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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.


Intron-based classification system for serpin genes from vertebrates and two urochordates illustrates six distinct groups namely V1-V6 and U1-U6, respectively. Black line and grey lines indicates vertebrate-specific and urochordate-specific intron positions, respectively. *indicates that the intron at the position 85c can differentiate between groups V1a and V1b. $ indicates that intron at position 274a is not found in Ci-Spn-2. Introns shared in more than one groups are marked. Only introns mapping to the conserved serpin fold (amino acids 33 to 394 of human α1-antitrypsin) are taken into consideration. Group wise distributions of major serpins are indicated.
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Figure 1: Intron-based classification system for serpin genes from vertebrates and two urochordates illustrates six distinct groups namely V1-V6 and U1-U6, respectively. Black line and grey lines indicates vertebrate-specific and urochordate-specific intron positions, respectively. *indicates that the intron at the position 85c can differentiate between groups V1a and V1b. $ indicates that intron at position 274a is not found in Ci-Spn-2. Introns shared in more than one groups are marked. Only introns mapping to the conserved serpin fold (amino acids 33 to 394 of human α1-antitrypsin) are taken into consideration. Group wise distributions of major serpins are indicated.

Mentions: Serpins from urochordates have unique gene structures as compared to vertebrate serpins (Fig. 1). Serpins from two urochordates are classified in six distinct groups and are named as group U1-U6. Group U1 serpins have five introns at positions 67a, 136b, 191c, 246a and 274a (missing in Ci-Spn-1). These intron positions are based on amino acid numbering of mature (without signal peptide) human A1AT, followed by intron phasing with suffixes a-c as reported in previous studies 5, 9. Two of these introns (at the positions 67c and 191c) are shared with vertebrate groups V4 and V5, respectively. Group U2 has a single serpin in two Ciona species with seven introns at the positions 56b, 97b, 156b, 204c, 259a, 301b and 344a. Group U3 has a single serpin in Ciona intestinalis only with six introns at the positions 73b, 151c, 217c, 254a, 292c and 322a. Similarly, group U4 has a single serpin in Ciona intestinalis only and it has six introns at the positions 83b, 144c, 191c, 247a, 283c and 339a, of which two positions are shared with vertebrate group V5. Group U5 genes are intron-less. Whereas group U6 have serpins with six introns at the positions 60a, 106c, 144c, 225a, 283c and 339a, with fourth and sixth introns are shared with vertebrate groups V6 and V5, respectively. Groups U4 and U6 share three introns at the positions 144c, 283c and 339a. By and large, Ciona serpins have a different set of intron positions as compared to vertebrate serpins 9 and only very few positions are shared with vertebrate serpins. Orthologs of vertebrate and urochordate serpins are listed in Fig 1; these orthologs are maintained in respective groups.


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

Kumar A, Bhandari A - J Genomics (2014)

Intron-based classification system for serpin genes from vertebrates and two urochordates illustrates six distinct groups namely V1-V6 and U1-U6, respectively. Black line and grey lines indicates vertebrate-specific and urochordate-specific intron positions, respectively. *indicates that the intron at the position 85c can differentiate between groups V1a and V1b. $ indicates that intron at position 274a is not found in Ci-Spn-2. Introns shared in more than one groups are marked. Only introns mapping to the conserved serpin fold (amino acids 33 to 394 of human α1-antitrypsin) are taken into consideration. Group wise distributions of major serpins are indicated.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: Intron-based classification system for serpin genes from vertebrates and two urochordates illustrates six distinct groups namely V1-V6 and U1-U6, respectively. Black line and grey lines indicates vertebrate-specific and urochordate-specific intron positions, respectively. *indicates that the intron at the position 85c can differentiate between groups V1a and V1b. $ indicates that intron at position 274a is not found in Ci-Spn-2. Introns shared in more than one groups are marked. Only introns mapping to the conserved serpin fold (amino acids 33 to 394 of human α1-antitrypsin) are taken into consideration. Group wise distributions of major serpins are indicated.
Mentions: Serpins from urochordates have unique gene structures as compared to vertebrate serpins (Fig. 1). Serpins from two urochordates are classified in six distinct groups and are named as group U1-U6. Group U1 serpins have five introns at positions 67a, 136b, 191c, 246a and 274a (missing in Ci-Spn-1). These intron positions are based on amino acid numbering of mature (without signal peptide) human A1AT, followed by intron phasing with suffixes a-c as reported in previous studies 5, 9. Two of these introns (at the positions 67c and 191c) are shared with vertebrate groups V4 and V5, respectively. Group U2 has a single serpin in two Ciona species with seven introns at the positions 56b, 97b, 156b, 204c, 259a, 301b and 344a. Group U3 has a single serpin in Ciona intestinalis only with six introns at the positions 73b, 151c, 217c, 254a, 292c and 322a. Similarly, group U4 has a single serpin in Ciona intestinalis only and it has six introns at the positions 83b, 144c, 191c, 247a, 283c and 339a, of which two positions are shared with vertebrate group V5. Group U5 genes are intron-less. Whereas group U6 have serpins with six introns at the positions 60a, 106c, 144c, 225a, 283c and 339a, with fourth and sixth introns are shared with vertebrate groups V6 and V5, respectively. Groups U4 and U6 share three introns at the positions 144c, 283c and 339a. By and large, Ciona serpins have a different set of intron positions as compared to vertebrate serpins 9 and only very few positions are shared with vertebrate serpins. Orthologs of vertebrate and urochordate serpins are listed in Fig 1; these orthologs are maintained in respective groups.

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.