaches and illustrate their advantages and disadvantages. Because of significant advances in the field, different technologies are now at the verge of generating data that are useful for exploring and investigating metabolic heterogeneity.
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Affiliation(s)
- Matthias Heinemann
- ETH Zurich, Institute of Molecular Systems Biology, Wolfgang-Pauli-Strasse 16, Zurich, Switzerland.
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653
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Ray S, Peters CA. Adaptations in microbiological populations exposed to dinitrophenol and other chemical stressors. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2010; 29:2161-2168. [PMID: 20872677 DOI: 10.1002/etc.280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Microbiological populations in natural and engineered systems may experience multiple exposures to chemical stressors, which may affect system functions. The impact of such exposures on the metabolism of a population of Pseudomonas aeruginosa was studied using respirometry. Two serial exposures to low concentrations of 2,4-dinitrophenol (DNP), pentachlorophenol (PCP), or N-ethyl maleimide (NEM) did not affect metabolism beyond that expected for a single exposure. However, at higher concentrations, three exposures to DNP led to a combination of metabolic stress and resilience in the population. At a low DNP concentration of 400 mg/L, multiple exposures led to increased stress but indicated no development of resilience. At a high DNP concentration of 1,200 mg/L, no biological activity was observed, indicating that the population did not survive the exposure. At intermediate concentrations of 800 and 900 mg/L DNP, stress was observed, but it was found to decrease after multiple exposures. This, combined with the observation that the size of the population decreased, indicated that resilience in the population had developed because of elimination of the weaker organisms in the population. In contrast, the lack of resilience at the lower DNP concentration was attributed to the survival of the strong as well as weak members, lowering the resilience of the population as a whole. The development of resilience within a window of stressor concentrations is an important finding with implications for predicting the performance of biotreatment processes and biosensor technologies and for interpreting ecotoxicity risk assessments.
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Affiliation(s)
- Sujata Ray
- Department of Civil Engineering, Indian Institute of Technology, Guwahati, Guwahati, Assam 781 039, India
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654
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Abstract
Growing populations of Bacillus subtilis exhibit bistability: motile cells co-exist with long chains of sessile cells. An epigenetic switch has been characterized that controls the transition between the two cell types.
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655
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Nielsen AT, Dolganov NA, Rasmussen T, Otto G, Miller MC, Felt SA, Torreilles S, Schoolnik GK. A bistable switch and anatomical site control Vibrio cholerae virulence gene expression in the intestine. PLoS Pathog 2010; 6:e1001102. [PMID: 20862321 PMCID: PMC2940755 DOI: 10.1371/journal.ppat.1001102] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 08/13/2010] [Indexed: 01/09/2023] Open
Abstract
A fundamental, but unanswered question in host-pathogen interactions is the timing, localization and population distribution of virulence gene expression during infection. Here, microarray and in situ single cell expression methods were used to study Vibrio cholerae growth and virulence gene expression during infection of the rabbit ligated ileal loop model of cholera. Genes encoding the toxin-coregulated pilus (TCP) and cholera toxin (CT) were powerfully expressed early in the infectious process in bacteria adjacent to epithelial surfaces. Increased growth was found to co-localize with virulence gene expression. Significant heterogeneity in the expression of tcpA, the repeating subunit of TCP, was observed late in the infectious process. The expression of tcpA, studied in single cells in a homogeneous medium, demonstrated unimodal induction of tcpA after addition of bicarbonate, a chemical inducer of virulence gene expression. Striking bifurcation of the population occurred during entry into stationary phase: one subpopulation continued to express tcpA, whereas the expression declined in the other subpopulation. ctxA, encoding the A subunit of CT, and toxT, encoding the proximal master regulator of virulence gene expression also exhibited the bifurcation phenotype. The bifurcation phenotype was found to be reversible, epigenetic and to persist after removal of bicarbonate, features consistent with bistable switches. The bistable switch requires the positive-feedback circuit controlling ToxT expression and formation of the CRP-cAMP complex during entry into stationary phase. Key features of this bistable switch also were demonstrated in vivo, where striking heterogeneity in tcpA expression was observed in luminal fluid in later stages of the infection. When this fluid was diluted into artificial seawater, bacterial aggregates continued to express tcpA for prolonged periods of time. The bistable control of virulence gene expression points to a mechanism that could generate a subpopulation of V. cholerae that continues to produce TCP and CT in the rice water stools of cholera patients. Most pathogenic microorganisms infect in a stepwise manner: colonization of host surfaces is followed by invasion and injury of host tissues and, late in the infectious process, dissemination to other hosts occurs. During its residence in the host, the pathogen produces essential virulence determinants and often replicates rapidly, leading to a vast expansion of its biomass. Although this scenario is well established also for Vibrio cholerae, the cause of a potentially fatal diarrheal illness, it has not previously been possible to identify precisely when or where virulence determinants are produced in the intestine. We addressed this question by investigating the expression of virulence genes by individual V. cholerae during infection of the small intestine. Virulence genes were found to be powerfully expressed early in the infectious process by bacteria in close proximity to epithelial surfaces. Increased replication rates were also localized to epithelial surfaces. During later stages of the infection, the population of V. cholerae bifurcates into two fractions: one subpopulation continues to express virulence genes, whereas these genes are silenced in the other subpopulation. The genetic program controlling the continued production of virulence genes may mediate the persistence of a hyper-infectious subpopulation of bacteria in the stools of cholera patients.
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Affiliation(s)
- Alex T. Nielsen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nadia A. Dolganov
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Thomas Rasmussen
- Technical University of Denmark, Department of Systems Biology, Kgs. Lyngby, Denmark
| | - Glen Otto
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Michael C. Miller
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Stephen A. Felt
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Stéphanie Torreilles
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gary K. Schoolnik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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656
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The pdh operon is expressed in a subpopulation of stationary-phase bacteria and is important for survival of sugar-starved Streptococcus mutans. J Bacteriol 2010; 192:4395-402. [PMID: 20581205 DOI: 10.1128/jb.00574-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus mutans is a facultative member of the oral plaque and is associated with dental caries. It is able to survive long periods of sugar starvation. We show here that inactivation of pdhD, putatively encoding a subunit of the pyruvate dehydrogenase complex, impairs survival of both batch cultures and biofilms. We show that pdhD and the downstream genes pdhA, pdhB, and pdhC form an operon that is predominantly transcribed in stationary phase. Analysis with fluorescent reporters revealed a bimodal expression pattern for the pdh promoter, with less than 1% of stationary-phase populations expressing pdh. When it was first detected, after 1 day of sugar starvation in batch culture, expression was mostly in individual bacteria. At later times, expressing bacteria were often in chains. The lengths of the chains increased with time. We infer that the pdh-expressing subpopulation is able grow and divide and to persist for extended times in stationary phase.
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657
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Origin and analysis of microbial population heterogeneity in bioprocesses. Curr Opin Biotechnol 2010; 21:100-13. [PMID: 20138500 DOI: 10.1016/j.copbio.2010.01.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 01/14/2010] [Accepted: 01/14/2010] [Indexed: 10/19/2022]
Abstract
Heterogeneity of industrial production cultures is accepted to a certain degree; however, the underlying mechanisms are seldom perceived or included in the development of new bioprocess control strategies. Population heterogeneity and its basics, perceptible in the diverse proficiency of cells, begins with asymmetric birth and is found to recess during the life cycle. Since inefficient subpopulations have significant impact on the productivity of industrial cultures, cellular heterogeneity needs to be detected and quantified by using high speed detection tools like flow cytometry. Possible origins of population heterogeneity, sophisticated fluorescent techniques for detection of individual cell states, and cutting-edge Omics-technologies for extended information beyond the resolution of fluorescent labelling are highlighted.
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658
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A mathematical and computational approach for integrating the major sources of cell population heterogeneity. J Theor Biol 2010; 266:41-61. [PMID: 20685607 DOI: 10.1016/j.jtbi.2010.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 04/08/2010] [Accepted: 06/01/2010] [Indexed: 11/20/2022]
Abstract
Several approaches have been used in the past to model heterogeneity in bacterial cell populations, with each approach focusing on different source(s) of heterogeneity. However, a holistic approach that integrates all the major sources into a comprehensive framework applicable to cell populations is still lacking. In this work we present the mathematical formulation of a cell population master equation (CPME) that describes cell population dynamics and takes into account the major sources of heterogeneity, namely stochasticity in reaction, DNA-duplication, and division, as well as the random partitioning of species contents into the two daughter cells. The formulation also takes into account cell growth and respects the discrete nature of the molecular contents and cell numbers. We further develop a Monte Carlo algorithm for the simulation of the stochastic processes considered here. To benchmark our new framework, we first use it to quantify the effect of each source of heterogeneity on the intrinsic and the extrinsic phenotypic variability for the well-known two-promoter system used experimentally by Elowitz et al. (2002). We finally apply our framework to a more complicated system and demonstrate how the interplay between noisy gene expression and growth inhibition due to protein accumulation at the single cell level can result in complex behavior at the cell population level. The generality of our framework makes it suitable for studying a vast array of artificial and natural genetic networks. Using our Monte Carlo algorithm, cell population distributions can be predicted for the genetic architecture of interest, thereby quantifying the effect of stochasticity in intracellular reactions or the variability in the rate of physiological processes such as growth and division. Such in silico experiments can give insight into the behavior of cell populations and reveal the major sources contributing to cell population heterogeneity.
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659
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Wade WF, O’Toole GA. Antibodies and immune effectors: shaping Gram-negative bacterial phenotypes. Trends Microbiol 2010; 18:234-9. [DOI: 10.1016/j.tim.2010.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 02/22/2010] [Accepted: 03/04/2010] [Indexed: 11/24/2022]
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660
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The threshold level of the sensor histidine kinase KinA governs entry into sporulation in Bacillus subtilis. J Bacteriol 2010; 192:3870-82. [PMID: 20511506 DOI: 10.1128/jb.00466-10] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Sporulation in Bacillus subtilis is controlled by a complex gene regulatory circuit that is activated upon nutrient deprivation. The initial process is directed by the phosphorelay, involving the major sporulation histidine kinase (KinA) and two additional phosphotransferases (Spo0F and Spo0B), that activates the master transcription factor Spo0A. Little is known about the initial event and mechanisms that trigger sporulation. Using a strain in which the synthesis of KinA is under the control of an IPTG (isopropyl-beta-d-thiogalactopyranoside)-inducible promoter, here we demonstrate that inducing the synthesis of the KinA beyond a certain level leads to the entry of the irreversible process of sporulation irrespective of nutrient availability. Moreover, the engineered cells expressing KinA under a sigma(H)-dependent promoter that is similar to but stronger than the endogenous kinA promoter induce sporulation during growth. These cells, which we designated COS (constitutive sporulation) cells, exhibit the morphology and properties of sporulating cells and express sporulation marker genes under nutrient-rich conditions. Thus, we created an engineered strain displaying two cell cycles (growth and sporulation) integrated into one cycle irrespective of culture conditions, while in the wild type, the appropriate cell fate decision is made depending on nutrient availability. These results suggest that the threshold level of the major sporulation kinase acts as a molecular switch to determine cell fate and may rule out the possibility that the activity of KinA is regulated in response to the unknown signal(s).
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661
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Zhang DL, Ross T, Bowman JP. Physiological aspects of Listeria monocytogenes during inactivation accelerated by mild temperatures and otherwise non-growth permissive acidic and hyperosmotic conditions. Int J Food Microbiol 2010; 141:177-85. [PMID: 20553835 DOI: 10.1016/j.ijfoodmicro.2010.05.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 04/14/2010] [Accepted: 05/14/2010] [Indexed: 11/25/2022]
Abstract
Application of simultaneous low pH (pH 3.5) and low water activity (a(w)=0.9; 2.5M NaCl) conditions to Listeria monocytogenes strains ScottA and FW03/0035, and growth permissive temperatures from 25 degrees C up to 45 degrees C result in increasingly accelerated inactivation rates. This phenomenon was related to i) increased cell permeability as suggested by ethidium homodimer-1 uptake and ii) de-energization as indicated by rapidly reduced ATP basal levels. Enrichment-based recovery experiments indicated that the stress conditions eventually lead to complete loss of reproductive capacity, possibly corresponding to an irreversible collapse of pH homeostasis. Transcriptomic analyses were used to obtain further insights into the physiology of the inactivation process occurring at 25 degrees C where inactivation times were more prolonged. QPCR, mRNA decay and microarray experiments revealed transcripts of tufA and other genes become substantially more stable during inactivation resulting from exposure to combined low pH/a(w) and from non-growth permissive temperature exposure. Genes that appear to be important for initial survival of combined low pH/a(w) were delineated by K-means clustering of expression data and included an overrepresentation of SigB-activated genes, the overall response of which fades with increasing time of inactivation exposure.
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Affiliation(s)
- Dong Lai Zhang
- Food Safety Centre, Tasmanian Institute of Agricultural Research, University of Tasmania, Hobart, Australia
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662
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Stupak EE, Stupak IV. Phenotypic switching of Escherichia coli cells containing cyclic digenic systems with negative feedback upon changes in cultivation conditions. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410050042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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663
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McMeekin T, Hill C, Wagner M, Dahl A, Ross T. Ecophysiology of food-borne pathogens: Essential knowledge to improve food safety. Int J Food Microbiol 2010; 139 Suppl 1:S64-78. [DOI: 10.1016/j.ijfoodmicro.2010.01.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 01/26/2010] [Accepted: 01/27/2010] [Indexed: 10/19/2022]
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664
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Havelaar AH, Brul S, de Jong A, de Jonge R, Zwietering MH, ter Kuile BH. Future challenges to microbial food safety. Int J Food Microbiol 2010; 139 Suppl 1:S79-94. [DOI: 10.1016/j.ijfoodmicro.2009.10.015] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 10/09/2009] [Accepted: 10/14/2009] [Indexed: 11/29/2022]
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665
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Eswaramoorthy P, Dinh J, Duan D, Igoshin OA, Fujita M. Single-cell measurement of the levels and distributions of the phosphorelay components in a population of sporulating Bacillus subtilis cells. MICROBIOLOGY-SGM 2010; 156:2294-2304. [PMID: 20413551 DOI: 10.1099/mic.0.038497-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Upon nutrient starvation, the Gram-positive bacterium Bacillus subtilis switches from growth to sporulation by activating a multicomponent phosphorelay consisting of a major sensor histidine kinase (KinA), two phosphotransferases (Spo0F and Spo0B) and a response regulator (Spo0A). Although the primary sporulation signal(s) produced under starvation conditions is not known, it is believed that the reception of a signal(s) on the sensor kinase results in the activation of autophosphorylation of the enzyme. The phosphorylated kinase transfers the phosphate group to Spo0A via the phosphorelay and thus triggers sporulation. With a combination of quantitative immunoblot analysis, microscopy imaging and computational analysis, here we found that each of the phosphorelay components tested increased gradually over the period of sporulation, and that Spo0F was expressed in a more heterogeneous pattern than KinA and Spo0B in a sporulating cell population. We determined molecule numbers and concentrations of each phosphorelay component under physiological sporulation conditions at the single-cell level. Based on these results, we suggest that successful entry into the sporulation state is manifested by a certain critical level of each phosphorelay component, and thus that only a subpopulation achieves a sufficient intracellular quorum of the phosphorelay components to activate Spo0A and proceed successfully to the entry into sporulation.
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Affiliation(s)
| | - Jeffrey Dinh
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | - Daniel Duan
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, Houston, TX 77251-1892, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
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666
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Ter Beek A, Brul S. To kill or not to kill Bacilli: opportunities for food biotechnology. Curr Opin Biotechnol 2010; 21:168-74. [DOI: 10.1016/j.copbio.2010.03.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 03/16/2010] [Accepted: 03/18/2010] [Indexed: 01/06/2023]
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667
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Chai Y, Norman T, Kolter R, Losick R. An epigenetic switch governing daughter cell separation in Bacillus subtilis. Genes Dev 2010; 24:754-65. [PMID: 20351052 DOI: 10.1101/gad.1915010] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Growing cells of Bacillus subtilis are a bistable mixture of individual motile cells in which genes for daughter cell separation and motility are ON, and chains of sessile cells in which these genes are OFF. How this ON/OFF switch is controlled has been mysterious. Here we report that a complex of the SinR and SlrR proteins binds to and represses genes involved in cell separation and motility. We also report that SinR and SlrR constitute a double-negative feedback loop in which SinR represses the gene for SlrR (slrR), and, by binding to (titrating) SinR, SlrR prevents SinR from repressing slrR. Thus, SlrR indirectly derepresses its own gene, creating a self-reinforcing loop. Finally, we show that, once activated, the loop remains locked in a high SlrR state in which cell separation and motility genes are OFF for extended periods of time. SinR and SlrR constitute an epigenetic switch for controlling genes involved in cell separation and motility.
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Affiliation(s)
- Yunrong Chai
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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668
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Veening JW, Kuipers OP. Gene position within a long transcript as a determinant for stochastic switching in bacteria. Mol Microbiol 2010; 76:269-72. [PMID: 20233302 DOI: 10.1111/j.1365-2958.2010.07113.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
How cultures of genetically identical cells bifurcate into distinct phenotypic subpopulations under uniform growth conditions is an important question in developmental biology of relevance even to relatively simple developmental systems, such as spore formation in bacteria. A growing Bacillus subtilis culture consists of either cells that are motile and can swim or cells that are non-motile and are chained together. In this issue of Molecular Microbiology, Cozy and Kearns show that the probability of a cell to become motile depends on the position of the sigD gene within the long (27 kb) motility operon. sigD encodes the alternative sigma factor sigma(D) that, together with RNA polymerase, drives expression of genes required for cell separation and the assembly of flagella. sigD is the penultimate gene of the B. subtilis motility operon and, in the control strain approximately, 70% of the cells are motile. When sigD was moved upstream within the operon, a larger fraction of cells became motile (up to 100%). This study highlights that the position of a gene within an operon can have a large impact on the control of gene expression. Furthermore, it suggests that RNA polymerase processivity or mRNA turnover can play important roles as sources of noise in bacterial development, and that gene position might be an unrecognized and possibly widespread mechanism to regulate phenotypic variation.
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Affiliation(s)
- Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Kluyver Centre for Genomics of Industrial Fermentation, University of Groningen, Haren, the Netherlands.
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669
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Cozy LM, Kearns DB. Gene position in a long operon governs motility development in Bacillus subtilis. Mol Microbiol 2010; 76:273-85. [PMID: 20233303 DOI: 10.1111/j.1365-2958.2010.07112.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Growing cultures of Bacillus subtilis bifurcate into subpopulations of motile individuals and non-motile chains of cells that are differentiated at the level of gene expression. The motile cells are ON and the chaining cells are OFF for transcription that depends on RNA polymerase and the alternative sigma factor sigma(D). Here we show that chaining cells were OFF for sigma(D)-dependent gene expression because sigma(D) levels fell below a threshold and sigma(D) activity was inhibited by the anti-sigma factor FlgM. The probability that sigma(D) exceeded the threshold was governed by the position of the sigD gene. The proportion of ON cells increased when sigD was artificially moved forward in the 27 kb fla/che operon. In addition, we identified a new sigma(D)-dependent promoter that increases sigD expression and may provide positive feedback to stabilize the ON state. Finally, we demonstrate that ON/OFF motility states in B. subtilis are a form of development because mosaics of stable and differentiated epigenotypes were evident when the normally dispersed bacteria were forced to grow in one dimension.
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Affiliation(s)
- Loralyn M Cozy
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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670
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Heterochronic phosphorelay gene expression as a source of heterogeneity in Bacillus subtilis spore formation. J Bacteriol 2010; 192:2053-67. [PMID: 20154131 DOI: 10.1128/jb.01484-09] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In response to limiting nutrient sources and cell density signals, Bacillus subtilis can differentiate and form highly resistant endospores. Initiation of spore development is governed by the master regulator Spo0A, which is activated by phosphorylation via a multicomponent phosphorelay. Interestingly, only part of a clonal population will enter this developmental pathway, a phenomenon known as sporulation bistability or sporulation heterogeneity. How sporulation heterogeneity is established is largely unknown. To investigate the origins of sporulation heterogeneity, we constructed promoter-green fluorescent protein (GFP) fusions to the main phosphorelay genes and perturbed their expression levels. Using time-lapse fluorescence microscopy and flow cytometry, we showed that expression of the phosphorelay genes is distributed in a unimodal manner. However, single-cell trajectories revealed that phosphorelay gene expression is highly dynamic or "heterochronic" between individual cells and that stochasticity of phosphorelay gene transcription might be an important regulatory mechanism for sporulation heterogeneity. Furthermore, we showed that artificial induction or depletion of the phosphorelay phosphate flow results in loss of sporulation heterogeneity. Our data suggest that sporulation heterogeneity originates from highly dynamic and variable gene activity of the phosphorelay components, resulting in large cell-to-cell variability with regard to phosphate input into the system. These transcriptional and posttranslational differences in phosphorelay activity appear to be sufficient to generate a heterogeneous sporulation signal without the need of the positive-feedback loop established by the sigma factor SigH.
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671
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Goulian M. Two-component signaling circuit structure and properties. Curr Opin Microbiol 2010; 13:184-9. [PMID: 20149717 DOI: 10.1016/j.mib.2010.01.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 01/15/2010] [Accepted: 01/15/2010] [Indexed: 12/18/2022]
Abstract
Various modeling and experimental studies have analyzed the reactions, interconnections, and motifs in two-component systems, with an eye toward understanding their physiological implications and the differences between alternative designs. Examples where recent progress has been made include aspects of autoregulation, signal integration in branched pathways, cross-talk suppression, and cross-regulation via connector proteins.
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Affiliation(s)
- Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USA.
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672
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Tracy BP, Gaida SM, Papoutsakis ET. Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. Curr Opin Biotechnol 2010; 21:85-99. [DOI: 10.1016/j.copbio.2010.02.006] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 01/29/2010] [Accepted: 02/02/2010] [Indexed: 02/01/2023]
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673
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Synthetic biology: tools to design, build, and optimize cellular processes. J Biomed Biotechnol 2010; 2010:130781. [PMID: 20150964 PMCID: PMC2817555 DOI: 10.1155/2010/130781] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 10/28/2009] [Indexed: 11/17/2022] Open
Abstract
The general central
dogma frames the emergent properties of life,
which make biology both necessary and difficult
to engineer. In a process engineering paradigm,
each biological process stream and process unit
is heavily influenced by regulatory interactions
and interactions with the surrounding
environment. Synthetic biology is developing the
tools and methods that will increase control
over these interactions, eventually resulting in
an integrative synthetic biology that will allow
ground-up cellular optimization. In this review,
we attempt to contextualize the areas of
synthetic biology into three tiers: (1) the
process units and associated streams of the
central dogma, (2) the intrinsic regulatory
mechanisms, and (3) the extrinsic physical and
chemical environment. Efforts at each of these
three tiers attempt to control cellular systems
and take advantage of emerging tools and
approaches. Ultimately, it will be possible to
integrate these approaches and realize the
vision of integrative synthetic biology when
cells are completely rewired for
biotechnological goals. This review will
highlight progress towards this goal as well as
areas requiring further research.
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674
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Coulon A, Gandrillon O, Beslon G. On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter. BMC SYSTEMS BIOLOGY 2010; 4:2. [PMID: 20064204 PMCID: PMC2832887 DOI: 10.1186/1752-0509-4-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2009] [Accepted: 01/08/2010] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gene promoters can be in various epigenetic states and undergo interactions with many molecules in a highly transient, probabilistic and combinatorial way, resulting in a complex global dynamics as observed experimentally. However, models of stochastic gene expression commonly consider promoter activity as a two-state on/off system. We consider here a model of single-gene stochastic expression that can represent arbitrary prokaryotic or eukaryotic promoters, based on the combinatorial interplay between molecules and epigenetic factors, including energy-dependent remodeling and enzymatic activities. RESULTS We show that, considering the mere molecular interplay at the promoter, a single-gene can demonstrate an elaborate spontaneous stochastic activity (eg. multi-periodic multi-relaxation dynamics), similar to what is known to occur at the gene-network level. Characterizing this generic model with indicators of dynamic and steady-state properties (including power spectra and distributions), we reveal the potential activity of any promoter and its influence on gene expression. In particular, we can reproduce, based on biologically relevant mechanisms, the strongly periodic patterns of promoter occupancy by transcription factors (TF) and chromatin remodeling as observed experimentally on eukaryotic promoters. Moreover, we link several of its characteristics to properties of the underlying biochemical system. The model can also be used to identify behaviors of interest (eg. stochasticity induced by high TF concentration) on minimal systems and to test their relevance in larger and more realistic systems. We finally show that TF concentrations can regulate many aspects of the stochastic activity with a considerable flexibility and complexity. CONCLUSIONS This tight promoter-mediated control of stochasticity may constitute a powerful asset for the cell. Remarkably, a strongly periodic activity that demonstrates a complex TF concentration-dependent control is obtained when molecular interactions have typical characteristics observed on eukaryotic promoters (high mobility, functional redundancy, many alternate states/pathways). We also show that this regime results in a direct and indirect energetic cost. Finally, this model can constitute a framework for unifying various experimental approaches. Collectively, our results show that a gene - the basic building block of complex regulatory networks - can itself demonstrate a significantly complex behavior.
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Affiliation(s)
- Antoine Coulon
- Université de Lyon, Université Lyon 1, Centre de Génétique Moléculaire et Cellulaire, CNRS UMR5534, F-69622 Lyon, France.
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675
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Pechmann S, Vendruscolo M. Derivation of a solubility condition for proteins from an analysis of the competition between folding and aggregation. MOLECULAR BIOSYSTEMS 2010; 6:2490-7. [DOI: 10.1039/c005160h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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676
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Lei J, He G, Liu H, Nie Q. A delay model for noise-induced bi-directional switching. NONLINEARITY 2009; 22:2845-2859. [PMID: 20592956 PMCID: PMC2893745 DOI: 10.1088/0951-7715/22/12/003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Many biological systems can switch between two distinct states. Once switched, the system remains stable for a period of time and may switch back to its original state. A gene network with bistability is usually required for the switching and stochastic effect in the gene expression may induce such switching. A typical bistable system allows one-directional switching, in which the switch from the low state to the high state or from the high state to the low state occurs under different conditions. It is usually difficult to enable bi-directional switching such that the two switches can occur under the same condition. Here, we present a model consisting of standard positive feedback loops and an extra negative feedback loop with a time delay to study its capability to produce bi-directional switching induced by noise. We find that the time delay in the negative feedback is critical for robust bi-directional switching and the length of delay affects its switching frequency.
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Affiliation(s)
- Jinzhi Lei
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, People's Republic of China
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677
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López D, Kolter R. Extracellular signals that define distinct and coexisting cell fates in Bacillus subtilis. FEMS Microbiol Rev 2009; 34:134-49. [PMID: 20030732 DOI: 10.1111/j.1574-6976.2009.00199.x] [Citation(s) in RCA: 198] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The soil-dwelling bacterium Bacillus subtilis differentiates into distinct subpopulations of specialized cells that coexist within highly structured communities. The coordination and interplay between these cell types requires extensive extracellular communication driven mostly by sensing self-generated secreted signals. These extracellular signals activate a set of sensor kinases, which respond by phosphorylating three major regulatory proteins, Spo0A, DegU and ComA. Each phosphorylated regulator triggers a specific differentiation program while at the same time repressing other differentiation programs. This allows a cell to differentiate in response to a specific cue, even in the presence of other, possibly conflicting, signals. The sensor kinases involved respond to an eclectic group of extracellular signals, such as quorum-sensing molecules, natural products, temperature, pH or scarcity of nutrients. This article reviews the cascades of cell differentiation pathways that are triggered by sensing extracellular signals. We also present a tentative developmental model in which the diverse cell types sequentially differentiate to achieve the proper development of the bacterial community.
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Affiliation(s)
- Daniel López
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.
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678
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Bistable expression of CsgD in biofilm development of Salmonella enterica serovar typhimurium. J Bacteriol 2009; 192:456-66. [PMID: 19897646 DOI: 10.1128/jb.01826-08] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial persistence in the environment and in the infected host is often aided by the formation of exopolymer-enclosed communities known as biofilms. Heterogeneous gene expression takes place in microcompartments formed within the complex biofilm structure. This study describes cell differentiation within an isogenic bacterial cell population based on the example of biofilm formation by Salmonella enterica serovar Typhimurium. We analyzed the expression of the major biofilm regulator CsgD at the single-cell level with a chromosomal CsgD-green fluorescent protein (GFP) translational fusion. In individual cells, CsgD-GFP expression is mostly found in the cytoplasm. Quantitative expression analysis and results from three different models of S. Typhimurium biofilms demonstrated that CsgD is expressed in a bistable manner during biofilm development. CsgD expression is, however, monomodal when CsgD is expressed in larger amounts due to a promoter mutation or elevated levels of the secondary signaling molecule c-di-GMP. High levels of CsgD-GFP are associated with cellular aggregation in all three biofilm models. Furthermore, the subpopulation of cells expressing large amounts of CsgD is engaged in cellulose production during red, dry, and rough (rdar) morphotype development and in microcolony formation under conditions of continuous flow. Consequently, bistability at the level of CsgD expression leads to a corresponding pattern of task distribution in S. Typhimurium biofilms.
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679
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Danchin A. Information of the chassis and information of the program in synthetic cells. SYSTEMS AND SYNTHETIC BIOLOGY 2009; 3:125-34. [PMID: 19816808 PMCID: PMC2759428 DOI: 10.1007/s11693-009-9036-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2009] [Revised: 07/08/2009] [Accepted: 07/27/2009] [Indexed: 02/01/2023]
Abstract
Synthetic biology aims at reconstructing life to put to the test the limits of our understanding. It is based on premises similar to those which permitted invention of computers, where a machine, which reproduces over time, runs a program, which replicates. The underlying heuristics explored here is that an authentic category of reality, information, must be coupled with the standard categories, matter, energy, space and time to account for what life is. The use of this still elusive category permits us to interact with reality via construction of self-consistent models producing predictions which can be instantiated into experiments. While the present theory of information has much to say about the program, with the creative properties of recursivity at its heart, we almost entirely lack a theory of the information supporting the machine. We suggest that the program of life codes for processes meant to trap information which comes from the context provided by the environment of the machine.
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Affiliation(s)
- Antoine Danchin
- CNRS URA2171/Institut Pasteur, 28 rue du Docteur Roux, Paris Cedex 15, 75724, France,
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680
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Petersen JM, Dubilier N. Methanotrophic symbioses in marine invertebrates. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:319-335. [PMID: 23765884 DOI: 10.1111/j.1758-2229.2009.00081.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Symbioses between marine animals and aerobic methane-oxidizing bacteria are found at hydrothermal vents and cold seeps in the deep sea where reduced, methane-rich fluids mix with the surrounding oxidized seawater. These habitats are 'oases' in the otherwise nutrient-poor deep sea, where entire ecosystems are fueled by microbial chemosynthesis. By associating with bacteria that gain energy from the oxidation of CH4 with O2 , the animal host is indirectly able to gain nutrition from methane, an energy source that is otherwise only available to methanotrophic microorganisms. The host, in turn, provides its symbionts with continuous access to both electron acceptors and donors that are only available at a narrow oxic - anoxic interface for free-living methanotrophs. Symbiotic methane oxidizers have resisted all attempts at cultivation, so that all evidence for these symbiotic associations comes from ultrastructural, enzymatic, physiological, stable isotope and molecular biological studies of the symbiotic host tissues. In this review, we present an overview of the habitats and invertebrate hosts in which symbiotic methane oxidizers have been found, and the methods used to investigate these symbioses, focusing on the symbioses of bathymodiolin mussels that have received the most attention among methanotrophic associations.
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Affiliation(s)
- Jillian M Petersen
- Symbiosis Group, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
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681
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López D, Vlamakis H, Losick R, Kolter R. Cannibalism enhances biofilm development in Bacillus subtilis. Mol Microbiol 2009; 74:609-18. [PMID: 19775247 DOI: 10.1111/j.1365-2958.2009.06882.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cannibalism is a mechanism to delay sporulation in Bacillus subtilis. Cannibal cells express the skf and sdp toxin systems to lyse a fraction of their sensitive siblings. The lysed cells release nutrients that serve to feed the community, effectively delaying spore formation. Here we provide evidence that the subpopulation of cells that differentiates into cannibals is the same subpopulation that produces the extracellular matrix that holds cells together in biofilms. Cannibalism and matrix formation are both triggered in response to the signalling molecule surfactin. Nutrients released by the cannibalized cells are preferentially used by matrix-producing cells, as they are the only cells expressing resistance to the Skf and Sdp toxins. As a result this subpopulation increases in number and matrix production is enhanced when cannibalism toxins are produced. The cannibal/matrix-producing subpopulation is also generated in response to antimicrobials produced by other microorganisms and may thus constitute a defense mechanism to protect B. subtilis from the action of antibiotics in natural settings.
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Affiliation(s)
- Daniel López
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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682
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Modeling of the genetic switch of bacteriophage TP901-1: A heteromer of CI and MOR ensures robust bistability. J Mol Biol 2009; 394:15-28. [PMID: 19747486 DOI: 10.1016/j.jmb.2009.08.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 08/23/2009] [Accepted: 08/27/2009] [Indexed: 11/22/2022]
Abstract
The lytic-lysogenic switch of the temperate lactococcal phage TP901-1 is fundamentally different from that of phage lambda. In phage TP901-1, the lytic promoter P(L) is repressed by CI, whereas repression of the lysogenic promoter P(R) requires the presence of both of the antagonistic regulator proteins, MOR and CI. We model the central part of the switch and compare the two cases for P(R) repression: the one where the two regulators interact only on the DNA and the other where the two regulators form a heteromer complex in the cytoplasm prior to DNA binding. The models are analyzed for bistability, and the predicted promoter repression folds are compared to experimental data. We conclude that the experimental data are best reproduced the latter case, where a heteromer complex forms in solution. We further find that CI sequestration by the formation of MOR:CI complexes in cytoplasm makes the genetic switch robust.
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683
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Wilhelm T. The smallest chemical reaction system with bistability. BMC SYSTEMS BIOLOGY 2009; 3:90. [PMID: 19737387 PMCID: PMC2749052 DOI: 10.1186/1752-0509-3-90] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 09/08/2009] [Indexed: 11/10/2022]
Abstract
Background Bistability underlies basic biological phenomena, such as cell division, differentiation, cancer onset, and apoptosis. So far biologists identified two necessary conditions for bistability: positive feedback and ultrasensitivity. Results Biological systems are based upon elementary mono- and bimolecular chemical reactions. In order to definitely clarify all necessary conditions for bistability we here present the corresponding minimal system. According to our definition, it contains the minimal number of (i) reactants, (ii) reactions, and (iii) terms in the corresponding ordinary differential equations (decreasing importance from i-iii). The minimal bistable system contains two reactants and four irreversible reactions (three bimolecular, one monomolecular). We discuss the roles of the reactions with respect to the necessary conditions for bistability: two reactions comprise the positive feedback loop, a third reaction filters out small stimuli thus enabling a stable 'off' state, and the fourth reaction prevents explosions. We argue that prevention of explosion is a third general necessary condition for bistability, which is so far lacking discussion in the literature. Moreover, in addition to proving that in two-component systems three steady states are necessary for bistability (five for tristability, etc.), we also present a simple general method to design such systems: one just needs one production and three different degradation mechanisms (one production, five degradations for tristability, etc.). This helps modelling multistable systems and it is important for corresponding synthetic biology projects. Conclusion The presented minimal bistable system finally clarifies the often discussed question for the necessary conditions for bistability. The three necessary conditions are: positive feedback, a mechanism to filter out small stimuli and a mechanism to prevent explosions. This is important for modelling bistability with simple systems and for synthetically designing new bistable systems. Our simple model system is also well suited for corresponding teaching purposes.
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Affiliation(s)
- Thomas Wilhelm
- Theoretical Systems Biology, Institute of Food Research, Norwich Research Park, Colney Lane, Norwich NR4 7UA, UK.
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684
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Zamboni N, Sauer U. Novel biological insights through metabolomics and 13C-flux analysis. Curr Opin Microbiol 2009; 12:553-8. [PMID: 19744879 DOI: 10.1016/j.mib.2009.08.003] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 07/31/2009] [Accepted: 08/06/2009] [Indexed: 11/28/2022]
Abstract
Metabolomics and (13)C-flux analysis have become instrumental for analyzing cellular metabolism and its regulation. Driven primarily by technical advances in mass spectrometry-based analytics, they provide unmatched readouts on metabolic state and activity. Functional genomics leverages metabolomics for the discovery of novel enzymes and unexpected secondary activities of annotated enzymes. (13)C-flux analyses are frequently used for empirical elucidation of pathways in poorly characterized species and for network-wide analysis of mechanisms that realize energy and redox balancing. Integration of metabolomics, (13)C-flux analysis and other data enable the condition-dependent characterization of regulatory circuits that ultimately govern the metabolic phenotype.
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Affiliation(s)
- Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
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685
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Abstract
Bacterial autolysis has recently been identified as a key mechanism that regulates different phases of biofilm development including microcolony formation and dispersal. However such autolytic measures are limited to a subfraction of cells within the entire biofilm population. Here we speculate on the role biofilm heterogeneity plays in limiting autolysis within biofilms and further describe the molecular regulation of suicidal and fratricidal mechanisms in biofilm development of Staphylococcus aureus and Enterococcus faecalis.
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686
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Abstract
Cellular differentiation is triggered by extracellular signals that cause target cells to adopt a particular fate. Differentiation in bacteria typically involves autocrine signaling in which all cells in the population produce and respond to the same signal. Here we present evidence for paracrine signaling in bacterial populations-some cells produce a signal to which only certain target cells respond. Biofilm formation in Bacillus involves two centrally important signaling molecules, ComX and surfactin. ComX triggers the production of surfactin. In turn, surfactin causes a subpopulation of cells to produce an extracellular matrix. Cells that produced surfactin were themselves unable to respond to it. Likewise, once surfactin-responsive cells commenced matrix production, they no longer responded to ComX and could not become surfactin producers. Insensitivity to ComX was the consequence of the extracellular matrix as mutant cells unable to make matrix responded to both ComX and surfactin. Our results demonstrate that extracellular signaling was unidirectional, with one subpopulation producing a signal and a different subpopulation responding to it. Paracrine signaling in a bacterial population ensures the maintenance, over generations, of particular cell types even in the presence of molecules that would otherwise cause those cells to differentiate into other cell types.
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Affiliation(s)
- Daniel López
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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687
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688
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Osera C, Amati G, Calvio C, Galizzi A. SwrAA activates poly-γ-glutamate synthesis in addition to swarming in Bacillus subtilis. Microbiology (Reading) 2009; 155:2282-2287. [DOI: 10.1099/mic.0.026435-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Poly-γ-glutamic acid (γ-PGA) is an extracellular polymer produced by various strains of Bacillus. Ιt was first described as the component of the capsule in Bacillus anthracis, where it plays a relevant role in virulence. γ-PGA is also a distinctive component of ‘natto’, a traditional Japanese food consisting of soybean fermented by Bacillus subtilis (natto). Domesticated B. subtilis strains do not synthesize γ-PGA although they possess the functional biosynthetic pgs operon. In the present work we explore the correlation between the genetic determinants, swrAA and degU, which allow a derivative of the domestic strain JH642 to display a mucoid colony morphology on LB agar plates due to the production of γ-PGA. Full activation of the pgs operon requires the co-presence of SwrAA and the phosphorylated form of DegU (DegU∼P). The presence of either DegU∼P or SwrAA alone has only marginal effects on pgs operon transcription and γ-PGA production. Although SwrAA was identified as necessary for swarming and full swimming motility together with DegU, we show that motility is not involved in γ-PGA production. Activation of γ-PGA synthesis is therefore a motility-independent phenotype in which SwrAA and DegU∼P display a cooperative effect.
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Affiliation(s)
- Cecilia Osera
- Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, via Ferrata 1, 27100 Pavia, Italy
| | - Giuseppe Amati
- Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, via Ferrata 1, 27100 Pavia, Italy
| | - Cinzia Calvio
- Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, via Ferrata 1, 27100 Pavia, Italy
| | - Alessandro Galizzi
- Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, via Ferrata 1, 27100 Pavia, Italy
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689
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Affiliation(s)
- Susan M Rosenberg
- Department of Molecular and Human Genetics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America.
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690
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Murray EJ, Kiley TB, Stanley-Wall NR. A pivotal role for the response regulator DegU in controlling multicellular behaviour. MICROBIOLOGY-SGM 2009; 155:1-8. [PMID: 19118340 DOI: 10.1099/mic.0.023903-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacteria control multicellular behavioural responses, including biofilm formation and swarming motility, by integrating environmental cues through a complex regulatory network. Heterogeneous gene expression within an otherwise isogenic cell population that allows for differentiation of cell fate is an intriguing phenomenon that adds to the complexity of multicellular behaviour. This review focuses on recent data about how DegU, a pleiotropic response regulator, co-ordinates multicellular behaviour in Bacillus subtilis. We review studies that challenge the conventional understanding of the molecular mechanisms underpinning the DegU regulatory system and others that describe novel targets of DegU during activation of biofilm formation by B. subtilis. We also discuss a novel role for DegU in regulating multicellular processes in the food-borne pathogen Listeria monocytogenes.
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Affiliation(s)
- Ewan J Murray
- Division of Molecular and Environmental Microbiology, College of Life Sciences, MSI/WTB/JBC Complex, University of Dundee, Dundee DD1 5EH, UK
| | - Taryn B Kiley
- Division of Molecular and Environmental Microbiology, College of Life Sciences, MSI/WTB/JBC Complex, University of Dundee, Dundee DD1 5EH, UK
| | - Nicola R Stanley-Wall
- Division of Molecular and Environmental Microbiology, College of Life Sciences, MSI/WTB/JBC Complex, University of Dundee, Dundee DD1 5EH, UK
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691
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Fraser D, Kaern M. A chance at survival: gene expression noise and phenotypic diversification strategies. Mol Microbiol 2009; 71:1333-40. [DOI: 10.1111/j.1365-2958.2009.06605.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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692
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de Jong W, Manteca A, Sanchez J, Bucca G, Smith CP, Dijkhuizen L, Claessen D, Wösten HAB. NepA is a structural cell wall protein involved in maintenance of spore dormancy inStreptomyces coelicolor. Mol Microbiol 2009; 71:1591-603. [DOI: 10.1111/j.1365-2958.2009.06633.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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693
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Abstract
Phenotypic noise and social evolution in microbes have recently attracted huge interdisciplinary interest. A new study highlights the interaction between these phenomena and its implications for self-destructive cooperation.
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Affiliation(s)
- Andy Gardner
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK.
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694
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The capabilities of chaos and complexity. Int J Mol Sci 2009; 10:247-291. [PMID: 19333445 PMCID: PMC2662469 DOI: 10.3390/ijms10010247] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 12/27/2008] [Accepted: 01/04/2009] [Indexed: 11/17/2022] Open
Abstract
To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis? To address these questions, chaos, complexity, self-ordered states, and organization must all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action must be delineated. Are there any formal (non physical, abstract, conceptual, algorithmic) components to chaos, complexity, self-ordering and organization, or are they entirely physicodynamic (physical, mass/energy interaction alone)? Chaos and complexity can produce some fascinating self-ordered phenomena. But can spontaneous chaos and complexity steer events and processes toward pragmatic benefit, select function over non function, optimize algorithms, integrate circuits, produce computational halting, organize processes into formal systems, control and regulate existing systems toward greater efficiency? The question is pursued of whether there might be some yet-to-be discovered new law of biology that will elucidate the derivation of prescriptive information and control. “System” will be rigorously defined. Can a low-informational rapid succession of Prigogine’s dissipative structures self-order into bona fide organization?
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695
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Leisner M, Stingl K, Frey E, Maier B. Stochastic switching to competence. Curr Opin Microbiol 2008; 11:553-9. [PMID: 18955155 DOI: 10.1016/j.mib.2008.09.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Revised: 09/24/2008] [Accepted: 09/28/2008] [Indexed: 11/15/2022]
Abstract
Distinct modes of gene expression enable isogenic populations of bacteria to maintain a diversity of phenotypes and to rapidly adapt to environmental changes. Competence development for DNA transformation in Bacillus subtilis has become a paradigm for a multimodal system which implements a genetic switch through a nonlinear positive feedback of a transcriptional master regulator. Recent advances in quantitative analysis at the single cell level in conjunction with mathematical modeling allowed a molecular level understanding of the switching probability between the noncompetent state and the competent state. It has been discovered that the genetic switching probability may be tuned by controlling noise in the transcription of the master regulator of competence, by timing of its expression, and by rewiring of the control circuit.
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Affiliation(s)
- Madeleine Leisner
- Institut für Allgemeine Zoologie und Genetik, Westfälische Wilhelms Universität, Schlossplatz 5, 48149 Münster, Germany
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696
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DegU and Spo0A jointly control transcription of two loci required for complex colony development by Bacillus subtilis. J Bacteriol 2008; 191:100-8. [PMID: 18978066 DOI: 10.1128/jb.01236-08] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilm formation is an example of a multicellular process which depends on cooperative behavior and differentiation within a bacterial population. Our findings indicate that there is a complex feedback loop that maintains the stoichiometry of the extracellular matrix and other proteins required for complex colony development by Bacillus subtilis. Analysis of the transcriptional regulation of two DegU-activated genes that are required for complex colony development by B. subtilis revealed additional involvement of global regulators that are central to controlling biofilm formation. Activation of transcription from both the yvcA and yuaB promoters requires DegU approximately phosphate, but transcription is inhibited by direct AbrB binding to the promoter regions. Inhibition of transcription by AbrB is relieved when Spo0A approximately phosphate is generated due to its known role in inhibiting abrB expression. Deletion of SinR, a key coordinator of motility and biofilm formation, enhanced transcription from both loci; however, no evidence of a direct interaction with SinR for either the yvcA or yuaB promoter regions was observed. The enhanced transcription in the sinR mutant background was subsequently demonstrated to be dependent on biosynthesis of the polysaccharide component that forms the major constituent of the B. subtilis biofilm matrix. Together, these findings indicate that a genetic network dependent on activation of both DegU and Spo0A controls complex colony development by B. subtilis.
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697
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Pedersen M, Hammer K. The role of MOR and the CI operator sites on the genetic switch of the temperate bacteriophage TP901-1. J Mol Biol 2008; 384:577-89. [PMID: 18930065 DOI: 10.1016/j.jmb.2008.09.071] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Revised: 09/22/2008] [Accepted: 09/23/2008] [Indexed: 10/21/2022]
Abstract
A genetic switch controls whether the temperate bacteriophage TP901-1 will enter a lytic or a lysogenic life cycle after infection of its host, Lactococcus lactis. We studied this bistable switch encoded in a small DNA fragment of 979 bp by fusing it to a reporter gene on a low-copy-number plasmid. The cloned DNA fragment contained the two divergently oriented promoters, P(R) and P(L), transcribing the lysogenic and lytic gene clusters; the two promoter-proximal genes, cI and mor; and the three CI operator sites, O(R), O(L) and O(D). We show that mor encodes a protein and that this protein in concert with CI is required for the bistability. Furthermore, interaction of CI at O(R) represses transcription from the lysogenic promoter, P(R). Thus, CI regulates its own transcription. Interaction of CI at O(L) represses transcription from the lytic promoter, P(L). The presence of only O(L) (absence of O(R) and O(D)) is enough to maintain a bistable system. The distantly located operator site, O(D), functions as a helper site by increasing binding of CI at O(R) and O(L). In the immune state, O(D) increases repression of the lytic promoter, P(L). Our results strongly support the model that a hexameric form of CI binds cooperatively to the three operator sites in the immune state forming a CI-DNA loop structure. Finally, we show that in the anti-immune state, repression of the lysogenic promoter is independent of the known CI operator sites but requires the presence of both CI and MOR.
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Affiliation(s)
- Margit Pedersen
- Center for Systems Microbiology, DTU BIOSYS, Technical University of Denmark, DK-2800 Lyngby,
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