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Published ahead of print on January 23, 2003, doi:10.1165/rcmb.2002-0205OC
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American Journal of Respiratory Cell and Molecular Biology. Vol. 29, pp. 71-80, 2003
© 2003 American Thoracic Society
DOI: 10.1165/rcmb.2002-0205OC

ORFeome-Based Search of Airway Epithelial Cell-Specific Novel Human ß-Defensin Genes

Cheng Yuan Kao, Yin Chen, Yu Hua Zhao and Reen Wu

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

Address correspondence to: Reen Wu, Ph.D., Center for Comparative Respiratory Biology and Medicine, Surge 1 Annex, Room 1121, University of California at Davis, One Shields Ave., Davis, CA 95616. E-mail: rwu{at}ucdavis.edu

ß-Defensin is one of the major host defense shields produced by various tissues and organs against microbial infection. To date, four human ß-defensins (DEFBs) 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 ß-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. Phylogenetic analysis supported a close relationship of these six new members with existing DEFB genes. Polymerase Chain Reaction 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. The novel DEFB genes identified in this study may significantly contribute to overall antimicrobial host defenses.

Abbreviations: human ß-defensin, DEFB • digoxygenin, DIG • expressed sequence tag, EST • glyceraldehyde-phosphate-dehydrogenase, GAPDH • hidden Markov model, HMM • Luria borth, LB • nonredundant, nr • polymerase chain reaction, PCR • saline sodium citrate, SSC




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