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Distribution, classification, domain architectures and evolution of prolyl oligopeptidases in prokaryotic lineages.

Kaushik S, Sowdhamini R - BMC Genomics (2014)

Bottom Line: We proposed significant extension of this gene family by characterizing 39 new POPs and 158 new α/β hydrolase members.Many genomes with multiple POPs were identified with high sequence variations and different cellular localizations.Such anomalous distribution of POP genes in different bacterial genomes shows differential expansion of POP gene family primarily by multiple horizontal gene transfer events.

View Article: PubMed Central - PubMed

Affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India. Swati.Kaushik@ucsf.edu.

ABSTRACT

Background: Prolyl oligopeptidases (POPs) are proteolytic enzymes, widely distributed in all the kingdoms of life. Bacterial POPs are pharmaceutically important enzymes, yet their functional and evolutionary details are not fully explored. Therefore, current analysis is aimed at understanding the distribution, domain architecture, probable biological functions and gene family expansion of POPs in bacterial and archaeal lineages.

Results: Exhaustive sequence analysis of 1,202 bacterial and 91 archaeal genomes revealed ~3,000 POP homologs, with only 638 annotated POPs. We observed wide distribution of POPs in all the analysed bacterial lineages. Phylogenetic analysis and co-clustering of POPs of different phyla suggested their common functions in all the prokaryotic species. Further, on the basis of unique sequence motifs we could classify bacterial POPs into eight subtypes. Analysis of coexisting domains in POPs highlighted their involvement in protein-protein interactions and cellular signaling. We proposed significant extension of this gene family by characterizing 39 new POPs and 158 new α/β hydrolase members.

Conclusions: Our study reflects diversity and functional importance of POPs in bacterial species. Many genomes with multiple POPs were identified with high sequence variations and different cellular localizations. Such anomalous distribution of POP genes in different bacterial genomes shows differential expansion of POP gene family primarily by multiple horizontal gene transfer events.

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Part of sequence alignment of POPs of the fifth cluster representing class specific motifs. Red boxes and arrows represent class specific motifs, only 90% conserved residues are colored.
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Fig7: Part of sequence alignment of POPs of the fifth cluster representing class specific motifs. Red boxes and arrows represent class specific motifs, only 90% conserved residues are colored.

Mentions: To further analyse the co-clustering trend of annotated bPOPs, we identified conserved class specific sequence motifs. An alignment stretch was considered as a ‘conserved motif’, if 95% of the sequences had conserved amino acids at least at three consecutive positions. From these highly conserved sequence motifs, we next identified class specific motifs. A ‘class-specific motif’ was defined as a sequence motif in a cluster, which was completely absent from all the other clusters. In the first and seventh clusters (Figure 6), no class-specific motifs were observed. Figure 7 shows a part of the alignment of fifth cluster of bPOPs representing class specific motifs. Detailed analysis of motifs of all the clusters was carried out to understand their relative position on the structure of bPOPs. Class-specific motifs of second, sixth, eighth and ninth cluster were localized in the hydrolase domain, while motifs of cluster third, fourth and fifth were distributed on both the domains (see Additional files 9 and 10 for details).Figure 7


Distribution, classification, domain architectures and evolution of prolyl oligopeptidases in prokaryotic lineages.

Kaushik S, Sowdhamini R - BMC Genomics (2014)

Part of sequence alignment of POPs of the fifth cluster representing class specific motifs. Red boxes and arrows represent class specific motifs, only 90% conserved residues are colored.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4522959&req=5

Fig7: Part of sequence alignment of POPs of the fifth cluster representing class specific motifs. Red boxes and arrows represent class specific motifs, only 90% conserved residues are colored.
Mentions: To further analyse the co-clustering trend of annotated bPOPs, we identified conserved class specific sequence motifs. An alignment stretch was considered as a ‘conserved motif’, if 95% of the sequences had conserved amino acids at least at three consecutive positions. From these highly conserved sequence motifs, we next identified class specific motifs. A ‘class-specific motif’ was defined as a sequence motif in a cluster, which was completely absent from all the other clusters. In the first and seventh clusters (Figure 6), no class-specific motifs were observed. Figure 7 shows a part of the alignment of fifth cluster of bPOPs representing class specific motifs. Detailed analysis of motifs of all the clusters was carried out to understand their relative position on the structure of bPOPs. Class-specific motifs of second, sixth, eighth and ninth cluster were localized in the hydrolase domain, while motifs of cluster third, fourth and fifth were distributed on both the domains (see Additional files 9 and 10 for details).Figure 7

Bottom Line: We proposed significant extension of this gene family by characterizing 39 new POPs and 158 new α/β hydrolase members.Many genomes with multiple POPs were identified with high sequence variations and different cellular localizations.Such anomalous distribution of POP genes in different bacterial genomes shows differential expansion of POP gene family primarily by multiple horizontal gene transfer events.

View Article: PubMed Central - PubMed

Affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India. Swati.Kaushik@ucsf.edu.

ABSTRACT

Background: Prolyl oligopeptidases (POPs) are proteolytic enzymes, widely distributed in all the kingdoms of life. Bacterial POPs are pharmaceutically important enzymes, yet their functional and evolutionary details are not fully explored. Therefore, current analysis is aimed at understanding the distribution, domain architecture, probable biological functions and gene family expansion of POPs in bacterial and archaeal lineages.

Results: Exhaustive sequence analysis of 1,202 bacterial and 91 archaeal genomes revealed ~3,000 POP homologs, with only 638 annotated POPs. We observed wide distribution of POPs in all the analysed bacterial lineages. Phylogenetic analysis and co-clustering of POPs of different phyla suggested their common functions in all the prokaryotic species. Further, on the basis of unique sequence motifs we could classify bacterial POPs into eight subtypes. Analysis of coexisting domains in POPs highlighted their involvement in protein-protein interactions and cellular signaling. We proposed significant extension of this gene family by characterizing 39 new POPs and 158 new α/β hydrolase members.

Conclusions: Our study reflects diversity and functional importance of POPs in bacterial species. Many genomes with multiple POPs were identified with high sequence variations and different cellular localizations. Such anomalous distribution of POP genes in different bacterial genomes shows differential expansion of POP gene family primarily by multiple horizontal gene transfer events.

Show MeSH