TY - JOUR
T1 - The DNA-binding domain as a functional indicator
T2 - The case of the AraC/XylS family of transcription factors
AU - Ibarra, J. Antonio
AU - Pérez-Rueda, Ernesto
AU - Segovia, Lorenzo
AU - Puente, J. Luis
N1 - Funding Information:
Acknowledgements We would like to thank Enrique Merino, Sa-rath Chandra Janga and Gabriel Moreno-Hagelsieb for helpful discussions and valuable comment, and Dan Drecktrah for reading and correcting the manuscript. This work was supported by grants from the Universidad Nacional Autónoma de México (DGAPA IN201703-3), from the Consejo Nacional de Ciencia y Tecnología (CONACyT 42918Q) and by an International Research Scholar Award (75301-565101) from the Howard Hughes Medical Institute (HHMI) to JLP. JAI was supported by postdoctoral fellowships from the HHMI and CONACyT. This work was partially supported by a grant (ASTF 224-2005) from EMBO to E. P-R.
PY - 2008/5
Y1 - 2008/5
N2 - The AraC/XylS family of transcription factors, which include proteins that are involved in the regulation of diverse biological processes, has been of considerable interest recently and has been constantly expanding by means of in silico predictions and experimental analysis. In this work, using a HMM based on the DNA binding domain of 58 experimentally characterized proteins from the AraC/XylS (A/X), 1974 A/X proteins were found in 149 out of 212 bacterial genomes. This domain was used as a template to generate a phylogenetic tree and as a tool to predict the putative regulatory role of the new members of this family based on their proximity to a particular functional cluster in the tree. Based on this approach we assigned a functional regulatory role for 75% of the TFs dataset. Of these, 33.7% regulate genes involved in carbon-source catabolism, 9.6% global metabolism, 8.3% nitrogen metabolism, 2.9% adaptation responses, 8.9% stress responses, and 11.7% virulence. The abundance of TFs involved in the regulation of metabolic processes indicates that bacteria have optimized their regulatory systems to control energy uptake. In contrast, the lower percentage of TFs required for stress, adaptation and virulence regulation reflects the specialization acquired by each subset of TFs associated with those processes. This approach would be useful in assigning regulatory roles to uncharacterized members of other transcriptional factor families and it might facilitate their experimental analysis.
AB - The AraC/XylS family of transcription factors, which include proteins that are involved in the regulation of diverse biological processes, has been of considerable interest recently and has been constantly expanding by means of in silico predictions and experimental analysis. In this work, using a HMM based on the DNA binding domain of 58 experimentally characterized proteins from the AraC/XylS (A/X), 1974 A/X proteins were found in 149 out of 212 bacterial genomes. This domain was used as a template to generate a phylogenetic tree and as a tool to predict the putative regulatory role of the new members of this family based on their proximity to a particular functional cluster in the tree. Based on this approach we assigned a functional regulatory role for 75% of the TFs dataset. Of these, 33.7% regulate genes involved in carbon-source catabolism, 9.6% global metabolism, 8.3% nitrogen metabolism, 2.9% adaptation responses, 8.9% stress responses, and 11.7% virulence. The abundance of TFs involved in the regulation of metabolic processes indicates that bacteria have optimized their regulatory systems to control energy uptake. In contrast, the lower percentage of TFs required for stress, adaptation and virulence regulation reflects the specialization acquired by each subset of TFs associated with those processes. This approach would be useful in assigning regulatory roles to uncharacterized members of other transcriptional factor families and it might facilitate their experimental analysis.
KW - AraC/XylS family
KW - DNA binding domain
KW - Functional genomics
KW - Phylogenomics
KW - Transcriptional regulators
UR - http://www.scopus.com/inward/record.url?scp=41549144323&partnerID=8YFLogxK
U2 - 10.1007/s10709-007-9185-y
DO - 10.1007/s10709-007-9185-y
M3 - Artículo
C2 - 17712603
AN - SCOPUS:41549144323
SN - 0016-6707
VL - 133
SP - 65
EP - 76
JO - Genetica
JF - Genetica
IS - 1
ER -