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Urochordate serpins are Classified into Six Groups Encoded by Exon-Intron Structures, Microsynteny and Bayesian Phylogenetic Analyses.

Kumar A, Bhandari A - J Genomics (2014)

Bottom Line: The exon/intron structures and genomic locus comparisons together with sequence phylogenetic analysis, suggested that urochordate serpins are classified into six groups (U1-U6), different from six groups (V1-V6) of vertebrate serpins.Human α1-antitrypsin shared lower sequence identities and similarities with urochordates serpins ranged from 14-29% and 30-49%, respectively.Based on protein sequences, genes and genomic architectures, we conclude that these two urochordates do not contain a single copy of genuine ortholog of the vertebrate serpins.

View Article: PubMed Central - PubMed

Affiliation: 1. Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany.

ABSTRACT
Members of serpin superfamily are involved in wide array of cellular processes to control proteolytic activities of eukaryotic organisms. Vertebrate serpins are extensively studied and reported to be classified into six groups (V1-V6) based on gene structures. However, there is no study conducted for serpins in urochordates (the closest living invertebrates related to vertebrates) to date. To unravel further the phylogenetic history of serpin genes, we characterized serpin genes from two urochordates (Ciona intestinalis and Ciona savignyi). There are 11 and 5 serpins in the C. intestinalis and C. savignyi, respectively. The exon/intron structures and genomic locus comparisons together with sequence phylogenetic analysis, suggested that urochordate serpins are classified into six groups (U1-U6), different from six groups (V1-V6) of vertebrate serpins. Human α1-antitrypsin shared lower sequence identities and similarities with urochordates serpins ranged from 14-29% and 30-49%, respectively. Based on protein sequences, genes and genomic architectures, we conclude that these two urochordates do not contain a single copy of genuine ortholog of the vertebrate serpins.

No MeSH data available.


Bayesian evolutionary history of serpins from vertebrates (V1-V6) and urochordates (U1-U6) illustrates separate groups are maintained. Six representatives of vertebrate serpin groups were used for this analysis. We used Hv- Spn-1 (Genbank ID: XP_002156931.1) from Hydra vulgaris as an outgroup.
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Figure 4: Bayesian evolutionary history of serpins from vertebrates (V1-V6) and urochordates (U1-U6) illustrates separate groups are maintained. Six representatives of vertebrate serpin groups were used for this analysis. We used Hv- Spn-1 (Genbank ID: XP_002156931.1) from Hydra vulgaris as an outgroup.

Mentions: To further examine the relationships of vertebrate and urochordate groups of serpins, we carried out sequence and phylogenetic analyses by combining six representative member of group V1 to V6 from human, namely monocyte/neutrophil elastase inhibitor (MNEI), α1-antitrypsin (A1AT), plasminogen activator inhibitor 1 (PAI1), pigment epithelium-derived factor (PEDF), antithrombin III (ATIII) and heat shock protein 47 (HSP47). The six-serpin groups of vertebrates and two urochordates are maintained as evident in the Bayesian phylogenetic tree (Fig. 4). The group U5 is close to vertebrate group V1 and it is evident from sequence identity scores in Table 4, with members of the group U5 shared 37.1%-41.4% sequence identities with human MNEI. Similarly, the group U6 is closely related to the vertebrate group V5, also evident on sequence identity scores in table 4. These identities are slightly higher and it is common that several invertebrate serpins have slightly higher sequence identities with vertebrate groups V1 and V5, as evident for Hv-Spn-1 (from Hydra vulgaris) shares 35.5% and 33.2% identities, respectively. Only sequence identities of 25-40% cant not assign orthologous status for serpins in such a large superfamily. Other traits of serpins (gene structure pattern and genomic localizations) are not matching between vertebrates and two urochordates. Hence, it is not possible to assign orthology across vertebrates and urochordate species for serpins.


Urochordate serpins are Classified into Six Groups Encoded by Exon-Intron Structures, Microsynteny and Bayesian Phylogenetic Analyses.

Kumar A, Bhandari A - J Genomics (2014)

Bayesian evolutionary history of serpins from vertebrates (V1-V6) and urochordates (U1-U6) illustrates separate groups are maintained. Six representatives of vertebrate serpin groups were used for this analysis. We used Hv- Spn-1 (Genbank ID: XP_002156931.1) from Hydra vulgaris as an outgroup.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4150122&req=5

Figure 4: Bayesian evolutionary history of serpins from vertebrates (V1-V6) and urochordates (U1-U6) illustrates separate groups are maintained. Six representatives of vertebrate serpin groups were used for this analysis. We used Hv- Spn-1 (Genbank ID: XP_002156931.1) from Hydra vulgaris as an outgroup.
Mentions: To further examine the relationships of vertebrate and urochordate groups of serpins, we carried out sequence and phylogenetic analyses by combining six representative member of group V1 to V6 from human, namely monocyte/neutrophil elastase inhibitor (MNEI), α1-antitrypsin (A1AT), plasminogen activator inhibitor 1 (PAI1), pigment epithelium-derived factor (PEDF), antithrombin III (ATIII) and heat shock protein 47 (HSP47). The six-serpin groups of vertebrates and two urochordates are maintained as evident in the Bayesian phylogenetic tree (Fig. 4). The group U5 is close to vertebrate group V1 and it is evident from sequence identity scores in Table 4, with members of the group U5 shared 37.1%-41.4% sequence identities with human MNEI. Similarly, the group U6 is closely related to the vertebrate group V5, also evident on sequence identity scores in table 4. These identities are slightly higher and it is common that several invertebrate serpins have slightly higher sequence identities with vertebrate groups V1 and V5, as evident for Hv-Spn-1 (from Hydra vulgaris) shares 35.5% and 33.2% identities, respectively. Only sequence identities of 25-40% cant not assign orthologous status for serpins in such a large superfamily. Other traits of serpins (gene structure pattern and genomic localizations) are not matching between vertebrates and two urochordates. Hence, it is not possible to assign orthology across vertebrates and urochordate species for serpins.

Bottom Line: The exon/intron structures and genomic locus comparisons together with sequence phylogenetic analysis, suggested that urochordate serpins are classified into six groups (U1-U6), different from six groups (V1-V6) of vertebrate serpins.Human α1-antitrypsin shared lower sequence identities and similarities with urochordates serpins ranged from 14-29% and 30-49%, respectively.Based on protein sequences, genes and genomic architectures, we conclude that these two urochordates do not contain a single copy of genuine ortholog of the vertebrate serpins.

View Article: PubMed Central - PubMed

Affiliation: 1. Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany.

ABSTRACT
Members of serpin superfamily are involved in wide array of cellular processes to control proteolytic activities of eukaryotic organisms. Vertebrate serpins are extensively studied and reported to be classified into six groups (V1-V6) based on gene structures. However, there is no study conducted for serpins in urochordates (the closest living invertebrates related to vertebrates) to date. To unravel further the phylogenetic history of serpin genes, we characterized serpin genes from two urochordates (Ciona intestinalis and Ciona savignyi). There are 11 and 5 serpins in the C. intestinalis and C. savignyi, respectively. The exon/intron structures and genomic locus comparisons together with sequence phylogenetic analysis, suggested that urochordate serpins are classified into six groups (U1-U6), different from six groups (V1-V6) of vertebrate serpins. Human α1-antitrypsin shared lower sequence identities and similarities with urochordates serpins ranged from 14-29% and 30-49%, respectively. Based on protein sequences, genes and genomic architectures, we conclude that these two urochordates do not contain a single copy of genuine ortholog of the vertebrate serpins.

No MeSH data available.