Phylogenetic analysis of Type IX Secretion System (T9SS) protein components revealed that PorR undergoes horizontal gene transfer
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Abstract
Porphyromonas gingivalis is one of the major bacteria that causes periodontitis. Chronic periodontitis is a severe form of periodontal disease that occurs due to prolong inflammatory conditions. If left untreated, deterioration of the supporting structures such as gingiva, bone, and ligament can ultimately lead to tooth loss. Virulence factors produce by P. gingivalis that are responsible for the pathophysiology of periodontitis are secreted by Type IX Secretion System (T9SS). T9SS-acquiring bacteria have been linked to several systemic diseases such as atherosclerosis, aspiration pneumonia, cancer, rheumatoid arthritis, and diabetes mellitus. This study aims to investigate the phylogenetic relationship and taxonomic distribution between putative members of T9SS component protein families. There are 20 protein components of T9SS being investigated in this study. We have constructed multiple sequence alignments for each component using homologs of those components. Then we proceed to phylogenetic analysis by constructing the maximum-likelihood (ML) trees. ML trees for 19 protein components of T9SS exhibit clustering of terminal nodes based on their respective classes under Bacteroidetes phylum. The ML tree of PorR, which is an aminotransferase that involved in Wbp pathway that produces structural sugar of A-LPS, exhibits different clustering pattern of terminal nodes where the nodes do not cluster based on their respective classes. Hence, PorR might evolve independently from the other T9SS protein components which might suggest that PorR is acquired by T9SS-acquiring bacteria through horizontal gene transfer. The part of P. gingivalis strain ATCC 33277 genome that contains porR gene has been extracted to support the possibility that porR gene has been horizontally transferred. Through homology searching using NCBI blastx, we found that seven genes (including porR) that involved in the biosynthesis of A-LPS that anchored the virulence factor secreted by T9SS to bacterial cell surface are flanked by insertion sequences (ISs) that encode IS5 family transposase. The IS5 transposons contain a single open reading frame that encodes for the transposase that will cleave the 12 bp inverted repeats that flanked the transposons. Consequently, this can mobilise the intervening DNA segment that contains porR gene and subsequently contributes to the possibility that porR gene is subjected to conjugative transfer. The taxonomic distribution of T9SS protein components revealed that they can be found across all classes under Bacteroidetes phylum. Additionally, we have identified species under Chitinophagia, Saprospiria, and unclassified that acquired homologs of T9SS protein components that, to our knowledge, have not been reported. In conclusion, this study can provide a better understanding about the phylogeny and taxonomic distribution of T9SS protein components.
Cite this as
2019. Phylogenetic analysis of Type IX Secretion System (T9SS) protein components revealed that PorR undergoes horizontal gene transfer. PeerJ Preprints 7:e27700v1 https://doi.org/10.7287/peerj.preprints.27700v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a full manuscript that we intend to submit to PeerJ.
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Supplemental Information
Fasta files, multiple sequence alignments and genome data generated and used in this work
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Reeki Emrizal conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper.
Nor Azlan Nor Muhammad conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft, sourced funding for project.
Data Deposition
The following information was supplied regarding data availability:
The fasta files for each T9SS protein family are provided in supplemental data S1. The multiple sequence alignments for each T9SS protein family are provided in supplemental data S2. Supplemental data S3 contains the genome data used in this study.
Funding
The authors received funding from Universiti Kebangsaan Malaysia (UKM), GGPM-2016-016 grant which supported this research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
