title: In silico analysis of sequential, structural and functional diversity of wheat cystatins and its implication in plant defense.
abstract: Phytocystatins constitute a multigene family that regulates the activity of endogenous and/or exogenous cysteine proteinases. Cereal crops like wheat are continuously threatened by a multitude of pathogens, therefore cystatins offer to play a pivotal role in deciding the plant response. In order to study the need of having diverse specificities and activities of various cystatins, we conducted comparative analysis of six wheat cystatins (WCs) with twelve rice, seven barley, one sorghum and ten corn cystatin sequences employing different bioinformatics tools. The obtained results identified highly conserved signature sequences in all the cystatins considered. Several other motifs were also identified, based on which the sequences could be categorized into groups in congruence with the phylogenetic clustering. Homology modeling of WCs revealed 3D structural topology so well shared by other cystatins. Protein-protein interaction of WCs with papain supported the notion that functional diversity is a con-sequence of existing differences in amino acid residues in highly conserved as well as relatively less conserved motifs. Thus there is a significant conservation at the sequential and structural levels; however, concomitant variations maintain the functional diversity in this protein family, which constantly modulates itself to reciprocate the diversity while counteracting the cysteine proteinases.
authors.affiliation: Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India.
authors.forename: Shriparna
authors.initials: S
authors.lastname: Dutt
authors.forename: V K
authors.initials: VK
authors.lastname: Singh
authors.forename: Soma S
authors.initials: SS
authors.lastname: Marla
authors.forename: Anil
authors.initials: A
authors.lastname: Kumar
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D015891:Cystatins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D057056:Cysteine Proteases; D004042:Dietary Fats, Unsaturated / Q000378:metabolism; D002523:Edible Grain / Q000235:genetics / Q000378:metabolism; D001467:Hordeum / Q000235:genetics / Q000378:metabolism; D005810:Multigene Family; D012275:Oryza / Q000235:genetics / Q000378:metabolism; D010206:Papain / Q000235:genetics / Q000378:metabolism; D010938:Plant Oils / Q000378:metabolism; D010944:Plants / Q000235:genetics / Q000378:metabolism*; D006109:Poaceae / Q000235:genetics / Q000378:metabolism; D017434:Protein Structure, Tertiary / Q000235:genetics; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D012106:Research; D014908:Triticum / Q000235:genetics / Q000378:metabolism; D003313:Zea mays / Q000235:genetics / Q000378:metabolism
chemical_list: D015891:Cystatins; D004042:Dietary Fats, Unsaturated; D010938:Plant Oils; D011506:Proteins; D057056:Cysteine Proteases; D010206:Papain
references.citation: J Biol Chem. 1987 Jul 15;262(20):9688-94
references.pmid: 3496337
references.citation: Proteins. 2006 May 15;63(3):662-70
references.pmid: 16470583
references.citation: Plant J. 2001 Sep;27(5):383-91
references.pmid: 11576423
references.citation: Biochem J. 1986 May 15;236(1):312
references.pmid: 3491603
references.citation: Protein Sci. 1997 Jan;6(1):5-12
references.pmid: 9007972
references.citation: FEBS Lett. 1991 Jul 22;285(2):213-9
references.pmid: 1855589
references.citation: Biochim Biophys Acta. 2005 Jul 10;1729(3):186-99
references.pmid: 15979170
references.citation: J Exp Bot. 2006;57(15):4245-55
references.pmid: 17099080
references.citation: J Mol Biol. 2000 Jul 21;300(4):1005-16
references.pmid: 10891285
references.citation: Mol Genet Genomics. 2005 Jun;273(5):423-32
references.pmid: 15887031
references.citation: Plant Mol Biol. 2002 Nov;50(4-5):687-98
references.pmid: 12374300
references.citation: Electrophoresis. 1997 Dec;18(15):2714-23
references.pmid: 9504803
references.citation: Planta. 2005 Jun;221(4):493-501
references.pmid: 15647900
references.citation: Plant Cell. 1999 Mar;11(3):431-44
references.pmid: 10072402
references.citation: Phytochemistry. 2003 Jul;63(6):643-52
references.pmid: 12842136
references.citation: Biosci Biotechnol Biochem. 2001 Jan;65(1):22-8
references.pmid: 11272836
references.citation: FEBS Lett. 2000 Feb 11;467(2-3):206-10
references.pmid: 10675539
references.citation: Arch Biochem Biophys. 1998 Nov 1;359(1):24-30
references.pmid: 9799556
references.citation: J Mol Biol. 2004 Jul 16;340(4):783-95
references.pmid: 15223320
references.citation: Eur J Biochem. 1992 Nov 1;209(3):933-7
references.pmid: 1425699
references.citation: Trends Biochem Sci. 1995 Sep;20(9):374
references.pmid: 7482707
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references.pmid: 10592235
references.citation: Plant J. 2006 Nov;48(3):403-13
references.pmid: 16965553
references.citation: J Exp Bot. 2002 Mar;53(368):407-13
references.pmid: 11847238
references.citation: Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36
references.pmid: 7584402
references.citation: Eur J Biochem. 2003 Jun;270(12):2593-604
references.pmid: 12787025
references.citation: FEBS Lett. 1989 Jan 30;243(2):234-8
references.pmid: 2917648
references.citation: FEBS J. 2007 Apr;274(8):1908-17
references.pmid: 17371549
references.citation: Annu Rev Phytopathol. 2003;41:615-39
references.pmid: 12730388
references.citation: Plant Physiol. 1996 Nov;112(3):1201-10
references.pmid: 8938418
references.citation: Biochem J. 1990 Oct 1;271(1):281-4
references.pmid: 2222419
references.citation: J Biochem. 1991 Feb;109(2):294-8
references.pmid: 1864841
references.citation: J Biochem. 1994 Sep;116(3):488-92
references.pmid: 7852264
references.citation: BMC Evol Biol. 2008 Jul 10;8:198
references.pmid: 18616807
references.citation: J Biol Chem. 1987 Dec 15;262(35):16793-7
references.pmid: 3500172
references.citation: Plant Mol Biol. 2001 Mar;45(5):599-608
references.pmid: 11414618
references.citation: Biomed Biochim Acta. 1991;50(4-6):613-20
references.pmid: 1801731
references.citation: Arch Biochem Biophys. 2004 Nov 1;431(1):145-59
references.pmid: 15464737
references.citation: EMBO J. 1988 Aug;7(8):2593-9
references.pmid: 3191914
references.citation: Plant Physiol. 2009 Oct;151(2):515-27
references.pmid: 19648229
references.citation: J Biol Chem. 1990 Sep 15;265(26):15832-7
references.pmid: 1697595
references.citation: Nat Biotechnol. 1999 Dec;17(12):1223-6
references.pmid: 10585723
references.citation: Mol Biol Evol. 2007 Aug;24(8):1596-9
references.pmid: 17488738
references.citation: Protein Eng. 1995 Dec;8(12):1303-7
references.pmid: 8869643
references.citation: Plant Physiol. 1993 Dec;103(4):1347-1353
references.pmid: 12232028
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):325-7
references.pmid: 11752327
references.citation: J Exp Bot. 2005 Jul;56(417):1821-9
references.pmid: 15897228
references.citation: Biochemistry. 2000 Dec 5;39(48):14753-60
references.pmid: 11101290
references.citation: Plant Physiol Biochem. 2007 Oct-Nov;45(10-11):790-8
references.pmid: 17870587
references.citation: Biochim Biophys Acta. 2003 Sep 23;1651(1-2):146-52
references.pmid: 14499599
references.citation: EMBO J. 1990 Jun;9(6):1939-47
references.pmid: 2347312
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: FEBS Lett. 2007 Jun 26;581(16):2914-8
references.pmid: 17543305
references.citation: Planta. 2006 May;223(6):1207-18
references.pmid: 16320069