In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon.
BACKGROUND
Motif-prediction algorithm capabilities for the analysis of bacterial regulatory networks and the prediction of new regulatory sites can be greatly enhanced by the use of comparative genomics approaches. In this study, we make use of a consensus-building algorithm and comparative genomics to conduct an in-depth analysis of the LexA-regulon of gamma proteobacteria, and we use the inferred results to study the evolution of this regulatory network and to examine the usefulness of the control sequences and gene contents of regulons in phylogenetic analysis.


RESULTS
We show, for the first time, the substantial heterogeneity that the LexA-regulon of gamma proteobacteria displays in terms of gene content and we analyze possible branching points in its evolution. We also demonstrate the feasibility of using regulon-related information to derive sound phylogenetic inferences.


BACKGROUND
Complementary analysis data and both the source code and the Windows-executable files of the consensus-building software are available at http://www.cnm.es/~ivan/RCGScanner/
Erill
Ivan
I
Biomedical Applications Group, Centro Nacional de Microelectrónica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
Escribano
Marcos
M
Campoy
Susana
S
Barbé
Jordi
J
D000465:Algorithms; D001426:Bacterial Proteins / Q000235:genetics*; D016384:Consensus Sequence; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D005240:Feasibility Studies; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D014644:Genetic Variation; D016680:Genome, Bacterial; D018085:Regulon / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012697:Serine Endopeptidases / Q000235:genetics*; D012984:Software; D012986:Software Validation; D000099160:LexA Repressor Protein
D001426:Bacterial Proteins; D012697:Serine Endopeptidases; D000099160:LexA Repressor Protein