Transcription regulation and environmental adaptation in bacteria

Cases, Ildefonso; Lorenzo, Vı́ctor de; Ouzounis, Christos A.

doi:10.1016/s0966-842x(03)00103-3

Cited by 171 publications

(148 citation statements)

References 17 publications

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“…10 and 11 show, our experiments with RAevol reproduce qualitatively the scaling laws observed in the prokaryotic kingdom (Cases et al, 2003;van Nimwegen, 2003;Konstantinidis and Tiedje, 2004;Molina and van Nimwegen, 2008). Small genomes with few genes only have a very basic regulation activity while large ones develop complex regulation networks with many genes.…”

Section: Discussionsupporting

confidence: 53%

“…However, the classical hypothesis is that the scaling has a selective origin. It is often assumed that these scaling laws result from a selection process linked to bacterial lifestyle: complex environments would require the coordination of multiple metabolic pathways (Cases et al, 2003). Alternatively, it has been argued that any increase in the genetic repertoire of an organism (e.g., a new metabolic pathway) generates a need for new transcription factors in order to regulate its activity within the existing metabolism (Maslov et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

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Scaling laws in bacterial genomes: A side-effect of selection of mutational robustness?

et al. 2010

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ARTICLE INFO ABSTRACT Keywords: Modelling Scaling laws Gene content Transcription Factors Mutational robustness EvolvabilityIn the past few years, numerous research projects have focused on identifying and understanding scaling properties in the gene content of prokaryote genomes and the intricacy of their regulation networks. Yet, and despite the increasing amount of data available, the origins of these scalings remain an open question. The RAevol model, a digital genetics model, provides us with an insight into the mechanisms involved in an evolutionary process. The results we present here show that (i) our model reproduces qualitatively these scaling laws and that (ii) these laws are not due to differences in lifestyles but to differences in the spontaneous rates of mutations and rearrangements. We argue that this is due to an indirect selective pressure for robustness that constrains the genome size.

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Section: Discussionsupporting

confidence: 53%

Section: Introductionmentioning

confidence: 99%

Scaling laws in bacterial genomes: A side-effect of selection of mutational robustness?

et al. 2010

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“…Survival in this unstable environment requires a wide range of rapid, adaptive responses which are triggered by regulatory proteins. These regulators respond to specific environmental and cellular signals that modulate transcription, translation, or some other event in gene expression, so that the physiological responses are modified appropriately (32,52,64,104,107,145,244,311,312,326,330,379,397,409,427).…”

Section: Introductionmentioning

confidence: 99%

The TetR Family of Transcriptional Repressors

Ramos

Martínez-Bueno

Molina‐Henares

et al. 2005

Microbiol Mol Biol Rev

974

1,133

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We have developed a general profile for the proteins of the TetR family of repressors. The stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix DNA binding motif and adjacent regions in the three-dimensional structures of TetR, QacR, CprB, and EthR, four family members for which the function and three-dimensional structure are known. We have detected a set of 2,353 nonredundant proteins belonging to this family by screening genome and protein databases with the TetR profile. Proteins of the TetR family have been found in 115 genera of gram-positive, α-, β-, and γ-proteobacteria, cyanobacteria, and archaea. The set of genes they regulate is known for 85 out of the 2,353 members of the family. These proteins are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The regulatory network in which the family member is involved can be simple, as in TetR (i.e., TetR bound to the target operator represses tetA transcription and is released in the presence of tetracycline), or more complex, involving a series of regulatory cascades in which either the expression of the TetR family member is modulated by another regulator or the TetR family member triggers a cell response to react to environmental insults. Based on what has been learned from the cocrystals of TetR and QacR with their target operators and from their three-dimensional structures in the absence and in the presence of ligands, and based on multialignment analyses of the conserved stretch of 47 amino acids in the 2,353 TetR family members, two groups of residues have been identified. One group includes highly conserved positions involved in the proper orientation of the helix-turn-helix motif and hence seems to play a structural role. The other set of less conserved residues are involved in establishing contacts with the phosphate backbone and target bases in the operator. Information related to the TetR family of regulators has been updated in a database that can be accessed at www.bactregulators.org

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“…In agreement with this general prediction, it has been shown that regulatory gene number in prokaryotic genomes grows disproportionally fast [2][3][4][5]. In particular, a recent study analyzed the scaling of gene counts n c for each of 44 functional protein categories in relation to the total number of genes n, across 64 bacterial genomes [5].…”

Section: Introductionmentioning

confidence: 69%