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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.


Genomic organizations of Ciona serpins. Ciona serpins (red arrows) were identified on different scaffolds surrounded by marker genes (arrows in different colors as they are non-homologous in different loci). White boxes indicate the corresponding locus on specific reftig with corresponding serpins in C. savignyi.
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Figure 2: Genomic organizations of Ciona serpins. Ciona serpins (red arrows) were identified on different scaffolds surrounded by marker genes (arrows in different colors as they are non-homologous in different loci). White boxes indicate the corresponding locus on specific reftig with corresponding serpins in C. savignyi.

Mentions: To support the grouping of serpins based on gene structures in two urochordates and to compare it with vertebrate serpins, we carried out micro-syntenic analyses. Ci-Spn-1 and Ci-Spn-2 were found to be adjacent to each other and having the same orientation in C. intestinalis. These genes are located in scaffold_63, flanked by a dyad of genes namely a basic-leucine zipper (bZIP) transcription factor and a Pleckstrin-like (PLCKL) gene on the one side, while on the other side, there is a dyad of genes - the lactase and vesicle coat complex COPII, subunit SEC23 (SEC23) (Fig. 2). In similar fashion, the reftig_194 of C. savignyi genome possess Cs-Spn-4 and Cs-Spn-3 with the same flanking. These members maintained on this syntenic organization form group U1. Ci-Spn-3 was located on scaffold_69, flanked by a dyad of genes - secreted frizzled-related protein (fCRD) and mitochondrial carrier protein CGI69 (CGI69) on the one side, while a dyad of genes - ZPR1 type Zn-finger (ZFR1) and RYK receptor-like tyrosine kinase precursor (preRYK) is located on the other side (Fig. 2). This genomic architecture is maintained in the reftig_99 with Cs-Spn-5 for C. savignyi. These serpins form group U2. The Ci-Spn-4 was located on scaffold_127 as a single serpin gene, flanked by a dyad of glucokinase regulatory protein (GKReg) and Zn-finger, C2H2 type (DZIP1) (Fig. 2), forming group U3. Group U4 has one serpin as Ci-Spn-5, which is located on scaffold_301 flanked by a triad of potassium voltage gated Kv channel (Kv+), NGAP like protein (NGAPL) and transcriptional regulator SOH1 (SOH1) on the one side, while the singe gene valyl-tRNA synthetase (VTRS) is situated on the other side (Fig. 2). The Ci-Spn-6, Ci-Spn-7, and Ci-Spn-8 are found on scaffold_88 adjacent to each other in the same orientation (Fig. 2) in C. intestinalis. These three serpins are flanked by a triad of genes - syntaxin 5 (STXBP1), chondromodulin-1 precursor (ChMH) and surfeit locus protein 4 (SUR4) on the one side and the other side has a dyad of genes as tetraspanin 15 (NET7) and secreted protein acidic and rich in cysteine (SPARC). This genomic structure is found in the reftig_72 with only Cs-Spn-1 for C. savignyi. These five serpins belongs to group U5.


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

Kumar A, Bhandari A - J Genomics (2014)

Genomic organizations of Ciona serpins. Ciona serpins (red arrows) were identified on different scaffolds surrounded by marker genes (arrows in different colors as they are non-homologous in different loci). White boxes indicate the corresponding locus on specific reftig with corresponding serpins in C. savignyi.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4150122&req=5

Figure 2: Genomic organizations of Ciona serpins. Ciona serpins (red arrows) were identified on different scaffolds surrounded by marker genes (arrows in different colors as they are non-homologous in different loci). White boxes indicate the corresponding locus on specific reftig with corresponding serpins in C. savignyi.
Mentions: To support the grouping of serpins based on gene structures in two urochordates and to compare it with vertebrate serpins, we carried out micro-syntenic analyses. Ci-Spn-1 and Ci-Spn-2 were found to be adjacent to each other and having the same orientation in C. intestinalis. These genes are located in scaffold_63, flanked by a dyad of genes namely a basic-leucine zipper (bZIP) transcription factor and a Pleckstrin-like (PLCKL) gene on the one side, while on the other side, there is a dyad of genes - the lactase and vesicle coat complex COPII, subunit SEC23 (SEC23) (Fig. 2). In similar fashion, the reftig_194 of C. savignyi genome possess Cs-Spn-4 and Cs-Spn-3 with the same flanking. These members maintained on this syntenic organization form group U1. Ci-Spn-3 was located on scaffold_69, flanked by a dyad of genes - secreted frizzled-related protein (fCRD) and mitochondrial carrier protein CGI69 (CGI69) on the one side, while a dyad of genes - ZPR1 type Zn-finger (ZFR1) and RYK receptor-like tyrosine kinase precursor (preRYK) is located on the other side (Fig. 2). This genomic architecture is maintained in the reftig_99 with Cs-Spn-5 for C. savignyi. These serpins form group U2. The Ci-Spn-4 was located on scaffold_127 as a single serpin gene, flanked by a dyad of glucokinase regulatory protein (GKReg) and Zn-finger, C2H2 type (DZIP1) (Fig. 2), forming group U3. Group U4 has one serpin as Ci-Spn-5, which is located on scaffold_301 flanked by a triad of potassium voltage gated Kv channel (Kv+), NGAP like protein (NGAPL) and transcriptional regulator SOH1 (SOH1) on the one side, while the singe gene valyl-tRNA synthetase (VTRS) is situated on the other side (Fig. 2). The Ci-Spn-6, Ci-Spn-7, and Ci-Spn-8 are found on scaffold_88 adjacent to each other in the same orientation (Fig. 2) in C. intestinalis. These three serpins are flanked by a triad of genes - syntaxin 5 (STXBP1), chondromodulin-1 precursor (ChMH) and surfeit locus protein 4 (SUR4) on the one side and the other side has a dyad of genes as tetraspanin 15 (NET7) and secreted protein acidic and rich in cysteine (SPARC). This genomic structure is found in the reftig_72 with only Cs-Spn-1 for C. savignyi. These five serpins belongs to group U5.

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.