ORFeome-based search of airway epithelial cell-specific novel human [beta]-defensin genes

Am J Respir Cell Mol Biol. 2003 Jul;29(1):71-80. doi: 10.1165/rcmb.2002-0205OC. Epub 2003 Jan 23.


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 (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 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. 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Anti-Bacterial Agents / pharmacology
  • Chromosomes, Human
  • Databases, Protein
  • Epithelial Cells / physiology
  • Escherichia coli / drug effects
  • Expressed Sequence Tags
  • Gene Expression Regulation
  • Genome, Human*
  • Humans
  • In Situ Hybridization
  • Lung / physiology
  • Markov Chains
  • Microbial Sensitivity Tests
  • Molecular Sequence Data
  • Multigene Family
  • Open Reading Frames*
  • Organ Specificity
  • Peptides / genetics
  • Pilot Projects
  • Respiratory Mucosa / cytology
  • Respiratory Mucosa / physiology*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Homology, Amino Acid
  • beta-Defensins / genetics*


  • Anti-Bacterial Agents
  • DEFB106
  • Peptides
  • beta-Defensins