Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals
<p>Abstract</p> <p>Background</p> <p>The degradome -the complete repertoire of proteases in an organism- is involved in multiple key biological and pathological processes. Previous studies in several organisms have yielded sets of curated protease sequences which may be...
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| Format: | Article |
| Language: | English |
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BMC
2010-04-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/220 |
| _version_ | 1819202737019027456 |
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| author | López-Otín Carlos Warren Wesley C Puente Xose S Velasco Gloria Quesada Víctor |
| author_facet | López-Otín Carlos Warren Wesley C Puente Xose S Velasco Gloria Quesada Víctor |
| author_sort | López-Otín Carlos |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The degradome -the complete repertoire of proteases in an organism- is involved in multiple key biological and pathological processes. Previous studies in several organisms have yielded sets of curated protease sequences which may be used to characterize the degradome in a novel genome by similarity. Differences between degradomes can then be related to physiological traits of the species under study. Therefore, the sequencing of the zebra finch genome allows the comparison between the degradomes of mammals and birds and may help to understand the biological peculiarities of the zebra finch.</p> <p>Results</p> <p>A set of curated protease sequences from humans and chicken was used to predict the sequences of 460 protease and protease-like genes in the zebra finch genome. This analysis revealed important differences in the evolution of mammalian and bird degradomes, including genomic expansions and deletions of caspases, cytotoxic proteases, kallikreins, matrix metalloproteases, and trypsin-like proteases. Furthermore, we found several zebra finch-specific features, such as duplications in <it>CASP3 </it>and <it>BACE</it>, and a large genomic expansion of acrosin.</p> <p>Conclusions</p> <p>We have compared the degradomes of zebra finch, chicken and several mammalian species, with the finding of multiple differences which illustrate the evolution of the protease complement of these organisms. Detailed analysis of these changes in zebra finch proteases has shown that they are mainly related to immunological, developmental, reproductive and neural functions.</p> |
| first_indexed | 2024-12-23T04:08:46Z |
| format | Article |
| id | doaj.art-efd6612c31934ecb9a4cf85a579b72bf |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-23T04:08:46Z |
| publishDate | 2010-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-efd6612c31934ecb9a4cf85a579b72bf2022-12-21T18:00:34ZengBMCBMC Genomics1471-21642010-04-0111122010.1186/1471-2164-11-220Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammalsLópez-Otín CarlosWarren Wesley CPuente Xose SVelasco GloriaQuesada Víctor<p>Abstract</p> <p>Background</p> <p>The degradome -the complete repertoire of proteases in an organism- is involved in multiple key biological and pathological processes. Previous studies in several organisms have yielded sets of curated protease sequences which may be used to characterize the degradome in a novel genome by similarity. Differences between degradomes can then be related to physiological traits of the species under study. Therefore, the sequencing of the zebra finch genome allows the comparison between the degradomes of mammals and birds and may help to understand the biological peculiarities of the zebra finch.</p> <p>Results</p> <p>A set of curated protease sequences from humans and chicken was used to predict the sequences of 460 protease and protease-like genes in the zebra finch genome. This analysis revealed important differences in the evolution of mammalian and bird degradomes, including genomic expansions and deletions of caspases, cytotoxic proteases, kallikreins, matrix metalloproteases, and trypsin-like proteases. Furthermore, we found several zebra finch-specific features, such as duplications in <it>CASP3 </it>and <it>BACE</it>, and a large genomic expansion of acrosin.</p> <p>Conclusions</p> <p>We have compared the degradomes of zebra finch, chicken and several mammalian species, with the finding of multiple differences which illustrate the evolution of the protease complement of these organisms. Detailed analysis of these changes in zebra finch proteases has shown that they are mainly related to immunological, developmental, reproductive and neural functions.</p>http://www.biomedcentral.com/1471-2164/11/220 |
| spellingShingle | López-Otín Carlos Warren Wesley C Puente Xose S Velasco Gloria Quesada Víctor Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals BMC Genomics |
| title | Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals |
| title_full | Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals |
| title_fullStr | Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals |
| title_full_unstemmed | Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals |
| title_short | Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals |
| title_sort | comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals |
| url | http://www.biomedcentral.com/1471-2164/11/220 |
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