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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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Bacterial POP homologs with signal peptides and transmembrane regions.
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Fig2: Bacterial POP homologs with signal peptides and transmembrane regions.

Mentions: Earlier studies have shown that bPOPs are associated with the signal peptides [13]. Signal peptides are sequence motifs that permit the proteins to translocate across endoplasmic reticulum in eukaryotes and to the cytoplasmic membrane in prokaryotes. Therefore, we examined all the collected POP homologs for the presence of signal peptides. Our results showed that 20% of the POP homologs were predicted to be associated with such signals, from which 225 (35%) were annotated POPs (Figure 2). Bacteroides (78%) and Acidobacteria (75%) had maximum number of POP homologs with signal peptides, while in some bacterial phyla (e.g. Fusobacteria, Spirochaetes, Thermotogae and Synergistes) signal peptides were completely absent. POP homologs from gram-positive bacterial phyla (Actinobacteria and Firmicutes) showed relatively less number of signal peptides.Figure 2


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

Kaushik S, Sowdhamini R - BMC Genomics (2014)

Bacterial POP homologs with signal peptides and transmembrane regions.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Bacterial POP homologs with signal peptides and transmembrane regions.
Mentions: Earlier studies have shown that bPOPs are associated with the signal peptides [13]. Signal peptides are sequence motifs that permit the proteins to translocate across endoplasmic reticulum in eukaryotes and to the cytoplasmic membrane in prokaryotes. Therefore, we examined all the collected POP homologs for the presence of signal peptides. Our results showed that 20% of the POP homologs were predicted to be associated with such signals, from which 225 (35%) were annotated POPs (Figure 2). Bacteroides (78%) and Acidobacteria (75%) had maximum number of POP homologs with signal peptides, while in some bacterial phyla (e.g. Fusobacteria, Spirochaetes, Thermotogae and Synergistes) signal peptides were completely absent. POP homologs from gram-positive bacterial phyla (Actinobacteria and Firmicutes) showed relatively less number of signal peptides.Figure 2

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