Bacterial regulatory networks are extremely flexible in evolution Export

@article{citeulike:1036644, abstract = {Over millions of years the structure and complexity of the transcriptional regulatory network (TRN) in bacteria has changed, reorganized and enabled them to adapt to almost every environmental niche on earth. In order to understand the plasticity of TRNs in bacteria, we studied the conservation of currently known TRNs of the two model organisms Escherichia coli K12 and Bacillus subtilis across complete genomes including Bacteria, Archaea and Eukarya at three different levels: individual components of the TRN, pairs of interactions and regulons. We found that transcription factors (TFs) evolve much faster than the target genes (TGs) across phyla. We show that global regulators are poorly conserved across the phylogenetic spectrum and hence TFs could be the major players responsible for the plasticity and evolvability of the TRNs. We also found that there is only a small fraction of significantly conserved transcriptional regulatory interactions among different phyla of bacteria and that there is no constraint on the elements of the interaction to co-evolve. Finally our results suggest that majority of the regulons in bacteria are rapidly lost implying a high-order flexibility in the TRNs. We hypothesize that during the divergence of bacteria certain essential cellular processes like the synthesis of arginine, biotine and ribose, transport of amino acids and iron, availability of phosphate, replication process and the SOS response are well conserved in evolution. From our comparative analysis, it is possible to infer that transcriptional regulation is more flexible than the genetic component of the organisms and its complexity and structure plays an important role in the phenotypic adaptation. 10.1093/nar/gkl423}, address = {Programa de Genomica Computacional, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Apdo. Postal 565-A, Avenue Universidad, Cuernavaca, Morelos, 62100 Mexico, Mexico. ilozada@ccg.unam.mx [corrected]}, author = {Lozada-Chavez, Irma and Janga, Sarath C. and Collado-Vides, Julio}, citeulike-article-id = {1036644}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkl423}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/34/12/3434.abstract}, citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/34/12/3434.full.pdf}, citeulike-linkout-3 = {http://nar.oxfordjournals.org/cgi/content/abstract/34/12/3434}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/16840530}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=16840530}, day = {13}, doi = {10.1093/nar/gkl423}, issn = {1362-4962}, journal = {Nucl. Acids Res.}, keywords = {bacterial, evolution-of-transcriptional-regulation, network-evolution, transcriptional-regulatory-network}, month = {July}, number = {12}, pages = {3434--3445}, posted-at = {2008-06-05 01:03:33}, priority = {2}, title = {Bacterial regulatory networks are extremely flexible in evolution}, url = {http://dx.doi.org/10.1093/nar/gkl423}, volume = {34}, year = {2006} }

TY - JOUR ID - citeulike:1036644 L3 - citeulike-article-id:1036644 N2 - Over millions of years the structure and complexity of the transcriptional regulatory network (TRN) in bacteria has changed, reorganized and enabled them to adapt to almost every environmental niche on earth. In order to understand the plasticity of TRNs in bacteria, we studied the conservation of currently known TRNs of the two model organisms Escherichia coli K12 and Bacillus subtilis across complete genomes including Bacteria, Archaea and Eukarya at three different levels: individual components of the TRN, pairs of interactions and regulons. We found that transcription factors (TFs) evolve much faster than the target genes (TGs) across phyla. We show that global regulators are poorly conserved across the phylogenetic spectrum and hence TFs could be the major players responsible for the plasticity and evolvability of the TRNs. We also found that there is only a small fraction of significantly conserved transcriptional regulatory interactions among different phyla of bacteria and that there is no constraint on the elements of the interaction to co-evolve. Finally our results suggest that majority of the regulons in bacteria are rapidly lost implying a high-order flexibility in the TRNs. We hypothesize that during the divergence of bacteria certain essential cellular processes like the synthesis of arginine, biotine and ribose, transport of amino acids and iron, availability of phosphate, replication process and the SOS response are well conserved in evolution. From our comparative analysis, it is possible to infer that transcriptional regulation is more flexible than the genetic component of the organisms and its complexity and structure plays an important role in the phenotypic adaptation. 10.1093/nar/gkl423 IS - 12 JF - Nucl. Acids Res. SN - 1362-4962 AD - Programa de Genomica Computacional, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Apdo. Postal 565-A, Avenue Universidad, Cuernavaca, Morelos, 62100 Mexico, Mexico. ilozada@ccg.unam.mx [corrected] EP - 3445 TI - Bacterial regulatory networks are extremely flexible in evolution VL - 34 SP - 3434 KW - bacterial KW - evolution-of-transcriptional-regulation KW - network-evolution KW - transcriptional-regulatory-network AU - Lozada-Chavez, Irma AU - Janga, Sarath AU - Collado-Vides, Julio PY - 2006/07/13/ UR - http://dx.doi.org/10.1093/nar/gkl423 ER -