Transmembrane START domain proteins: in silico identification, characterization and expression analysis under stress conditions in chickpea (Cicer arietinum L.)

References

• Stocco DM. StAR protein and the regulation of steroid hormone biosynthesis. Ann Rev Physiol 2001; 63:193-213
   PubMed Web of Science ®Google Scholar
• Schrick K, Nguyen D, Karlowski WM, Mayer KFX. START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors. Genome Biol 2004; 5:R41; PMID:15186492
   PubMed Web of Science ®Google Scholar
• Roderick SL, Chan WW, Agate DS, Olsen LR, Vetting MW, Rajashankar KR, Cohen DE. Structure of human phosphatidylcholine transfer protein in complex with its ligand. Nat Struct Biol 2002; 9:507-11; PMID:12055623
   PubMedGoogle Scholar
• Romanowski MJ, Soccio RE, Breslow JL, Burley SK. Crystal structure of the Mus musculus cholesterol-regulated START protein 4 (StarD4) containing a StAR-related lipid transfer domain. Proc Natl Acad Sci U S A 2002; 99:6949-54; PMID:12011453; http://dx.doi.org/10.1073/pnas.052140699
   PubMed Web of Science ®Google Scholar
• Eyster KM. The membrane and lipids as integral participants in signal transduction: lipid signal transduction for the non-lipid biochemist. Adv Physiol Educ 2007; 31:5-16; PMID:17327576; http://dx.doi.org/10.1152/advan.00088.2006
   PubMed Web of Science ®Google Scholar
• Hanada K, Kumagai K, Yasuda S, Miura Y, Kawano M, Fukasawa M, Nishijima M. Molecular machinery for non-vesicular trafficking of ceramide. Nature 2003; 426:803-9; PMID:14685229; http://dx.doi.org/10.1038/nature02188
   PubMed Web of Science ®Google Scholar
• Tabunoki H, Sugiyama H, Tanaka Y, Fujii H, Banno Y, Jouni ZE, Kobayashi M, Sato R, Maekawa H, Tsuchida K. Isolation, characterization, and cDNA sequence of a carotenoid binding protein from the silk gland of Bombyx mori larvae. J Biol Chem 2002; 277:32133-40; PMID:12052833; http://dx.doi.org/10.1074/jbc.M204507200
   PubMed Web of Science ®Google Scholar
• Ponting CP, Aravind L. START: a lipid-binding domain in StAR, HD-ZIP and signalling proteins. Trends Biochem Sci 1999; 24:130-2; PMID:10322415; http://dx.doi.org/10.1016/S0968-0004(99)01362-6
   PubMed Web of Science ®Google Scholar
• Roth GE, Gierl MS, Vollborn L, Meise M, Lintermann R, Korge G. The Drosophila gene Start1: a putative cholesterol transporter and key regulator of ecdysteroid synthesis. Proc Natl Acad Sci 2004; 101:1601-6; PMID:14745013; http://dx.doi.org/10.1073/pnas.0308212100
   PubMed Web of Science ®Google Scholar
• Venkata BP, Schrick K. START domains in lipid / sterol transfer and signaling in plants. 2006; In: Proceedings of the 17th International Symposium on Plant Lipids, Michigan State University Press.
   Google Scholar
• Ito M, Sentoku N, Nishimura A, Hong S-K, Sato Y, Matsuoka M. Position dependent expression of GL2-type homeobox gene, Roc1: significance for protoderm differentiation and radial pattern formation in early rice embryogenesis. Plant J 2002; 29:497-507; PMID:11846882; http://dx.doi.org/10.1046/j.1365-313x.2002.01234.x
   PubMed Web of Science ®Google Scholar
• Kubo H. ANTHOCYANINLESS2, a Homeobox gene affecting anthocyanin distribution and root development in arabidopsis. Plant Cell 1999; 11(7):1217-26; PMID:10402424
   PubMed Web of Science ®Google Scholar
• Rerie WG, Feldmann KA, Marks MD. The GLABRA2 gene encodes a homeo domain protein required for normal trichome development in Arabidopsis. Genes Dev 1994; 8:1388-99; PMID:7926739; http://dx.doi.org/10.1101/gad.8.12.1388
   PubMed Web of Science ®Google Scholar
• McConnell JR, Emery J, Eshed Y, Bao N, Bowman J, Barton MK. Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. Nature 2001; 411:709-13; PMID:11395776; http://dx.doi.org/10.1038/35079635
   PubMed Web of Science ®Google Scholar
• Tang D, Ade J, Frye CA, Innes RW. Regulation of plant defense responses in Arabidopsis by EDR2, a PH and START domain-containing protein. Plant J 2005; 44:245-57; PMID:16212604; http://dx.doi.org/10.1111/j.1365-313X.2005.02523.x
   PubMed Web of Science ®Google Scholar
• Hurwitz N, Pellegrini-Calace M, Jones DT. Towards genome-scale structure prediction for transmembrane proteins. Philos Trans R Soc Lond B Biol Sci 2006; PMID:16524835
   PubMed Web of Science ®Google Scholar
• Wang W, Esch JJ, Shiu S-H, Agula H, Binder BM, Chang C, Patterson SE, Bleecker AB. Identification of important regions for ethylene binding and signaling in the transmembrane domain of the ETR1 ethylene receptor of Arabidopsis. Plant Cell 2006; 18:3429-42; PMID:17189345; http://dx.doi.org/10.1105/tpc.106.044537
   PubMed Web of Science ®Google Scholar
• Hothorn M, Belkhadir Y, Dreux M, Dabi T, Noel JP, Wilson IA, Chory J. Structural basis of steroid hormone perception by the receptor kinase BRI1. Nature 2011; 474:467-71; PMID:21666665; http://dx.doi.org/10.1038/nature10153
   PubMed Web of Science ®Google Scholar
• De Clercq I, Vermeirssen V, Van Aken O, Vandepoele K, Murcha MW, Law SR, Inzé A, Ng S, Ivanova A, Rombaut D, et al. The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. Plant Cell 2013; 25:3472-90; PMID:24045019; http://dx.doi.org/10.1105/tpc.113.117168
   PubMed Web of Science ®Google Scholar
• Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, et al. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 2013; 31:240-6; PMID:23354103; http://dx.doi.org/10.1038/nbt.2491
   PubMed Web of Science ®Google Scholar
• Jain M, Misra G, Patel RK, Priya P, Jhanwar S, Khan AW, Shah N, Singh VK, Garg R, Jeena G, et al. A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant J 2013; 74:715-29; PMID:23489434
   PubMed Web of Science ®Google Scholar
• Stanke M, Steinkamp R, Waack S, Morgenstern B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res 2004; 32:W309-12; PMID:15215400; http://dx.doi.org/10.1093/nar/gkh379
   PubMed Web of Science ®Google Scholar
• Besemer J, Borodovsky M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 2005; 33:W451-4; PMID:15980510; http://dx.doi.org/10.1093/nar/gki487
   PubMedGoogle Scholar
• Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997; 268:78-94; PMID:9149143; http://dx.doi.org/10.1006/jmbi.1997.0951
   PubMed Web of Science ®Google Scholar
• Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, et al. The Pfam protein families database. Nucleic Acids Res 2012; 40:D290-301; PMID:22127870; http://dx.doi.org/10.1093/nar/gkr1065
   PubMedGoogle Scholar
• Schultz J, Milpetz F, Bork P, Ponting CP. SMART, a simple modular architecture research tool: Identification of signaling domains. Proc Natl Acad Sci 1998; 95:5857-64; PMID:9600884; http://dx.doi.org/10.1073/pnas.95.11.5857
   PubMed Web of Science ®Google Scholar
• Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 2001; 305:567-80; PMID:11152613; http://dx.doi.org/10.1006/jmbi.2000.4315
   PubMed Web of Science ®Google Scholar
• Kyte J, Doolittle R. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982; 157:105-32; PMID:7108955; http://dx.doi.org/10.1016/0022-2836(82)90515-0
   PubMed Web of Science ®Google Scholar
• McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 2000; 16:404-5; PMID:10869041; http://dx.doi.org/10.1093/bioinformatics/16.4.404
   PubMed Web of Science ®Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725-29; PMID:24132122; http://dx.doi.org/10.1093/molbev/mst197
   PubMed Web of Science ®Google Scholar
• Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009; 37:W202-8; PMID:19458158; http://dx.doi.org/10.1093/nar/gkp335
   PubMed Web of Science ®Google Scholar
• Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 2002; 30:325-7; PMID:11752327; http://dx.doi.org/10.1093/nar/30.1.325
   PubMed Web of Science ®Google Scholar
• Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G, Bhatia S, Chattopadhyay D, Tyagi AK, Jain M. Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol 2011; 156:1661-78; PMID:21653784; http://dx.doi.org/10.1104/pp.111.178616
   PubMed Web of Science ®Google Scholar
• Garg R, Sahoo A, Tyagi AK, Jain M. Validation of internal control genes for quantitative gene expression studies in chickpea (Cicer arietinum L.). Biochem Biophys Res Commun 2010; 396:283-8; PMID:20399753
   PubMed Web of Science ®Google Scholar
• Satheesh V, Chidambaranathan P, Jagannadham PT, Kohli D, Jain PK, Bhat SR, Srinivasan R. A polyketide cyclase/dehydrase and lipid transport superfamily gene of Arabidopsis and its orthologue of chickpea exhibit rapid response to wounding. Ind J Genet Pl Breed 2014; 74:463-70; http://dx.doi.org/10.5958/0975-6906.2014.00871.2.
   Web of Science ®Google Scholar
• Chen X, Chen Z, Zhao H, Zhao Y, Cheng B, Xiang Y. Genome-Wide analysis of soybean hd-zip gene family and expression profiling under salinity and drought treatments. PLoS One 2014; 9(2): e87156; PMID:24498296; http://dx.doi.org/10.3390/ijms1303317610.1371/journal.pone.0087156
   PubMedGoogle Scholar
• Kwon Y, Yu S-I, Lee H, Yim JH, Zhu J-K, Lee B-H. Arabidopsis serine decarboxylase mutants implicate the roles of ethanolamine in plant growth and development. Int J Mol Sci 2012; 13:3176-88; PMID:22489147; http://dx.doi.org/10.3390/ijms13033176
   PubMed Web of Science ®Google Scholar
• Mo P, Zhu Y, Liu X, Zhang A, Yan C, Wang D. Identification of two phosphatidylinositol/phosphatidylcholine transfer protein genes that are predominately transcribed in the flowers of Arabidopsis thaliana. J Plant Physiol 2007; 164: 478-86; PMID:16697077; http://dx.doi.org/10.1016/j.jplph.2006.03.014
   PubMed Web of Science ®Google Scholar
• Nakamura Y, Andres F, Kanehara K, Liu YC, Dormann P, Coupland G. Arabidopsis florigen FT binds to diurnally oscillating phospholipids that accelerate flowering. Nat Commun 2014; 5:3553; PMID:24698997; http://dx.doi.org/10.1038/ncomms4553
   PubMed Web of Science ®Google Scholar
• Dixit AK, Jayabaskaran C. Phospholipid mediated activation of calcium dependent protein kinase 1 (CaCDPK1) from chickpea: a new paradigm of regulation. PLoS One 2012; 7:e51591; PMID:23284721; http://dx.doi.org/10.1371/journal.pone.0051591
   PubMedGoogle Scholar