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BMC Genomics 2009 Feb 17;10:81. doi: 10.1186/1471-2164-10-81.
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Genome-wide identification of Xenopus matrix metalloproteinases: conservation and unique duplications in amphibians.

Fu L , Das B , Mathew S , Shi YB .

BACKGROUND: Matrix metalloproteinases (MMPs) are members of the superfamily of Zn2+ dependent extracellular or membrane-bound endopeptidases which have been implicated to play critical roles in vertebrate development and human pathogenesis. A number of MMP genes have been found to be upregulated in some or all organs during frog metamorphosis, suggesting that different MMPs may have different functions in various organs/tissues. The recent advances in EST (expressed sequence tag) sequencing and the completion of the genome of Xenopus (X.) tropicalis prompted us to systematically analyze the existence of MMPs in the Xenopus genome. RESULTS: We examined X. laevis and X. tropicalis ESTs and genomic sequences for MMPs and obtained likely homologs for 20 out of the 25 MMPs known in higher vertebrates. Four of the five missing MMPs, i.e. MMPs 8, 10, 12 and 27, were all encoded on human Chromosome 11 and the other missing MMP, MMP22 (a chicken MMP), was also absent in human genome. In addition, we identified several novel MMPs which appears to be derived from unique duplications over evolution, are present in the genomes of both Xenopus species. CONCLUSION: We identified the homologs of most of the mammalian MMPs in Xenopus and discovered a number of novel MMPs. Our results suggest that MMP genes undergo dynamic changes over evolution. It will be of interest in the future to investigate whether MMP expression and functions during vertebrate development are conserved. The sequence information reported here should facilitate such an endeavor in the near future.

PubMed ID: 19222855
PMC ID: PMC2656525
Article link: BMC Genomics
Grant support: [+]

Species referenced: Xenopus
Genes referenced: furin mmp1 mmp11 mmp13 mmp15 mmp16 mmp17 mmp2 mmp20 mmp21 mmp23b mmp24 mmp25 mmp28 mmp3 mmp7 mmp8 mmp9.2

Article Images: [+] show captions
References [+] :
Amano, Metamorphosis-associated and region-specific expression of calbindin gene in the posterior intestinal epithelium of Xenopus laevis larva. 1998, Pubmed, Xenbase