Discovery of five conserved beta -defensin gene clusters using a computational search strategy

Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2129-33. doi: 10.1073/pnas.042692699.


The innate immune system includes antimicrobial peptides that protect multicellular organisms from a diverse spectrum of microorganisms. beta-Defensins comprise one important family of mammalian antimicrobial peptides. The annotation of the human genome fails to reveal the expected diversity, and a recent query of the draft sequence with the blast search engine found only one new beta-defensin gene (DEFB3). To define better the beta-defensin gene family, we adopted a genomics approach that uses hmmer, a computational search tool based on hidden Markov models, in combination with blast. This strategy identified 28 new human and 43 new mouse beta-defensin genes in five syntenic chromosomal regions. Within each syntenic cluster, the gene sequences and organization were similar, suggesting each cluster pair arose from a common ancestor and was retained because of conserved functions. Preliminary analysis indicates that at least 26 of the predicted genes are transcribed. These results demonstrate the value of a genomewide search strategy to identify genes with conserved structural motifs. Discovery of these genes represents a new starting point for exploring the role of beta-defensins in innate immunity.

Publication types

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

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Computers
  • Conserved Sequence
  • Contig Mapping
  • Cysteine / chemistry
  • Exons
  • Humans
  • Markov Chains
  • Mice
  • Models, Genetic
  • Molecular Sequence Data
  • Multigene Family
  • Phylogeny
  • Sequence Homology, Amino Acid
  • Software
  • beta-Defensins / chemistry*
  • beta-Defensins / genetics*


  • beta-Defensins
  • Cysteine

Associated data

  • GENBANK/AF318068