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Journal of Biomedicine and Biotechnology
Volume 2012 (2012), Article ID 103132, 14 pages
doi:10.1155/2012/103132
Research Article
Computer-Based Annotation of Putative AraC/XylS-Family Transcription Factors of Known Structure but Unknown Function
Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy; Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, 8331150 Santiago, Chile
Received 28 September 2011; Revised 9 December 2011; Accepted 13 December 2011
Academic Editor: Sergio Pantano
Copyright © 2012 Andreas Schüller et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Linked References
- H. M. Berman, J. D. Westbrook, M. J. Gabanyi et al., “The protein structure initiative structural genomics knowledgebase,” Nucleic Acids Research, vol. 37, no. 1, pp. D365–D368, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- M. T. Gallegos, R. Schleif, A. Bairoch, K. Hofmann, and J. L. Ramos, “AraC/Xyls family of transcriptional regulators,” Microbiology and Molecular Biology Reviews, vol. 61, no. 4, pp. 393–410, 1997. View at Scopus
- J. A. Ibarra, E. Pérez-Rueda, L. Segovia, and J. L. Puente, “The DNA-binding domain as a functional indicator: the case of the AraC/XylS family of transcription factors,” Genetica, vol. 133, no. 1, pp. 65–76, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- R. G. Martin and J. L. Rosner, “The AraC transcriptional activators,” Current Opinion in Microbiology, vol. 4, no. 2, pp. 132–137, 2001. View at Publisher · View at Google Scholar · View at Scopus
- S. M. Egan, “Growing repertoire of AraC/XylS activators,” Journal of Bacteriology, vol. 184, no. 20, pp. 5529–5532, 2002. View at Publisher · View at Google Scholar · View at Scopus
- M. N. Alekshun and S. B. Levy, “Regulation of chromosomally mediated multiple antibiotic resistance: the mar regulon,” Antimicrobial Agents and Chemotherapy, vol. 41, no. 10, pp. 2067–2075, 1997. View at Scopus
- C. He, J. C. Hus, J. S. Li et al., “A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli Ada,” Molecular Cell, vol. 20, no. 1, pp. 117–129, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- S. Rhee, R. G. Martin, J. L. Rosner, and D. R. Davies, “A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 18, pp. 10413–10418, 1998. View at Publisher · View at Google Scholar · View at Scopus
- H. Takinowaki, Y. Matsuda, T. Yoshida, Y. Kobayashi, and T. Ohkubo, “The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein,” Protein Science, vol. 15, no. 3, pp. 487–497, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- R. Tobes and J. L. Ramos, “AraC-XylS database: a family of positive transcriptional regulators in bacteria,” Nucleic Acids Research, vol. 30, no. 1, pp. 318–321, 2002. View at Scopus
- J. Yang, M. Tauschek, and R. M. Robins-Browne, “Control of bacterial virulence by AraC-like regulators that respond to chemical signals,” Trends in Microbiology, vol. 19, no. 3, pp. 128–135, 2011. View at Publisher · View at Google Scholar · View at PubMed
- S. J. Suhrer, M. Wiederstein, M. Gruber, and M. J. Sippl, “COPS—a novel workbench for explorations in fold space,” Nucleic Acids Research, vol. 37, no. 2, pp. W539–W544, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- M. J. Sippl, “On distance and similarity in fold space,” Bioinformatics, vol. 24, no. 6, pp. 872–873, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- M. J. Sippl and M. Wiederstein, “A note on difficult structure alignment problems,” Bioinformatics, vol. 24, no. 3, pp. 426–427, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- R. Apweiler, M. J. Martin, C. O'Donovan et al., “Ongoing and future developments at the Universal Protein Resource,” Nucleic Acids Research, vol. 39, supplement 1, pp. D214–D219, 2011. View at Publisher · View at Google Scholar · View at PubMed
- M. A. Marti-Renom, M. S. Madhusudhan, and A. Sali, “Alignment of protein sequences by their profiles,” Protein Science, vol. 13, no. 4, pp. 1071–1087, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- Molecular Operating Environment (MOE), Chemical Computing Group, Montreal, Canada.
- R. D. Finn, J. Mistry, J. Tate et al., “The Pfam protein families database,” Nucleic Acids Research, vol. 38, no. 1, pp. D211–D222, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- K. Katoh, K. Misawa, K. I. Kuma, and T. Miyata, “MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform,” Nucleic Acids Research, vol. 30, no. 14, pp. 3059–3066, 2002. View at Scopus
- K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods,” Molecular Biology and Evolution, vol. 28, no. 10, pp. 2731–2739, 2011. View at Publisher · View at Google Scholar · View at PubMed
- H. C. Wang, K. Li, E. Susko, and A. J. Roger, “A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny,” BMC Evolutionary Biology, vol. 8, no. 1, article 331, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- F. Abascal, R. Zardoya, and D. Posada, “ProtTest: selection of best-fit models of protein evolution,” Bioinformatics, vol. 21, no. 9, pp. 2104–2105, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- I. Letunic and P. Bork, “Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation,” Bioinformatics, vol. 23, no. 1, pp. 127–128, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- A. M. Waterhouse, J. B. Procter, D. M. A. Martin, M. Clamp, and G. J. Barton, “Jalview Version 2-A multiple sequence alignment editor and analysis workbench,” Bioinformatics, vol. 25, no. 9, pp. 1189–1191, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- A. Sali and T. L. Blundell, “Comparative protein modelling by satisfaction of spatial restraints,” Journal of Molecular Biology, vol. 234, no. 3, pp. 779–815, 1993. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- J. Wang, P. Cieplak, and P. A. Kollman, “How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?” Journal of Computational Chemistry, vol. 21, no. 12, pp. 1049–1074, 2000. View at Scopus
- X. J. Lu and W. K. Olson, “3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures,” Nature Protocols, vol. 3, no. 7, pp. 1213–1227, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- T. Norambuena and F. Melo, “The Protein-DNA Interface database,” BMC Bioinformatics, vol. 11, article 262, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- F. Melo and E. Feytmans, “Novel knowledge-based mean force potential at atomic,” Journal of Molecular Biology, vol. 267, no. 1, pp. 207–222, 1997. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- E. Capriotti, T. Norambuena, M. A. Marti-Renom, and F. Melo, “All-atom knowledge-based potential for RNA structure prediction and assessment,” Bioinformatics, vol. 27, no. 8, pp. 1086–1093, 2011. View at Publisher · View at Google Scholar · View at PubMed
- G. E. Crooks, G. Hon, J. M. Chandonia, and S. E. Brenner, “WebLogo: a sequence logo generator,” Genome Research, vol. 14, no. 6, pp. 1188–1190, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- R. G. Martin and J. L. Rosner, “Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data,” Molecular Microbiology, vol. 44, no. 6, pp. 1611–1624, 2002. View at Publisher · View at Google Scholar · View at Scopus
- B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, “Ultrafast and memory-efficient alignment of short DNA sequences to the human genome,” Genome Biology, vol. 10, no. 3, article R25, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- P. Kersey, L. Bower, L. Morris et al., “Integr8 and Genome Reviews: integrated views of complete genomes and proteomes,” Nucleic Acids Research, vol. 33, pp. D297–D302, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- S. Hunter, R. Apweiler, T. K. Attwood et al., “InterPro: the integrative protein signature database,” Nucleic Acids Research, vol. 37, no. 1, pp. D211–D215, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, and M. Tanabe, “KEGG for integration and interpretation of large-scale molecular data sets,” Nucleic Acids Research, vol. 40, no. 1, pp. D109–D114, 2011.
- B. Dangi, A. M. Gronenborn, J. L. Rosner, and R. G. Martin, “Versatility of the carboxy-terminal domain of the α subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA,” Molecular Microbiology, vol. 54, no. 1, pp. 45–59, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- H. J. Kwon, M. H. J. Bennik, B. Demple, and T. Ellenberger, “Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA,” Nature Structural Biology, vol. 7, no. 5, pp. 424–430, 2000. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- M. E. Rodgers and R. Schleif, “Solution structure of the DNA binding domain of AraC protein,” Proteins, vol. 77, no. 1, pp. 202–208, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- M. J. Lowden, K. Skorupski, M. Pellegrini, M. G. Chiorazzo, R. K. Taylor, and F. J. Kull, “Structure of Vibrio cholerae ToxT reveals a mechanism for fatty acid regulation of virulence genes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 7, pp. 2860–2865, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- A. Ochiai, T. Itoh, A. Kawamata, W. Hashimoto, and K. Murata, “Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization,” Applied and Environmental Microbiology, vol. 73, no. 12, pp. 3803–3813, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- K. Kobayashi, M. Ogura, H. Yamaguchi et al., “Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems,” Journal of Bacteriology, vol. 183, no. 24, pp. 7365–7370, 2001. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- V. Chow, G. Nong, and J. F. Preston, “Structure, function, and regulation of the aldouronate utilization gene cluster from Paenibacillus sp. strain JDR-2,” Journal of Bacteriology, vol. 189, no. 24, pp. 8863–8870, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- S. Poncet, M. Soret, P. Mervelet, J. Deutscher, and P. Noirot, “Transcriptional activator YesS is stimulated by histidine-phosphorylated HPr of the Bacillus subtilis phosphotransferase system,” Journal of Biological Chemistry, vol. 284, no. 41, pp. 28188–28197, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- K. M. Vlassak, C. Snoeck, E. Luyten, P. de Wilde, P. van Rhijn, and J. Vanderleyden, “The Rhizobium sp. BR816 NodD3 gene is regulated by a transcriptional regulator of the AraC/XylS family,” in Biological Nitrogen Fixation for the 21st Century, C. Elmerich, A. Kondorosi, and W. E. Newton, Eds., Proceedings of the 11th International Congress on Nitrogen Fixation, Institut Pasteur, Paris, France, July 20-25, 1997, Springer, 1998.
- H. Blanca-Ordóñez, J. J. Oliva-García, D. Pérez-Mendoza et al., “pSymA-dependent mobilization of the Sinorhizobium meliloti pSymB megaplasmid,” Journal of Bacteriology, vol. 192, no. 23, pp. 6309–6312, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- C. Schmeisser, H. Liesegang, D. Krysciak et al., “Rhizobium sp. strain NGR234 possesses a remarkable number of secretion systems,” Applied and Environmental Microbiology, vol. 75, no. 12, pp. 4035–4045, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- I. Nagy, G. Schoofs, F. Compernolle, P. Proost, J. Vanderleyden, and R. De Mot, “Degradation of the thiocarbamate herbicide EPTC (S-ethyl dipropylcarbamothioate) and biosafening by Rhodococcus sp. Strain NI86/21 involve an inducible cytochrome P-450 system and aldehyde dehydrogenase,” Journal of Bacteriology, vol. 177, no. 3, pp. 676–687, 1995. View at Scopus
- D. A. Garsin, “Ethanolamine utilization in bacterial pathogens: roles and regulation,” Nature Reviews Microbiology, vol. 8, no. 4, pp. 290–295, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- D. Büttner and U. Bonas, “Getting across—bacterial type III effector proteins on their way to the plant cell,” EMBO Journal, vol. 21, no. 20, pp. 5313–5322, 2002. View at Publisher · View at Google Scholar · View at Scopus
- S. Cunnac, C. Boucher, and S. Genin, “Characterization of the cis-acting regulatory element controlling HrpB-mediated activation of the type III secretion system and effector genes in Ralstonia solanacearum,” Journal of Bacteriology, vol. 186, no. 8, pp. 2309–2318, 2004. View at Publisher · View at Google Scholar · View at Scopus
- M. J. Soto, J. Sanjuán, and J. Olivares, “Rhizobia and plant-pathogenic bacteria: common infection weapons,” Microbiology, vol. 152, no. 11, pp. 3167–3174, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- F. W. Larimer, P. Chain, L. Hauser et al., “Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris,” Nature Biotechnology, vol. 22, no. 1, pp. 55–61, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- Y. Oda, S. K. Samanta, F. E. Rey et al., “Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris,” Journal of Bacteriology, vol. 187, no. 22, pp. 7784–7794, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- K. L. Griffith and R. E. Wolf, “A comprehensive alanine scanning mutagenesis of the Escherichia coli transcriptional activator SoxS: identifying amino acids important for DNA binding and transcription activation,” Journal of Molecular Biology, vol. 322, no. 2, pp. 237–257, 2002. View at Publisher · View at Google Scholar · View at Scopus
- N. M. Luscombe, R. A. Laskowski, and J. M. Thornton, “Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level,” Nucleic Acids Research, vol. 29, no. 13, pp. 2860–2874, 2001. View at Scopus
- G. Y. Heo, W. C. Kim, G. J. Joo et al., “Deletion of xylR gene enhances expression of xylose isomerase in Streptomyces lividans TK24,” Journal of Microbiology and Biotechnology, vol. 18, no. 5, pp. 837–844, 2008. View at Scopus
- O. Sand, M. Gingras, N. Beck, C. Hall, and N. Trun, “Phenotypic characterization of overexpression or deletion of the Escherichia coli crcA, cspE and crcB genes,” Microbiology, vol. 149, no. 8, pp. 2107–2117, 2003. View at Scopus
- P. Sliz, R. Engelmann, W. Hengstenberg, and E. F. Pai, “The structure of enzyme IIA(lactose) from Lactococcus lactis reveals a new fold and points to possible interactions of a multicomponent system,” Structure, vol. 5, no. 6, pp. 775–788, 1997.
- R. Rivilla, J. M. Sutton, and J. A. Downie, “Rhizobium leguminosarum NodT is related to a family of outer-membrane transport proteins that includes TolC, PrtF, CyaE and AprF,” Gene, vol. 161, no. 1, pp. 27–31, 1995. View at Publisher · View at Google Scholar · View at Scopus
- L. P. Solomonson and M. J. Barber, “Assimilatory nitrate reductase: functional properties and regulation,” Annual Review of Plant Physiology and Plant Molecular Biology, vol. 41, no. 1, pp. 225–253, 1990. View at Scopus
- M. Deshmukh, S. Turkarslan, D. Astor, M. Valkova-Valchanova, and F. Daldal, “The dithiol:disulfide oxidoreductases DsbA and DsbB of Rhodobacter capsulatus are not directly involved in cytochrome c biogenesis, but their inactivation restores the cytochrome c biogenesis defect of CcdA-null mutants,” Journal of Bacteriology, vol. 185, no. 11, pp. 3361–3372, 2003. View at Publisher · View at Google Scholar · View at Scopus
- F. E. Rey, E. K. Heiniger, and C. S. Harwood, “Redirection of metabolism for biological hydrogen production,” Applied and Environmental Microbiology, vol. 73, no. 5, pp. 1665–1671, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- H. S. Jeong and Y. Jouanneau, “Enhanced nitrogenase activity in strains of Rhodobacter capsulatus that overexpress the rnf genes,” Journal of Bacteriology, vol. 182, no. 5, pp. 1208–1214, 2000. View at Publisher · View at Google Scholar · View at Scopus