Literature DB >> 20825349

Noise and robustness in prokaryotic regulatory networks.

Rafael Silva-Rocha1, Víctor de Lorenzo.   

Abstract

Robustness is the quality of any relational object (biological or otherwise) to maintain its components, its structure, and its function despite both external changes and endogenous fluctuations. Live systems are surprisingly robust, as they are able to not only preserve their physicochemical architecture in the face of variable nutritional and environmental conditions, but also tolerate stochastic variability in the concentrations of their components, fix errors resulting from hazardous events, and make virtually perfect copies of themselves. These qualities have started to be comprehended in full only since the application of network theory formalisms to regulatory phenomena. This review addresses the distinct role of network architecture (topology, logic) and biochemical/kinetic parameters in the materialization of various archetypical robust gene expression circuits in prokaryotes. Some take-home lessons for the construction of artificial regulatory networks (one of the trademarks of synthetic biology) are to be derived from such state of affairs.

Mesh:

Year:  2010        PMID: 20825349     DOI: 10.1146/annurev.micro.091208.073229

Source DB:  PubMed          Journal:  Annu Rev Microbiol        ISSN: 0066-4227            Impact factor:   15.500


  44 in total

1.  Bacterial degradation of benzoate: cross-regulation between aerobic and anaerobic pathways.

Authors:  J Andrés Valderrama; Gonzalo Durante-Rodríguez; Blas Blázquez; José Luis García; Manuel Carmona; Eduardo Díaz
Journal:  J Biol Chem       Date:  2012-02-02       Impact factor: 5.157

2.  Making variability less variable: matching expression system and host for oxygenase-based biotransformations.

Authors:  Martin Lindmeyer; Daniel Meyer; Daniel Kuhn; Bruno Bühler; Andreas Schmid
Journal:  J Ind Microbiol Biotechnol       Date:  2015-04-16       Impact factor: 3.346

Review 3.  Foundations for the design and implementation of synthetic genetic circuits.

Authors:  Adrian L Slusarczyk; Allen Lin; Ron Weiss
Journal:  Nat Rev Genet       Date:  2012-05-18       Impact factor: 53.242

4.  Microalgal consortia differentially modulate progressive adsorption of hexavalent chromium.

Authors:  Adi Nath; Pravin Kumar Tiwari; Awadhesh Kumar Rai; Shanthy Sundaram
Journal:  Physiol Mol Biol Plants       Date:  2017-02-06

Review 5.  Culture history and population heterogeneity as determinants of bacterial adaptation: the adaptomics of a single environmental transition.

Authors:  Ben Ryall; Gustavo Eydallin; Thomas Ferenci
Journal:  Microbiol Mol Biol Rev       Date:  2012-09       Impact factor: 11.056

6.  Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities.

Authors:  Chang F Quo; Chanchala Kaddi; John H Phan; Amin Zollanvari; Mingqing Xu; May D Wang; Gil Alterovitz
Journal:  Brief Bioinform       Date:  2012-07       Impact factor: 11.622

7.  Downward causation by information control in micro-organisms.

Authors:  Luc Jaeger; Erin R Calkins
Journal:  Interface Focus       Date:  2011-09-29       Impact factor: 3.906

Review 8.  Programmed heterogeneity: epigenetic mechanisms in bacteria.

Authors:  Josep Casadesús; David A Low
Journal:  J Biol Chem       Date:  2013-04-16       Impact factor: 5.157

9.  Decomposing noise in biochemical signaling systems highlights the role of protein degradation.

Authors:  Michał Komorowski; Jacek Miękisz; Michael P H Stumpf
Journal:  Biophys J       Date:  2013-04-16       Impact factor: 4.033

Review 10.  Stress-induced remodeling of the bacterial proteome.

Authors:  Monica S Guo; Carol A Gross
Journal:  Curr Biol       Date:  2014-05-19       Impact factor: 10.834

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