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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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Distribution of POP homologs in prokaryotic lineages. A) Distribution of archaeal POP homologs. B) Distribution of bacterial POP homologs. C) Distribution of POP family members.
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Fig1: Distribution of POP homologs in prokaryotic lineages. A) Distribution of archaeal POP homologs. B) Distribution of bacterial POP homologs. C) Distribution of POP family members.

Mentions: We noticed that all the collected POP homologs were widely distributed across all the major lineages of bacteria and archaea with apparent loss in Nanoarchaeota. Phylum Actinobacteria was identified to be the most populated with ~1000 POP homologs (Figure 1), while in archaea, many POP homologs were captured from Euryarchaeota and Crenarchaeota. In POP family, POPs were more abundant (44%) in prokaryotic lineages than DPPs (24%) and OPBs (10%) (Figure 1c Additional file 5). We could also capture all the 638 annotated POPs from prokaryotes.Figure 1


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

Kaushik S, Sowdhamini R - BMC Genomics (2014)

Distribution of POP homologs in prokaryotic lineages. A) Distribution of archaeal POP homologs. B) Distribution of bacterial POP homologs. C) Distribution of POP family members.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Distribution of POP homologs in prokaryotic lineages. A) Distribution of archaeal POP homologs. B) Distribution of bacterial POP homologs. C) Distribution of POP family members.
Mentions: We noticed that all the collected POP homologs were widely distributed across all the major lineages of bacteria and archaea with apparent loss in Nanoarchaeota. Phylum Actinobacteria was identified to be the most populated with ~1000 POP homologs (Figure 1), while in archaea, many POP homologs were captured from Euryarchaeota and Crenarchaeota. In POP family, POPs were more abundant (44%) in prokaryotic lineages than DPPs (24%) and OPBs (10%) (Figure 1c Additional file 5). We could also capture all the 638 annotated POPs from prokaryotes.Figure 1

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