DETECTION OF SPLICE FORMS IN TWO ß- DEFENSINS IN EGYPTIAN NATIVE AND FRISIAN CROSSBRED CATTLE cDNA SEQUENCES
Abstract
Bovine neutrophil β-defensin-11 (BNBD-11) and β-defensin-12 (BNBD- 12) were investigated in Egyptian native and Frisian crossbred cattle. BNBD-11 and BNBD-12 genes have been expressed in several tissues of both breeds. CLUSTAL-W analysis revealed that native and crossbred cattle trachea BNBD-11 and BNBD-12 cDNA sequences have 85% and 65% identity, respectively. Crossbred cattle BNBD-12 showed an insertion of 15 nt compared to native cattle. Sequence alignment of native and crossbred cattle trachea BNBD-11 cDNA showed 66% identities in native and 72% in crossbred cattle compared to Bos taurus BNBD-11 (183 nt, exon I-II), PA: |AJ567992.1|. Whereas native and crossbred cattle trachea BNBD-12 cDNA sequences showed 64% identities in native and 62% in crossbred (excluding 15nt) cattle compared to "Bos taurus BNBD-12 exon I & II". Alternative splicing of native and crossbred cattle trachea BNBD-11 & 12 cDNA sequences is confirmed by the presence of the 12nt (which are absent in Bos taurus) at 3' end of intron-I sequence immediately preceding the 5' end of exon- II. The translated amino acid sequences of both native and crossbred cattle trachea BNBD-11 and BNBD-12 cDNAs were found to be different from those reported in Bos taurus BNBD-11& 12. Several internal stop codons were found in crossbred cattle BNBD-11& 12 cDNA, whereas no stop codons were noticed in native cattle BNBD-11 or BNBD-12. These stop codons may act on the amino acid chain to stop growing prematurely, resulting in the production of a defective protein. The absence of stop codons within the coding region in native cattle may be the cause of their higher resistance to diseases when compared to crossbred ones.References
Abou Mossallam, A. A., E. R. Mahfouz, M. A. Bibars and S. M. El Nahas (2007). Retention of Intron-1 in Cathelicidin-4 mRNA of Egyptian Native and Frisian Crossbred Cattle. J. Appl. Sci. Res., 3: 1400- 1406.
Bauer, F., K. Schweimer, E. Klüver, J. R. Conejo-Garcia, W. G. Forssmann, P. Rösch, K. Adermann and H. Sticht (2001). Structure determination of human and murine ßdefensins reveals structural conservation in the absence of significant sequence similarity. Protein Science, 10: 2470-2479.
Boue, S., I. Letunic and P. Bork (2003). Alternative splicing and evolution. Bioessays, 25: 1031-1034.
Brett, D., J. Hanke, G. Lehmann, S. Haase, S. Delbruck, S. Krueger, J. Reich and P. Bork (2000). EST comparison indicates 38% of human mRNAs contain possible alternative spliceforms. FEBS Lett., 474: 83-86.
Brett, D., H. Pospisil, J. Valcarcel, J. Reich and P. Bork (2002). Alternative splicing and genome complexity. Nat Genet., 30: 29-30.
Brian, C. S., P. M. Joseph, A. B. Jennifer, D. W. Jesse, P. J. Hong, J. W. Michael, L. C. Thomas and B. M. Jr. Paul (2002). Discovery of five conserved β-defensin gene clusters using a computational search strategy. Proc. Natl. Acad. Sci., USA, 99: 2129-2133.
Calarco, J. A, Y. Xing, M. Cáceres, J. P. Calarco, X. Xiao, Q. Pan, C. Lee, T. M. Preuss and B. J. Blencowe (2007). Global analysis of alternative splicing differences between humans and chimpanzees. Genes and Development, 21: 2963-2975.
Carnes, J., M. Jacobson, L. Leinwand and M. Yarus (2003). Stop codon suppression via inhibition of eRF1 expression. RNA, 9: 648- 653.
Das, S., G. S. Vince, I. Lewis-Jones, M. D. Bates and R. Gazvani (2007). The expression of human alpha and beta defensin in the endometrium and their effect on implantation. J. Assist. Reprod. Genet., 24: 533-539.
de Roos, A. D. G. (2005). Origins of introns based on the definition of exon modules and their conserved interfaces. Bioinformatics, 21: 2-9. Faustino, N. A. and T. A. Cooper (2003). Pre-mRNA splicing and human disease. Genes Dev., 17: 419-437.
Gallagher, D. S. Jr, A. M. Ryan, G. Diamond, C. L. Bevins and J. E. Womack (1995). Somatic cell mapping of beta-defensin genes to cattle syntenic group U25 and fluorescence in situ localization to chromosome 27. Mamm. Genome, 6: 554-556.
Ganz, T. (2003). Defensins: antimicrobial peptides of innate immunity. Nat. Rev. Immunol. 3: 710-720.
Ganz, T., M. E. Selsted, D. Szklarek, S. S. Harwig, K. Daher, D. F. Bainton and R. I. Lehrer (1985). Defensins. Natural peptide antibiotics of human neutrophils. J. Clin. Invest., 76: 1427-1435.
Gasteiger, E., A. Gattiker, C. Hoogland, I. Ivanyi, R. D. Appel and A. Bairoch (2003). ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res., 31: 3784-3788.
Hanke, J., D. Brett, I. Zastrow, A. Aydin, S. Delbruck, G. Lehmann, F. Luft, J. Reich and P. Bork (1999). Alternative splicing of human genes-more the rule than the exception? Trends Genet., 15: 389-390.
http://defensins.bii.a-star.edu.sg/
http://searchlauncher.bcm.tmc.edu/sequtil/Options/sixframe.html
http://www.ebi.ac.uk/Tools/clustalw/index.html
Kan, Z., D. States and W. Gish (2002). Selecting for functional alternative splices in ESTs. Genome Res., 12: 1837-1845.
Kondrashov, F. A. and E. V. Koonin (2003). Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. Trends Genet., 19: 115-119.
Koren, E., G. Lev-Maor and G. Ast (2007). The Emergence of Alternative 39 and 59 Splice Site Exons from Constitutive Exons. PLOS Computational Biology, 3: 0895-0908.
Kurlender, L., C. Borgono, I. P. Michael, C. Obiezu, M. B. Elliott, G. M. Yousef and E. P. S. Diamandi (2005). A survey of alternative transcripts of human tissue kallikrein genes. Biochimica et Biophsica Acta (BBA) - Reviews on Cancer, 1755: 1-14.
Lander, E. S., L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody (2001). Initial sequencing and analysis of the human genome. Nature, 409: 860-921.
Lee, C. Y., E. A. Clough, P. Yellon, T. M. Teslovich, D. A. Stephan and E. H. Baehrecke (2003). Genome-wide analyses of steroid- and radiationtriggered programmed cell death in Drosophila. Curr. Biol., 13: 350-357.
Luenser, K., J. Fickel and A. Ludwig (2005). Evolution of caprine and ovine beta-defensin genes. Immunogenetics, 57: 487-98.
Modrek, B., A. Resch, C. Grasso and C. Lee (2001). Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res., 29: 2850-2859.
Modrek, B. and C. Lee (2002). A genomic view of alternative splicing. Nat. Genet., 30: 13-19. Nei, M. (2007). The new mutation theory of phenotypic evolution. Proc. Natl. Acad. Sci., USA, 104: 12235-12242.
Nurtdinov, R. N., I. I. Artamonova, A. A. Mironov and M. S. Gelfand (2003). Low conservation of alternative splicing patterns in the human and mouse genomes. Human Molecular Genetics, 12: 1313-1320.
Ogata, K. B, B. A. Linzer, R. I. Zuberi, T. Ganz, R. I. Lehrer and A. Catanzaro (1992). Activity of defensins from human neutrophilic granulocytes against Mycobacterium avium-Mycobacterium intracellulare. Infect Immun., 60: 4720-4725.
Savkur, R. S., Y. Wu, K. S. Bramlett, M. Wang, S. Yao, D. Perkins, M. Totten, G. Searfoss III, T. P. Ryan, E. W. Su and T. P. Burris (2003). Alternative splicing within the ligand binding domain of the human constitutive and rostane receptor*1. Molecular Genetics and Metabolism, 80: 216-226.
Selsted, M. E., S. S. Harwig, T. Ganz, J. W. Schilling and R. I. Lehrer (1985). Primary structures of three human neutrophil defensins. J. Clin. Invest., 76: 1436-1439.
Soding, J. and A. N. Lupas (2003). More than the sum of their parts: On the evolution of proteins from peptides. Bioessays, 25: 837-846.
Tang, Y. Q. and M. E. Selsted (1993). Characterization of the Disulfide Motif in BNBD-12, an Antimicrobial 6-Defensin Peptide from Bovine Neutrophils. J. Biol. Chem., 268: 6649-6653.
Taylor, M. S., C. P. Ponting and R. R. Copley (2004). Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes. Genome Res., 14: 555-566.
Zavolan, M., S. Kondo, C. Schonbach, J. Adachi, D. A. Hume, R. G., Members, G. Group, Y. Hayashizaki and T. Gaasterland (2003). Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res., 13: 1290-1300.
