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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 phylogenetic history of serpins from C. intestinalis and C. savignyi. Human α1-antitrypsin was used as the outgroup. The color boxes represent Ciona serpins in different scaffolds, which cluster in this phylogenetic tree together.
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Figure 3: Bayesian phylogenetic history of serpins from C. intestinalis and C. savignyi. Human α1-antitrypsin was used as the outgroup. The color boxes represent Ciona serpins in different scaffolds, which cluster in this phylogenetic tree together.

Mentions: Furthermore, a Bayesian phylogenetic tree of urochordate serpins (Fig. 3) was created, which corroborates with clustering into six groups U1-U6 as supported by gene structures and chromosomal mapping. This tree has lowest percentage posterior probabilities of 55. Human α1-antitrypsin was used as outgroup. Hence, this tree also supports urochordate-specific classification system of 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 phylogenetic history of serpins from C. intestinalis and C. savignyi. Human α1-antitrypsin was used as the outgroup. The color boxes represent Ciona serpins in different scaffolds, which cluster in this phylogenetic tree together.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4150122&req=5

Figure 3: Bayesian phylogenetic history of serpins from C. intestinalis and C. savignyi. Human α1-antitrypsin was used as the outgroup. The color boxes represent Ciona serpins in different scaffolds, which cluster in this phylogenetic tree together.
Mentions: Furthermore, a Bayesian phylogenetic tree of urochordate serpins (Fig. 3) was created, which corroborates with clustering into six groups U1-U6 as supported by gene structures and chromosomal mapping. This tree has lowest percentage posterior probabilities of 55. Human α1-antitrypsin was used as outgroup. Hence, this tree also supports urochordate-specific classification system of 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.