Research articleComparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals

Background: The degradome -the complete repertoire of proteases in an organismis 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. Results: 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 finchspecific features, such as duplications in CASP3 and BACE, and a large genomic expansion of acrosin. Conclusions: 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. Background The degradome is defined as the set of proteases present in an organism [1]. The coining of this term reflects the enormous biological and pathological relevance of proteolysis that pervades virtually every aspect of life, including development, apoptosis, host defense, nutrition, reproduction and central nervous system biology [2]. From a genomic perspective, the degradome provides a relatively simple representative subset of the coding genome of a species. Thus, the human degradome contains about 570 proteases, and can be studied with semiautomated methods. On the other hand, and despite proteases share a common biochemical function, their catalytic domains exhibit high sequence diversity. This diversity is further increased by the frequent attachment of auxiliary, non-proteolytic domains to the catalytic moieties [3]. It is also remarkable that while some of the protease genes are clustered, most of them are randomly distributed throughout the annotated genomes [4-7]. Hence, the degradome forms a representative subset of the coding genome of a species, both in terms of sequence and genomic organization. Furthermore, since the role of multiple proteases in biological processes is well documented, the comparative study of degradomes may improve our understanding of these processes in different organisms. The zebra finch (Taeniopygia guttata) is a bird which has been extensively used as a model organism for neurological [8], reproductive [9], and immune [10] studies. Therefore, the characterization of the zebra finch degradome may provide valuable information on the role of proteases in key biological processes. * Correspondence: clo@uniovi.es 1 Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006-Oviedo, Spain Full list of author information is available at the end of the article Quesada et al. BMC Genomics 2010, 11:220 http://www.biomedcentral. com/1471-2164/11/220 Page 2 of 9 In this work, we report the analysis of the complete set of protease and protease-like genes in the zebra finch genome and its comparison to the chicken and human degradomes. Where appropriate, other mammalian degradomes have also been considered to expand the scope of this protease-based comparative genomic analysis. Results and Discussion As expected, we have found that the zebra finch degradome is similar to the chicken degradome. According to our preliminary prediction, the zebra finch and chicken degradomes contain about 460 proteases. Reciprocal best hit analysis of these results with the Ensembl predicted protein complement of chicken showed that 380 zebra finch proteases have a reciprocal best hit orthologue in the chicken degradome. In contrast, 80 predicted zebra finch proteases have no clear orthologue in chicken. Most of these proteases belong to large complex families, in which orthology assignment is difficult to establish. It must also be noted that gene gains and losses may be confused with lack of genomic data and assembly artefacts. However, some of these zebra finch specific proteases seem to have clearly arisen from species-specific duplications. Comparison of these degradomes with the human degradome has yielded further information about the evolution of proteases and has led to hypothesis about their putative roles in zebra finch physiology. Thus, most of the major differences characteristic of the zebra finch and chicken degradomes compared to mammalian degradomes affect proteases involved in a few key biological processes, including apoptosis, host defense, teeth formation, reproduction, and neural development. Apoptosis The detailed comparative analysis of proteases involved in apoptosis has revealed a series of zebra finch and avian characteristic features. Thus, group I caspases, involved in the processing of inflammatory cytokines, is composed of CASP1, -4, -5, and -12 in humans [11] and only one (CASP1) in chicken. We have not found any sequence corresponding to group I caspases in the current assembly of zebra finch nor in zebra finch ChrUn assembly or sequence traces, nor in EST databases. However, the genomic contig in which this sequence should be located is rich in unsequenced stretches. Since this protease is expected to play a very important role in apoptosis induced by bacterial infections, it seems likely that the gene encoding caspase-1 exists in an unsequenced stretch of the zebra finch genome. Nevertheless, further experimental validation will be necessary to clarify this important question. On the other hand, the degradomes of zebra finch and chicken contain several caspases which are not present in humans [12] (Figure 1). Thus, CASP18 is present in both birds. The phylogenetic analysis of this gene is consistent with the proposed evolutionary history of this gene, which is present in opossum and absent in placental mammals [12]. Another gene absent in mammals is CASP17, which can be found in chicken. Surprisingly, we have not found any orthologue of CASP17 in the zebra finch genome. In contrast, there is evidence for a tandem duplication of CASP3 in the zebra finch genome, but not in the genomes of chicken or human. Taken together, these results suggest that the mechanisms leading to caspase-dependent apoptosis in birds might depend on more proteases than in mammals. In fact, the evolution of caspases in mammals includes complex events, like the pseudogenization of CASP12 in most of the human population but not in other hominoids [13]. These changes may influence processes such as immune system maturation and inflammatory response. In this regard, it is noteFigure 1 Phylogenetic relationship between zebra finch (zf_), chicken (gg_), and human (hs_) caspases. Numbers indicate the robustness of each node assessed by bootstrap. Two caspase-3-like genes from opossum (md_) are included. Casp, caspase; malt, paracaspase; cflar, casper; iceyh, homolog ICEY. The phylogenetic tree was rooted with the paracaspase family. md casp3b md casp3a 100