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Open Access Highly Accessed Research article

Genome-wide identification of Xenopus matrix metalloproteinases: conservation and unique duplications in amphibians

Liezhen Fu, Biswajit Das, Smita Mathew and Yun-Bo Shi*

Author Affiliations

Section on Molecular Morphogenesis, PCRM, NICHD, NIH, Bldg. 18T, Rm. 106, Bethesda, MD 20892, USA

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BMC Genomics 2009, 10:81  doi:10.1186/1471-2164-10-81

Published: 17 February 2009

Abstract

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.