Molecular characterization of RNA binding motif protein 3 (RBM3) gene from Pashmina goat Ruby Zargar, Uneeb Urwat, Firdose Malik, Riaz A. Shah, M.H. Bhat, Niyaz A. Naykoo, Firdous Khan, H.M. Khan, Syed Mudasir Ahmed, Ramesh Kumar Vijh, Nazir A. Ganai * Division of Animal Biotechnology, SKUAST-K, Shuhama, Alesteng, Kashmir ARTICLE INFO Article history: Received 15 February 2014 Accepted 26 November 2014 Keywords: Pashmina Hypothermia RNA binding motif protein 3 Expression analysis Comparative modeling A B ST R AC T Pashmina goat inhabits the high altitude cold arid desert of Ladakh, India. This goat is known for its finest and costliest under fiber. Though the under fiber may be a part of its complex thermoregulation mech- anism, the genetics of its adaptability under cold conditions is not known. As an attempt to understand its adaptive genetics, and the role of RNA-binding proteins at the cellular response, this study was con- ducted to characterize the RBM3 gene in Pashmina goat and its expression during hypothermia. The ORF of Pashmina RBM3 gene was 273 bp. Phylogenetic analysis revealed that Pashmina RBM3 is closely related to Bos taurus RBM3. Pashmina RBM3 was characterized by comparative modeling studies. The final 3-D model contained two α-helices and four β-sheets. qRT-PCR data showed that Pashmina RBM3 gene ex- pression was significantly higher (P < 0.05) at moderate (30 °C) hypothermic stress conditions as compared with deep (15 °C) hypothermia. © 2014 Elsevier Ltd. All rights reserved. 1. Introduction Pashmina (Cashmere) goat (Capra hircus) is found at higher al- titudes of the Himalayas in Northern India, Nepal and Pakistan. In India, Pashmina goat is mainly found in the Ladakh region of Jammu and Kashmir (Banerjee, 1991). Ladakh is located in Himalayan range of mountains at an altitude of about 3000–6000 m above the mean sea level. The annual rainfall in this area is quite low (up to 8–9 cm) and the temperature levels fluctuate between +35 °C in summers and -40 °C in winters. The high wind velocity with low precipita- tion rate, low humidity, low oxygen tension and fluctuating temperature makes this cold arid high altitude region hostile for man as well as to livestock species. Under such harsh environmen- tal conditions, Pashmina goats still manage to survive by adapting different adaptation strategies. In general organisms have developed sophisticated strategies to adapt themselves to various environmental temperature shifts. In mammals as well as other organisms, cold stress changes the lipid composition of cellular membrane, suppresses the rate of protein synthesis and ultimately the cell growth (Aloia and Raison, 1989; Burdon, 1987; Rao and Engelberg, 1965; Watanabe and Okada, 1967). In eukaryotic cells, gene expression is regulated both at transcrip- tional as well as post transcriptional level (Burd and Dreyfuss, 1994). All these processes are mediated by various RNA-binding proteins and by small RNAs as stable ribonucleoprotein (RNP) complexes (Dreyfuss, 1986; Gorlach et al., 1993; Mattaj, 1990). RNA-binding proteins have been known to play important roles in the cellular response at low temperatures. In case of E. coli, the CspA destabi- lizes RNA secondary structures during hypothermia and thereby facilitate translation (Bae et al., 1997). In Xenopus oocytes, Y-box binding proteins contain a cold-shock domain which controls trans- lation during hypothermia (Matsumoto and Wolffe, 1998) whereas in case of mammals, two cold-induced RNA-binding proteins, CIRBP and RBM3, were found to function during hypothermia (Dresios et al., 2005; Lleonart, 2010; Smart et al., 2007). Both proteins are struc- turally highly similar and belong to the glycine rich RNA-binding protein family. Members of this family are characterized by one RNA recognition motif adjacent to a C-terminal arginine and a glycine- rich domain. Moreover, both CIRBP and RBM3 are thought to be the modulators of gene expression during mild hypothermic condi- tions and have been proposed to function as mRNA chaperone molecules to help maintain or enhance protein translation during periods of cellular stress (Danno et al., 1997; Nishiyama et al., 1997; Smart et al., 2007). Hypothermia generally down-regulates protein synthesis and metabolism in mammalian cells (Fujita, 1999; Giuliodori et al., 2004; Golovlev, 2003; Gualerzi et al., 2003; Homma et al., 2003; Murata et al., 2006; Phadtare, 2004; Phadtare et al., 1999; Ulusu and Tezcan, 2001; Weber and Marahiel, 2003) but the Abbreviations: RBM3, RNA binding motif protein 3; RBP, RNA binding protein; CIRBP, cold induced RNA binding protein; qRT-PCR, quantitative real-time PCR; ORF, open reading frame; RNP, ribonucleoprotein; cDNA, complementary DNA; RMSD, root mean square deviation; CDD, Conserved Domain Database; PDB, Protein Database * Corresponding author. Division of Animal Biotechnology, SKUAST-K, Shuhama, Alesteng, Kashmir. Tel.: +0194 2262642; fax: +0194 2262207. E-mail address: naganai@skuastkashmir.ac.in (N.A. Ganai). http://dx.doi.org/10.1016/j.rvsc.2014.11.016 0034-5288/© 2014 Elsevier Ltd. All rights reserved. Research in Veterinary Science 98 (2015) 51–58 Contents lists available at ScienceDirect Research in Veterinary Science journal homepage: www.elsevier.com/locate/rvsc