151
|
Kalisky T, Dekel E, Alon U. Cost–benefit theory and optimal design of gene regulation functions. Phys Biol 2007; 4:229-45. [DOI: 10.1088/1478-3975/4/4/001] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
152
|
Wykoff DD, Rizvi AH, Raser JM, Margolin B, O’Shea EK. Positive feedback regulates switching of phosphate transporters in S. cerevisiae. Mol Cell 2007; 27:1005-13. [PMID: 17889672 PMCID: PMC2034509 DOI: 10.1016/j.molcel.2007.07.022] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 06/10/2007] [Accepted: 07/18/2007] [Indexed: 11/30/2022]
Abstract
The regulation of transporters by nutrient-responsive signaling pathways allows cells to tailor nutrient uptake to environmental conditions. We investigated the role of feedback generated by transporter regulation in the budding yeast phosphate-responsive signal transduction (PHO) pathway. Cells starved for phosphate activate feedback loops that regulate high- and low-affinity phosphate transport. We determined that positive feedback is generated by PHO pathway-dependent upregulation of Spl2, a negative regulator of low-affinity phosphate uptake. The interplay of positive and negative feedback loops leads to bistability in phosphate transporter usage--individual cells express predominantly either low- or high-affinity transporters, both of which can yield similar phosphate uptake capacity. Cells lacking the high-affinity transporter, and associated negative feedback, exhibit phenotypes that arise from hysteresis due to unopposed positive feedback. In wild-type cells, population heterogeneity generated by feedback loops may provide a strategy for anticipating changes in environmental phosphate levels.
Collapse
|
153
|
Nachman I, Regev A, Ramanathan S. Dissecting Timing Variability in Yeast Meiosis. Cell 2007; 131:544-56. [DOI: 10.1016/j.cell.2007.09.044] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 07/18/2007] [Accepted: 09/21/2007] [Indexed: 10/22/2022]
|
154
|
Affiliation(s)
- Jerome T Mettetal
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | |
Collapse
|
155
|
Murphy KF, Balázsi G, Collins JJ. Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A 2007; 104:12726-31. [PMID: 17652177 PMCID: PMC1931564 DOI: 10.1073/pnas.0608451104] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Understanding the behavior of basic biomolecular components as parts of larger systems is one of the goals of the developing field of synthetic biology. A multidisciplinary approach, involving mathematical and computational modeling in parallel with experimentation, is often crucial for gaining such insights and improving the efficiency of artificial gene network design. Here we used such an approach and developed a combinatorial promoter design strategy to characterize how the position and multiplicity of tetO(2) operator sites within the GAL1 promoter affect gene expression levels and gene expression noise in Saccharomyces cerevisiae. We observed stronger transcriptional repression and higher gene expression noise as a single operator site was moved closer to the TATA box, whereas for multiple operator-containing promoters, we found that the position and number of operator sites together determined the dose-response curve and gene expression noise. We developed a generic computational model that captured the experimentally observed differences for each of the promoters, and more detailed models to successively predict the behavior of multiple operator-containing promoters from single operator-containing promoters. Our results suggest that the independent binding of single repressors is not sufficient to explain the more complex behavior of the multiple operator-containing promoters. Taken together, our findings highlight the importance of joint experimental-computational efforts and some of the challenges of using a bottom-up approach based on well characterized, isolated biomolecular components for predicting the behavior of complex, synthetic gene networks, e.g., the whole can be different from the sum of its parts.
Collapse
Affiliation(s)
- Kevin F Murphy
- Department of Biomedical Engineering, Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
| | | | | |
Collapse
|
156
|
Schoen C, Joseph B, Claus H, Vogel U, Frosch M. Living in a changing environment: insights into host adaptation in Neisseria meningitidis from comparative genomics. Int J Med Microbiol 2007; 297:601-13. [PMID: 17572149 DOI: 10.1016/j.ijmm.2007.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 04/25/2007] [Accepted: 04/25/2007] [Indexed: 11/18/2022] Open
Abstract
Neisseria meningitidis (the meningococcus) colonizes the human nasopharynx of about 10% of the human population. However, for reasons that are still mostly unknown meningococci occasionally enter the cerebrospinal fluid leading to often fatal bacterial meningitis especially in children and young adults. The genetic basis for the observed differences in the pathogenic potential of different strains has only partially been unravelled so far. With the advent of whole genome sequencing technologies, complete genome sequences from three pathogenic meningococcal strains have become available and allow for a comprehensive analysis of the genomic and genetic differences occurring within this species. In this review, the general properties of the meningococcal genomes so far sequenced is given with an emphasis on the chromosomal rearrangements that have occurred, and the genomic islands and prophages that have been identified. The concomitant development of microarray technology for comparative genome hybridization studies of a large set of different meningococcal isolates as well as strains from other Neisseria species has extended our understanding of meningococcal population genetics on a genome-wide scale thus bridging the gap between meningococcal epidemiology and genomics. Finally, we briefly discuss the potential impact of meningococcal life style on its genome architecture and how in turn this genomic make-up might lead to a virulent phenotype making N. meningitidis an accidental pathogen. The overall properties of the meningococcal genome are characterized by genomic variability and instability, resulting in increased functional flexibility within this species.
Collapse
Affiliation(s)
- Christoph Schoen
- Institut für Hygiene und Mikrobiologie, Universität Würzburg, Josef-Schneider-Str. 2, Bau E1, D-97080 Würzburg, Germany.
| | | | | | | | | |
Collapse
|
157
|
|
158
|
Abstract
An example is provided where, with antagonistic selection and epistatic interaction of alleles at two loci, an autosomal allele can rise in frequency, persist in the population, and even continue to fixation, despite having an apparently lower average fitness than the alternative allele, in a process similar to Parrondo's paradox.
Collapse
Affiliation(s)
- Floyd A Reed
- Department of Biology, University of Maryland, College Park, Maryland 20742-5815, USA.
| |
Collapse
|
159
|
Abstract
According to classical evolutionary theory, phenotypic variation originates from random mutations that are independent of selective pressure. However, recent findings suggest that organisms have evolved mechanisms to influence the timing or genomic location of heritable variability. Hypervariable contingency loci and epigenetic switches increase the variability of specific phenotypes; error-prone DNA replicases produce bursts of variability in times of stress. Interestingly, these mechanisms seem to tune the variability of a given phenotype to match the variability of the acting selective pressure. Although these observations do not undermine Darwin's theory, they suggest that selection and variability are less independent than once thought.
Collapse
Affiliation(s)
- Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | | |
Collapse
|
160
|
|
161
|
Blake WJ, Balázsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ. Phenotypic consequences of promoter-mediated transcriptional noise. Mol Cell 2007; 24:853-65. [PMID: 17189188 DOI: 10.1016/j.molcel.2006.11.003] [Citation(s) in RCA: 453] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2006] [Revised: 08/07/2006] [Accepted: 11/01/2006] [Indexed: 01/26/2023]
Abstract
A more complete understanding of the causes and effects of cell-cell variability in gene expression is needed to elucidate whether the resulting phenotypes are disadvantageous or confer some adaptive advantage. Here we show that increased variability in gene expression, affected by the sequence of the TATA box, can be beneficial after an acute change in environmental conditions. We rationally introduce mutations within the TATA region of an engineered Saccharomyces cerevisiae GAL1 promoter and measure promoter responses that can be characterized as being either highly variable and rapid or steady and slow. We computationally illustrate how a stable transcription scaffold can result in "bursts" of gene expression, enabling rapid individual cell responses in the transient and increased cell-cell variability at steady state. We experimentally verify computational predictions that the rapid response and increased cell-cell variability enabled by TATA-containing promoters confer a clear benefit in the face of an acute environmental stress.
Collapse
|
162
|
Abstract
Various practical challenges involved in controlling living organisms must be surmounted if synthetic biology is to be productive. Efforts to manipulate living organisms have raised the question of whether engineering principles of hierarchy, abstraction and design can be applied to biological systems. Here, we consider the practical challenges to controlling living organisms that must be surmounted, or at least managed, if synthetic biology and cellular bioengineering are to be productive.
Collapse
Affiliation(s)
- Adam P Arkin
- Howard Hughes Medical Institute, Department of Bioengineering, University of California, Berkeley, CA 94720, USA.
| | | |
Collapse
|
163
|
Samoilov MS, Price G, Arkin AP. From fluctuations to phenotypes: the physiology of noise. ACTA ACUST UNITED AC 2006; 2006:re17. [PMID: 17179490 DOI: 10.1126/stke.3662006re17] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
There are fundamental physical reasons why biochemical processes might be subject to noise and stochastic fluctuations. Indeed, it has long been understood that random molecular-scale mechanisms, such as those that drive genetic mutation, lie at the heart of population-scale evolutionary dynamics. What we can now appreciate is how stochastic fluctuations inherent in biochemical processes contribute to cellular and organismal phenotypes. Advancements in techniques for empirically measuring single cells and in corresponding theoretical methods have enabled the rigorous design and interpretation of experiments that provide incontrovertible proof that there are important endogenous sources of stochasticity that drive biological processes at the scale of individual organisms. Recently, some studies have progressed beyond merely ascertaining the presence of noise in biological systems; they trace its role in cellular physiology as it is passed through and processed by the biomolecular pathways-from the underlying origins of stochastic fluctuations in random biomolecular interactions to their ultimate manifestations in characteristic species phenotypes. These emerging results suggest new biological network design principles that account for a constructive role played by noise in defining the structure, function, and fitness of biological systems. They further show that stochastic mechanisms open novel classes of regulatory, signaling, and organizational choices that can serve as efficient and effective biological solutions to problems that are more complex, less robust, or otherwise suboptimal to deal with in the context of purely deterministic systems. Research in Drosophila melanogaster eye color-vision development and Bacillus subtilis competence induction has elegantly traced the role of noise in vital physiological processes from fluctuations to phenotypes, and is used here to highlight these developments.
Collapse
|
164
|
Abstract
In biological networks, any manifestations of behaviors substantially 'deviant' from the predictions of continuous-deterministic classical chemical kinetics (CCK) are typically ascribed to systems with complex dynamics and/or a small number of molecules. Here we show that in certain cases such restrictions are not obligatory for CCK to be largely incorrect. By systematically identifying properties that may cause significant divergences between CCK and the more accurate discrete-stochastic chemical master equation (CME) system descriptions, we comprehensively characterize potential CCK failure patterns in biological settings, including consequences of the assertion that CCK is closer to the 'mode' rather than the 'average' of stochastic reaction dynamics, as generally perceived. We demonstrate that mechanisms underlying such nonclassical effects can be very simple, are common in cellular networks and result in often unintuitive system behaviors. This highlights the importance of deviant effects in biotechnologically or biomedically relevant applications, and suggests some approaches to diagnosing them in situ.
Collapse
Affiliation(s)
- Michael S Samoilov
- Howard Hughes Medical Institute, Department of Bioengineering, University of California at Berkeley, Center for Synthetic Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
| | | |
Collapse
|
165
|
Klausen M, Gjermansen M, Kreft JU, Tolker-Nielsen T. Dynamics of development and dispersal in sessile microbial communities: examples from Pseudomonas aeruginosa and Pseudomonas putida model biofilms. FEMS Microbiol Lett 2006; 261:1-11. [PMID: 16842351 DOI: 10.1111/j.1574-6968.2006.00280.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Surface-associated microbial communities in many cases display dynamic developmental patterns. Model biofilms formed by Pseudomonas aeruginosa and Pseudomonas putida in laboratory flow-chamber setups represent examples of such behaviour. Dependent on the experimental conditions the bacteria in these model biofilms develop characteristic multicellular structures through a series of distinct steps where cellular migration plays an important role. Despite the appearance of these characteristic developmental patterns in the model biofilms the available evidence suggest that the biofilm forming organisms do not possess comprehensive genetic programs for biofilm development. Instead the bacteria appear to have evolved a number of different mechanisms to optimize surface colonization, of which they express a subset in response to the prevailing environmental conditions. These mechanisms include the ability to regulate cellular adhesiveness and migration in response to micro-environmental signals including those secreted by the bacteria themselves.
Collapse
Affiliation(s)
- Mikkel Klausen
- Centre for Biomedical Microbiology, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark
| | | | | | | |
Collapse
|
166
|
van Hoek MJA, Hogeweg P. In silico evolved lac operons exhibit bistability for artificial inducers, but not for lactose. Biophys J 2006; 91:2833-43. [PMID: 16877514 PMCID: PMC1578483 DOI: 10.1529/biophysj.105.077420] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bistability in the lac operon of Escherichia coli has been widely studied, both experimentally and theoretically. Experimentally, bistability has been observed when E. coli is induced by an artificial, nonmetabolizable, inducer. However, if the lac operon is induced with lactose, the natural inducer, bistability has not been demonstrated. We derive an analytical expression that can predict the occurrence of bistability both for artificial inducers and lactose. We find very different conditions for bistability in the two cases. Indeed, for artificial inducers bistability is predicted, but for lactose the condition for bistability is much more difficult to satisfy. Moreover, we demonstrate that in silico evolution of the lac operon generates an operon that avoids bistability with respect to lactose, but does exhibit bistability with respect to artificial inducers. The activity of this evolved operon strikingly resembles the experimentally observed activity of the operon. Thus our computational experiments suggest that the wild-type lac operon, which regulates lactose metabolism, is not a bistable switch. Nevertheless, for engineering purposes, this operon can be used as a bistable switch with artificial inducers.
Collapse
Affiliation(s)
- M J A van Hoek
- Theoretical Biology/Bioinformatics Group, Utrecht University, Utrecht, The Netherlands.
| | | |
Collapse
|
167
|
Smits WK, Kuipers OP, Veening JW. Phenotypic variation in bacteria: the role of feedback regulation. Nat Rev Microbiol 2006; 4:259-71. [PMID: 16541134 DOI: 10.1038/nrmicro1381] [Citation(s) in RCA: 397] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To survive in rapidly changing environmental conditions, bacteria have evolved a diverse set of regulatory pathways that govern various adaptive responses. Recent research has reinforced the notion that bacteria use feedback-based circuitry to generate population heterogeneity in natural situations. Using artificial gene networks, it has been shown that a relatively simple 'wiring' of a bacterial genetic system can generate two or more stable subpopulations within an overall genetically homogeneous population. This review discusses the ubiquity of these processes throughout nature, as well as the presumed molecular mechanisms responsible for the heterogeneity observed in a selection of bacterial species.
Collapse
Affiliation(s)
- Wiep Klaas Smits
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
| | | | | |
Collapse
|
168
|
Kussell E, Leibler S. Phenotypic diversity, population growth, and information in fluctuating environments. Science 2005; 309:2075-8. [PMID: 16123265 DOI: 10.1126/science.1114383] [Citation(s) in RCA: 836] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Organisms in fluctuating environments must constantly adapt their behavior to survive. In clonal populations, this may be achieved through sensing followed by response or through the generation of diversity by stochastic phenotype switching. Here we show that stochastic switching can be favored over sensing when the environment changes infrequently. The optimal switching rates then mimic the statistics of environmental changes. We derive a relation between the long-term growth rate of the organism and the information available about its fluctuating environment.
Collapse
Affiliation(s)
- Edo Kussell
- Laboratory of Living Matter and Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, Box 34, New York, NY 10021-6399, USA.
| | | |
Collapse
|
169
|
Wolf DM, Vazirani VV, Arkin AP. A microbial modified prisoner's dilemma game: how frequency-dependent selection can lead to random phase variation. J Theor Biol 2005; 234:255-62. [PMID: 15757682 DOI: 10.1016/j.jtbi.2004.11.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Accepted: 11/18/2004] [Indexed: 11/19/2022]
Abstract
Random phase variation (RPV) is a control strategy in which the expression of a cell state or phenotype randomly alternates between discrete 'on' and 'off' states. Though this mode of control is common for bacterial virulence factors like pili and toxins, precise conditions under which RPV confers an advantage have not been well defined. In Part I of this study, we predicted that fluctuating environments select for RPV if transitions between different selective environments cannot be reliably sensed (J. Theor. Biol. (2005)). However, selective forces both inside and outside of human hosts are also likely to be frequency dependent in the sense that the fitnesses of some bacterial states are greatest when rare. Here we show that RPV at slow rates can provide a survival advantage in such a frequency-dependent environment by generating population heterogeneity, essentially mimicking a polymorphism. More surprisingly, RPV at a faster 'optimal' rate can shift the population composition toward an optimal growth rate that exceeds that possible for polymorphic populations, but this optimal strategy is not evolutionarily stable. The population would be most fit if all cells randomly phase varied at the optimal rate, but individual cells have a growth-rate incentive to defect (mutate) to other switching rates or non-phase variable phenotype expression, leading to an overall loss of fitness of the individual and the population. This scenario describes a modified Prisoner's Dilemma game (Evolution and the Theory of Games, Cambridge University Press, Cambridge, New York, 1982, viii, 224pp.; Nature 398 (6726) (1999) 367), with random phase variation at optimal switching rates serving as the cooperation strategy.
Collapse
Affiliation(s)
- Denise M Wolf
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | | | | |
Collapse
|