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BioMed Research International
Volume 2013 (2013), Article ID 145037, 15 pages
Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors
Department of Biology Science, Fuyang Normal College, No. 100 West Qing He Road, Fuyang 236037, China
Received 30 April 2013; Revised 25 July 2013; Accepted 9 August 2013
Academic Editor: Andre Van Wijnen
Copyright © 2013 Wuyi Liu and Deyu Chen. 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.
- W. R. Atchley and W. M. Fitch, “A natural classification of the basic helix-loop-helix class of transcription factors,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 10, pp. 5172–5176, 1997.
- M. E. Massari and C. Murre, “Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms,” Molecular and Cellular Biology, vol. 20, no. 2, pp. 429–440, 2000.
- V. Ledent and M. Vervoort, “The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis,” Genome Research, vol. 11, no. 5, pp. 754–770, 2001.
- V. Ledent, O. Paquet, and M. Vervoort, “Phylogenetic analysis of the human basic helix-loop-helix proteins,” Genome biology, vol. 3, no. 6, pp. 301–318, 2002.
- S. Jones, “An overview of the basic helix-loop-helix proteins,” Genome Biology, vol. 5, no. 6, article 226, 2004.
- E. Simionato, V. Ledent, G. Richards et al., “Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics,” BMC Evolutionary Biology, vol. 7, article 33, 18 pages, 2007.
- W. Liu and C. Zhao, “Molecular phylogenetic analysis of zebra finch basic helix-loop-helix transcription factors,” Biochemical Genetics, vol. 49, no. 3-4, pp. 226–241, 2011.
- Y. Wang, K. Chen, Q. Yao, W. Wang, and Z. Zhu, “The basic helix-loop-helix transcription factor family in the honey bee, Apis mellifera,” Journal of Insect Science, vol. 8, no. 40, pp. 1–12, 2008.
- C. Dang, Y. Wang, D. Zhang, Q. Yao, and K. Chen, “A genome-wide survey on basic helix-loop-helix transcription factors in giant panda,” PLoS ONE, vol. 6, no. 11, Article ID e26878, 2011.
- A. Liu, Y. Wang, C. Dang et al., “A genome-wide identification and analysis of the basic helix-loop-helix transcription factors in the ponerine ant, Harpegnathos saltator,” BMC Evolutionary Biology, vol. 12, no. 165, pp. 1–14, 2012.
- L. Carretero-Paulet, A. Galstyan, I. Roig-Villanova, J. F. Martínez-García, J. R. Bilbao-Castro, and D. L. Robertson, “Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae,” Plant Physiology, vol. 153, no. 3, pp. 1398–1412, 2010.
- C. Murre, P. Schonleber McCaw, and D. Baltimore, “A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD, and myc proteins,” Cell, vol. 56, no. 5, pp. 777–783, 1989.
- W. R. Atchley, W. Terhalle, and A. Dress, “Positional dependence, cliques, and predictive motifs in the bHLH protein domain,” Journal of Molecular Evolution, vol. 48, no. 5, pp. 501–516, 1999.
- W. R. Atchley, K. R. Wollenberg, W. M. Fitch, W. Terhalle, and A. W. Dress, “Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis,” Molecular Biology and Evolution, vol. 17, no. 1, pp. 164–178, 2000.
- G. Toledo-Ortiz, E. Huq, and P. H. Quail, “The Arabidopsis basic/helix-loop-helix transcription factor family,” Plant Cell, vol. 15, no. 8, pp. 1749–1770, 2003.
- W.-Y. Liu, “Identification and evolutionary analysis of the Xenopus tropicalis bHLH transcription factors,” Yi Chuan, vol. 34, no. 1, pp. 59–71, 2012.
- M. J. Buck and W. R. Atchley, “Phylogenetic analysis of plant basic helix-loop-helix proteins,” Journal of Molecular Evolution, vol. 56, no. 6, pp. 742–750, 2003.
- M. A. Heim, M. Jakoby, M. Werber, C. Martin, B. Weisshaar, and P. C. Bailey, “The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity,” Molecular Biology and Evolution, vol. 20, no. 5, pp. 735–747, 2003.
- J. Li, Q. Liu, M. Qiu, Y. Pan, Y. Li, and T. Shi, “Identification and analysis of the mouse basic/Helix-Loop-Helix transcription factor family,” Biochemical and Biophysical Research Communications, vol. 350, no. 3, pp. 648–656, 2006.
- X. Li, X. Duan, H. Jiang et al., “Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis,” Plant Physiology, vol. 141, no. 4, pp. 1167–1184, 2006.
- Y. Wang, K. Chen, Q. Yao, W. Wang, and Z. Zhu, “The basic helix-loop-helix transcription factor family in Bombyx mori,” Development Genes and Evolution, vol. 217, no. 10, pp. 715–723, 2007.
- Y. Wang, K. Chen, Q. Yao, X. Zheng, and Z. Yang, “Phylogenetic analysis of Zebrafish basic helix-loop-helix transcription factors,” Journal of Molecular Evolution, vol. 68, no. 6, pp. 629–640, 2009.
- N. Pires and L. Dolan, “Origin and diversification of basic-helix-loop-helix proteins in plants,” Molecular biology and evolution, vol. 27, no. 4, pp. 862–874, 2010.
- J. K. Sailsbery, W. R. Atchley, and R. A. Dean, “Phylogenetic analysis and classification of the fungal bHLH domain,” Molecular Biology and Evolution, vol. 29, no. 5, pp. 1301–1318, 2012.
- X. Zheng, Y. Wang, Q. Yao, Z. Yang, and K. Chen, “A genome-wide survey on basic helix-loop-helix transcription factors in rat and mouse,” Mammalian Genome, vol. 20, no. 4, pp. 236–246, 2009.
- S. Carruthers and D. L. Stemple, “Genetic and genomic prospects for Xenopus tropicalis research,” Seminars in Cell and Developmental Biology, vol. 17, no. 1, pp. 146–153, 2006.
- J. B. Bowes, K. A. Snyder, E. Segerdell et al., “Xenbase: a xenopus biology and genomics resource,” Nucleic Acids Research, vol. 36, no. 1, pp. D761–D767, 2008.
- U. Hellsten, R. M. Harland, M. J. Gilchrist et al., “The genome of the western clawed frog Xenopus tropicalis,” Science, vol. 328, no. 5978, pp. 633–636, 2010.
- J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins, “The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools,” Nucleic Acids Research, vol. 25, no. 24, pp. 4876–4882, 1997.
- K. B. Nicholas and H. B. Nicholas, “GeneDoc: a tool for editing and annotating multiple sequence alignments,” Distributed by the author, 1997.
- G. Dennis Jr., B. T. Sherman, D. A. Hosack et al., “DAVID: database for annotation, visualization, and integrated discovery,” Genome Biology, vol. 4, no. 5, p. 3, 2003.
- D. W. Huang, B. T. Sherman, and R. A. Lempicki, “Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources,” Nature Protocols, vol. 4, no. 1, pp. 44–57, 2009.
- X. Mao, T. Cai, J. G. Olyarchuk, and L. Wei, “Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary,” Bioinformatics, vol. 21, no. 19, pp. 3787–3793, 2005.
- J. Wu, X. Mao, T. Cai, J. Luo, and L. Wei, “KOBAS server: a web-based platform for automated annotation and pathway identification,” Nucleic Acids Research, vol. 34, pp. W720–W724, 2006.
- C. Xie, X. Mao, J. Huang et al., “KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases,” Nucleic Acids Research, vol. 39, no. 2, pp. W316–W322, 2011.
- C. von Mering, L. J. Jensen, B. Snel et al., “STRING: known and predicted protein-protein associations, integrated and transferred across organisms,” Nucleic Acids Research, vol. 33, pp. D433–D437, 2005.
- D. Szklarczyk, A. Franceschini, M. Kuhn et al., “The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored,” Nucleic Acids Research, vol. 39, no. 1, pp. D561–D568, 2011.
- D. Szklarczyk, A. Franceschini, M. Kuhn et al., “STRING v9.1: protein-protein interaction networks, with increased coverage and integration,” Nucleic Acids Research, vol. 41, no. 1, pp. D808–D815, 2013.
- Y. Fujii, T. Shimizu, T. Toda, M. Yanagida, and T. Hakoshima, “Structural basis for the diversity of DNA recognition by bZIP transcription factors,” Nature Structural Biology, vol. 7, no. 10, pp. 889–893, 2000.
- F. Fisher and C. R. Goding, “Single amino acid substitutions alter helix-loop-helix protein specificity for bases flanking the core CANNTG motif,” EMBO Journal, vol. 11, no. 11, pp. 4103–4109, 1992.
- A. R. Ferre-D'Amare, G. C. Prendergast, E. B. Ziff, and S. K. Burley, “Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain,” Nature, vol. 362, no. 6424, pp. 38–45, 1993.
- F. Ahmadpour, R. Ghirlando, A. T. de Jong, M. Gloyd, J. A. Shin, and A. Guarné, “Crystal structure of the minimalist Max-e47 protein chimera,” PLoS ONE, vol. 7, no. 2, Article ID e32136, 2012.
- T. Ellenberger, D. Fass, M. Arnaud, and S. C. Harrison, “Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer,” Genes and Development, vol. 8, no. 8, pp. 970–980, 1994.
- S. Guindon and O. Gascuel, “A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood,” Systematic Biology, vol. 52, no. 5, pp. 696–704, 2003.
- D. T. Jones, W. R. Taylor, and J. M. Thornton, “The rapid generation of mutation data matrices from protein sequences,” Computer Applications in the Biosciences, vol. 8, no. 3, pp. 275–282, 1992.
- K. Tamura, J. Dudley, M. Nei, and S. Kumar, “MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0,” Molecular Biology and Evolution, vol. 24, no. 8, pp. 1596–1599, 2007.
- J. P. Huelsenbeck and F. Ronquist, “MRBAYES: bayesian inference of phylogenetic trees,” Bioinformatics, vol. 11, no. 8, pp. 754–755, 2001.
- J. A. Campos-Ortega, “Mechanisms of early neurogenesis in Drosophila melanogaster,” Journal of Neurobiology, vol. 24, no. 10, pp. 1305–1327, 1993.
- R. Sousa-Nunes, L. Y. Cheng, and A. P. Gould, “Regulating neural proliferation in the Drosophila CNS,” Current Opinion in Neurobiology, vol. 20, no. 1, pp. 50–57, 2010.
- S. Lin and T. Lee, “Generating neuronal diversity in the Drosophila central nervous system,” Developmental Dynamics, vol. 241, no. 1, pp. 57–68, 2012.
- T. Shimizu, A. Toumoto, K. Ihara et al., “Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition,” EMBO Journal, vol. 16, no. 15, pp. 4689–4697, 1997.
- B. Morgenstern and W. R. Atchley, “Evolution of bHLH transcription factors: modular evolution by domain shuffling?” Molecular Biology and Evolution, vol. 16, no. 12, pp. 1654–1663, 1999.
- Y. Lu and M. D. Rausher, “Evolutionary rate variation in anthocyanin pathway genes,” Molecular Biology and Evolution, vol. 20, no. 11, pp. 1844–1853, 2003.
- M. A. Streisfeld and M. D. Rausher, “Relaxed constraint and evolutionary rate variation between basic helix-loop-helix floral anthocyanin regulators in Ipomoea,” Molecular Biology and Evolution, vol. 24, no. 12, pp. 2816–2826, 2007.
- M. A. Streisfeld, D. Liu, and M. D. Rausher, “Predictable patterns of constraint among anthocyanin-regulating transcription factors in Ipomoea,” New Phytologist, vol. 191, no. 1, pp. 264–274, 2011.