Identification of conserved domains and motifs for TaWdhn13 gene in Triticum aestivum by in silico analysis.
Bioinformatics is an interdisciplinary research area, which may be defined as the interface between biological and computational sciences. It greatly helps in management of complex and scattered biological data, sequence analysis, algorithmic designing . Domains, traditionally known as structurally independently folding units, are conserved functional units that may contain or more motifs. Domains are functional structural units. These units are conserved at the level of sequence and structure. Motifs are conserved across proteins at the level of sequence or structure or both. They include both short stretches of fixed residue length that act as sites for post-translational modification, phosphorylation, and longer sequence that form secondary structure for protein-DNA, protein-ion or protein-lipid interaction [7, 9]. TaWdhn13 gene has a crucial role as the cold-acclimation process in the wheat. TaWdhn13 gene is transcriptionally activated and produces the accumulated proteins and metabolites and protection cell structure from freezing damage . In this study, we identify and characterize the conserved domain and motifs of TaWdhn13 gene.
Download the complete sequence for TaWdhn13 gene (with accession number: AB297677) in the NCBI database.
Identification of the conserved domain:
To identify conserved domain, we used the Conserved domain database (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.c gi).
Identification of the motifs in TaWdhn13 gene:
To analyze the nucleotide sequence we searched for the motifs and the motif search software (http://www.genome.jp/tools/motif) was used to identify the motifs in nucleotide sequence.
Results and Discussion
Our results showed TaWdhn13 conserved domain incudes: Dehydrin superfamily (Fig. 1).
In silico analysis showed the motif structure for this gene includes (Table 1 and Fig. 2):
a) 2FE-2S_FER_1 Motif, or ferredoxins, iron-sulfur binding region signature. Motif 2Fe-2S is a structural motif, from the comparison of the coding proteins between rice and spinach chlorine monooxygenase (CMOs), rice CMO potentially shares two conservative motifs including a Rieske-type [2Fe-2S]  cluster and a mononuclear non-heme Fe binding sequence. These motifs are considered to be essential for the function of CMO .
b) INTEGRIN_BETA Motif. Integrins are expressed on the cell surface as a noncovalently linked heterodimer consisting of [alpha] and [beta] subunit, which conveys specificity in cell-cell adhesion, cell-extracellular matrix (ECM) adhesion, immune cell recruitment, extravasation, and signaling .
c) CTCK_1 Motif or C-terminal cystine knot signature. The cystine-knot motif, made up of three intertwined disulfide bridges, is a unique feature of several toxins, cyclotides and growth factors, and occurs in a variety of species, including fungi, insects, molluscs and mammals .
d) ANAPHYLATOXIN_1 Motif. In the mammalian cell, Anaphylatoxins are able to trigger j) degranulation (release of substances) of endothelial cells, mast cells or phagocytes, which produce a local inflammatory response .
e) AGOUTI_1 Motif. The AGOUTI_1 Motif is a signaling motif and normally expressed in skin cells and interacts with the first melanocortin receptor (MCR1) to control pigmentation .
f) IGFBP_N_1 Motif. Insulin-like growth factor (IGF) 1-binding proteins (IGFBPs) are a group of six homologous, yet distinct proteins (IGFBPs1-6) which bind both IGF-I and IGF-II with high affinity .
g) VWFC_1 Motif. VWFC motif has conserved cysteine which was found in many cereal crops like rice .
h) EGF_1 Motif. The EGF_1 motif or EGF-like domain signature 1 is an evolutionary conserved protein domain, which derives its name from the epidermal growth factor where it was first described. It comprises about 30 to 40 amino-acid residues and has been found in a large number of mostly animal proteins .
i) DEFENSIN Motif. Defensins motifs are small Cysteine-rich cationic proteins found in both vertebrates and invertebrates. They have also been reported in plants. They are, and function as, host defense peptides. They are active against bacteria, fungi and many enveloped and nonenveloped viruses .
This computational analysis focuses on identified a number of motifs structure and conserved domains in TaWdhn13 gene. In silico analysis provides an efficient way to indicating motifs sequence and conserved domains in genome [11,12]. However, by using the in silico analysis we can predicating and identified the motifs structure and conserved domain in gene sequence.
In this study a total of 9 motifs structure and one conserved domain identified in TaWdhn13 gene sequence.
Our results showed in TaWdhn13gene, motifs structure includes: 2FE2S_FER_1 Motif, INTEGRIN_BETA Motif, CTCK_1 Motif, ANAPHYLATOXIN_1 Motif, AGOUTI_1 Motif, IGFBP_N_1 Motif, VWFC_1 Motif, EGF_1 Motif and DEFENSIN Motif. Also conserved domain in this gene include: Dehydrin superfamily.
[1.] Kobayashi, F., M. Ishibashi, S. Takumi, 2012. Transcriptional activation Cor/Lea genes and increase stress tolerance through expression of a wheat DREB2 homolog in transgenic tobacco. Transgenic Research, 17(5): 755-767.
[2.] Zhengxin, C.H., 2012. Development of a Database Course for Bioinformatics. Procedia Computer Science, 9: 532-539.
[3.] Mario, C., W. Rodrigo, S. Joakim, 2012. Biomedical and Bioinformatics Challenges to Computer Science. Procedia Computer Science, 1: 931-933.
[4.] Shalini, L., K.R. Acharya, 2011. Tying the knot the cystine signature and molecular-recognition processes of the vascular endothelial growth factor family of angiogenic cytokines. FEBS Journal., 278: 4304-4322.
[5.] Marwa, N.M.E., A.A. E-seuodi, A.A. Abd-Elhady, S.E.A. Edris, N.R. Abdelhamid, A.H.M. Hassan, 2011. Utilization of Some EST Derived SSR Markers to Detect Glutenin Gene Loci in Wheat. Journal of Applied Sciences Research, 7(12): 2147-2155.
[6.] Ti-Cao, Z., Q. Qiao, Y. Zhong, 2012. Detecting adaptive evolution and functional divergence in aminocyclopropane-1-carboxylate synthase (ACS) gene family. Computional Biology and chemistry, 38: 10-16.
[7.] Cannataro, M., R.W. dos Santos, J. Sundnes, 2009. Bioinformatics' challenges to computer science: Bioinformatics tools and biomedical modeling,in: G. Allen, J. Nabrzyski, E. Seidel, G. D. van Albada, J. Dongarra, P. M. A. Sloot (Eds.), ICCS (1), Vol. 5544 of Lecture Notes in Computer Science, Springer, pp: 807-809.
[8.] Fan, C.H., Y.Z. Xing, H.L. Mao, T.T. Lu and B. Han, 2006. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet., 112: 1164-1171.
[9.] McNulty, J.C., P.J. Jackson, D.A. Thompson, B. Chai, I. Gantz, G.S. Barsh, P.E. Dawson and G.L. Millhauser, 2005. Structures of the agouti signaling protein. J Mol Biol., 346: 1059-1070.
[10.] Adam, L.F., K. Heidi, C. Tresa, 2004. Cellular integrins function as entry receptors for human cytomegalovirus via a highly conserved disintegrin-like domain. PANS, 101: 15470-15475.
[11.] Zhu, J.K., 2002. Salt and drought stress signal transduction in plants. Annu. Rev. Plant. Biol., 53: 247-273.
[12.] Lloyd, G., P. Landini, S. Bushby, 2001. Activation and repression of transcription initiation in bacteria. Essays Biochem., 37: 17-31.
[13.] Gray, J., P.S. Close, S.P. Briggs, G.S. Johal, 1997. A novel suppressor of cell death in plants encoded by the Lls1 gene of maize. Cell, 89: 25-31.
[14.] Rathinasabapathi, B., M. Burnet, B.L. Russell, D.A. Gage, P.C. Liao, G.J. Nye, P. Scott, J.H. Golbeck, A.D. Hanson, 1997. Choline monooxygenase, an unusual iron-sulfur enzyme catalyzing the first step of glycine betaine synthesis in plants: prosthetic group characterization and cDNA cloning. Proc Natl Acad Sci USA., 94: 3454-3458.
[15.] Downing, A.K., V. Knott, J.M. Werner, C.M. Cardy, I.D. Campbell, P.A. Handford, 1996. Solution structure of a pair of calcium-binding epidermal growth factor-like domains: implications for the Marfan syndrome and other genetic disorders. Cell., 85(4): 597-605.
[16.] Rechler, M.M., 1995. In Molecular Endocrinology: Basic Concepts and Clinical Correlations (Weintraub, B. D., ed) pp. 155-180, Raven Press, Ltd., New York
[17.] Hugli, T.E., 1986. Biochemistry and Biology of Anaphylatoxins. Complement., 3(3): 111-27.
[18.] Selsted, M.E., S.S. Harwing, T. Ganz, J.W. Schiling and R.I. Lehrer, 1985. Primary structure of three human neutrophil defensins. J.Clin. Invest., 76: 1436-1439.
(1) Hassan Rasouli, (1) Danial Kahrizi, (2) Parivash Ghadernia
(1) Agronomy and Plant Breeding and Biotechnology Department (APBBD), College of Agriculture and Natural Resources, Razi University, Kermanshah, Iran.
(2) Department of Microbiology in Bruojerd Islamic Azad University
Hassan Rasouli, Agronomy and Plant Breeding and Biotechnology Department (APBBD), College of Agriculture and Natural Resources, Razi University, Kermanshah, Iran.
E-mail address: firstname.lastname@example.org
Table 1: Location and sequence to identified motifs in the TaWdhn13 gene. Motif Motif Sequence Symbol location 2FE-2S FER 1 1491..149 CAGGTCGGC A Motif 9 CTAGTCGGC 1579..158 CTGGACAGC 7 2123..213 1 INTEGRIN_BETA 856..870 CCGCCGCCTCCTCCC B Motif 1771..178 CAGGGGCACGGCGC 4 CTCK_1 Motif 1602..164 CCACTCACAAGAGCACACGTGGT C GCTTTCTCCACCCTCC ANAPHYLATOXIN 869..901 CCGCGCGATCACGGCGCCGA D CGCGCCGCCAGCC _1 Motif 1063..109 CCGAGTGCACCGATCTCGGAGT GGATCGAGTAGCC 7 CCCCACTTTATGAGCTAGTCGGC AGTCACCTGCCCACC 1565..160 2 AGOUTI1 Motif 836..878 CCTAGCGCCTCTCACCACCGCC E GCCGCCTCCTCCCGCGCGATC IGFBP_N_1 Motif 890..905 GCGCCGCCAGCCGCGC F VWFC_1 Motif 564..616 CCACTCGGGAGCAGCTTGAC G GAGTTCTACCAACACTTTCC AGACATCCAGCT 805..859 C 806..859 CCGACTCCCCTTAGGAGCCAGA ACCCTAAACCCTAGCGCCT CTCACCACCGC 841..891 CGC 843..897 CGACTCCCCTTAGGAGCCAGAA CCCTAAACCCTAGCGCCTCTC ACCACCGCC 844..901 GC 848..905 CGCCTCTCACCACCGCCGCCG CCTCCTCCCGCGCGATCACG GCGCCGACGC 859..915 CCTCTCACCACCGCCGCCGCC TCCTCCCGCGCGATCACGG CGCCGACGCGCC 860..915 GCC 862..915 CTCTCACCACCGCCGCCGCCTCC TCCCGCGCGATCACGGCG CCGACGCGCCG 863..915 CCAGCC 874..928 CACCACCGCCGCCGCCTCCTCCC GCGCGATCACGGCGCCGAC GCGCCGCCAG 901..945 CCGCGC 907..945 CCGCCTCCTCCCGCGCGATCAC GGCGCCGACGCGCCGCCAG CCGCGCTCAAC 910..968 CTCTC 911..968 CGCCTCCTCCCGCGCGATCACG GCGCCGACGCGCCGCCAG CCGCGCTCAACC 922..975 TCTC 923..975 CCTCCTCCCGCGCGATCA CGGCGCCGACGCGCCGC CAGCCGCGCTCAACCTC 925..975 TC 1499..154 CTCCTCCCGCGCGATCACGG CGCCGACGCGCCGCCAG CCGCGCTCAACCTCT 6 C 1502..154 CGATCACGGCGCCGACGCG CCGCCAGCCGCGCTCA ACCTCTCACCAACCCAC 6 CTC 1511..156 CGCGCTCAACCTCTCACCA ACCCACCTCTCATCCCTAC AACCTAC 8 CAACCTCTCACCAACCCACC TCTCATCCCTACAACCTAC 1527..157 CCTCTCACCAACCCACCTCT CATCCCTACAACCTACTGTT GAGGCCCGGTGAC 0 CCTAGC 1528..157 CTCTCACCAACCCACCTCTCAT CCCTACAACCTACTGTTGA GGCCCGGTGACC 0 CTAGC 1565..160 CCACCTCTCATCCCTACAA CCTACTGTTGAGGCCCGG TGACCCTAGCTCCTAC 7 C 1587..164 CACCTCTCATCCCTACAACC TACTGTTGAGGCCCGGT GACCCTAGCTCCTACC 0 CCTCTCATCCCTACAACC TACTGTTGAGGCCCGGT GACCCTAGCTCCTACC 1599..164 CAGCCACTCATGCGAGCA CACGTCGCGCCCTGCA CTGCATGCCGCGGC 3 CCACTCATGCGAGCACACG TCGCGCCCTGCACTG CATGCCGCGGC 1601..164 CGAGCACACGTCGCGCC CTGCACTGCATGCCGCG GCGATTCGTCCATCTAAC 3 CACCCC 1602..164 CCTGCACTGCATGCCGC GGCGATTCGTCCATCTAA CCACCCCAC 3 CTGCACTGCATGCCGCG GCGATTCGTCCATCTAAC CACCCCAC 1657..170 CCCCACTTTATGAGCTA GTCGGCAGTCACCT GCCCACCCACTC 8 CAGTCACCTGCCCACCCACT CACAAGAGCACACGTG GTGCTTTCTCCACCCTC 1666..170 C 8 CACCCACTCACAAGA GCACACGTGGTGCTTTC TCCACCCTCCAAC 1812..186 CCCACTCACAAGAGCACA CGTGGTGCTTTCTCCACC CTCCAAC 0 CCACTCACAAGAGCAC ACGTGGTGCTTTCT CCACCCTCCAAC 1980..203 CGCCTCGTGCTGCACTTG CTTTACACAGCCACC TTCCTCACACAACCAGGAC 4 CTGCACTTGCTTTACACA GCCACCTTCCTCACACAA CCAGGAC 1981..203 CATCACGGAGAAGCTCC CCCGTGGCCATGGTG ATCACCAGCAGGCCACC 4 CCAGCACACCACTGGAA TGAGCGGCTCGAAGACG CATGCCACCACAGCCAC 1986..203 CACC 4 CAGCACACCACTGGAAT GAGCGGCTCGAAGACG CATGCCACCACAGCCACC 2128..217 ACC 5 CACCACTGGAATGAGCGG CTCGAAGACGCATGCCA CCACAGCCACCACC CAGCACTAAGCCCAGCC GGTCTGCCCACGCC CGCGCCCGACCCGCTAC EGF_1 Motif 344..355 CGCGCCCTGGCC H 410..421 CACCAGCGGTGC 461..472 CACCAGTAGTGC 811..822 CCCCTTAGGAGC 1568..157 CACTTTATGAGC 9 CACACGTGGTGC 1615..162 CACAACCAGGAC 6 CACCAGCAGGCC 1697..170 8 1846..185 7 DEFENSIN Motif 2131..215 CACTAAGCCCAGC I 9 CGGTCTGCCCACGCCC
|Printer friendly Cite/link Email Feedback|
|Title Annotation:||Original Article|
|Author:||Rasouli, Hassan; Kahrizi, Danial; Ghadernia, Parivash|
|Publication:||Advances in Environmental Biology|
|Date:||Apr 1, 2013|
|Previous Article:||Degradation of crude oil in the presence of lead (Pb) and cadmium (Cd) by a metal-adapted consortium culture.|
|Next Article:||Evaluation of antioxidant activity, free radical scavenging and cuprac of two compounds isolated from Scorzonera undulata ssp deliciosa.|