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Published ahead of print on January 23, 2003, doi:10.1165/rcmb.2002-0205OC

Am. J. Respir. Cell Mol. Biol., Volume 29, Number 1, July 2003, 71-80

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Submitted on October 4, 2002
Revised on January 22, 2003

ORFeome Based Search of Airway Epithelial Cell-Specific Novel Human {beta}-Defensin Genes

Cheng Y Kao1, Yin Chen1, Yu H Zhao1, and Reen Wu1*

1 Center for Comparative Respiratory Biology and Medicine, University of California at Davis, Davis, CA, USA

* To whom correspondence should be addressed. E-mail: rwu{at}ucdavis.edu.

{beta}-Defensin is one of the major host defense shields produced by various tissues and organs against microbial infection. To date, four human {beta}-defensins (DEFB) gene products that share a consensus six-cysteine motif have been discovered. The hidden Markov model (HMM) profile was constructed from the common features of those known {beta}-defensin peptides to search for additional novel DEFB genes. A genome-wide search of the profile against ORFeome-based peptide databases (e.g. Ensembl project) led to the identification of six new DEFB members that also shared the conserved six-cysteine motif. The phylogenetic analysis supported a close relationship of these six new members with existing DEFB genes. PCR studies of human tissue cDNA panels confirmed the expression of all six novel DEFB genes in various tissues. Two of them, DEFB106 and DEFB109, were expressed in the lung. A pilot study with cRNA probes for in situ hybridization and a synthetic propeptide for the functional characterization demonstrated the tissue-/cell-specific expression and the strong antimicrobial activity of DEFB106. These results support the utility of ORFeome-based HMM search in gene discovery for members of a specific gene family. These novel DEFB genes identified in this study may significantly contribute to overall antimicrobial host defenses.




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