Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus

PLoS One. 2020 Jan 14;15(1):e0223033. doi: 10.1371/journal.pone.0223033. eCollection 2020.

Abstract

Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane. Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at the lssXYZABD locus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detect lssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non-pneumophila Legionella, which has led to the assumption that this system is a virulence factor exclusively possessed by L. pneumophila. Here we discovered RtxA and its associated T1SS in a novel Legionella taurinensis strain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverse Legionella spp. The ABC transporter of the novel Legionella T1SS Legionella repeat protein secretion system shares structural similarity to those of diverse T1SS families, including the alkaline protease T1SS in Pseudomonas aeruginosa. The Legionella bacteriocin (1-3) secretion systems T1SSs are novel putative bacteriocin transporting T1SSs as their ABC transporters include C-39 peptidase domains in their N-terminal regions, with LB2SS and LB3SS likely constituting a nitrile hydratase leader peptide transport T1SSs. The LB1SS is more closely related to the colicin V T1SS in Escherichia coli. Of 45 Legionella spp. whole genomes examined, 19 (42%) were determined to possess lssB and lssD homologs. Of these 19, only 7 (37%) are known pathogens. There was no difference in the proportions of disease associated and non-disease associated species that possessed the RtxA T1SS (p = 0.4), contrary to the current consensus regarding the RtxA T1SS. These results draw into question the nature of RtxA and its T1SS as a singular virulence factor. Future studies should investigate mechanistic explanations for the association of RtxA with virulence.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • ATP-Binding Cassette Transporters / genetics
  • Bacterial Proteins / genetics*
  • Cell Membrane / genetics
  • Computational Biology
  • Escherichia coli / genetics
  • Genome, Bacterial / genetics
  • Hemolysin Proteins / genetics*
  • Humans
  • Legionella / genetics*
  • Legionella / pathogenicity
  • Legionella pneumophila / genetics
  • Legionellosis / genetics*
  • Legionellosis / microbiology
  • Sequence Analysis
  • Type I Secretion Systems / genetics*
  • Virulence Factors / genetics
  • Whole Genome Sequencing

Substances

  • ATP-Binding Cassette Transporters
  • Bacterial Proteins
  • Hemolysin Proteins
  • Type I Secretion Systems
  • Virulence Factors
  • ApxI toxin, Bacteria

Supplementary concepts

  • Legionella taurinensis

Associated data

  • figshare/10.6084/m9.figshare.9162161.v1
  • figshare/10.6084/m9.figshare.9162146.v1
  • figshare/10.6084/m9.figshare.9162152.v1

Grants and funding

This study was supported by the US National Science Foundation via RAPID Award no. 1556258: Recipient: A.P.; a Graduate Research Fellowship Program Grant (DGE 0822220): Recipient: E.G.; Supplementary funding associated with award #1336650: Recipient: A.P. Additional support was provided by the Alfred P. Sloan Foundation Microbiology of the Built Environment program (https://sloan.org/programs/research/microbiology-of-the-built-environment#apply): Recipient: E.G.; the American Water Works Association Abel Wolman Fellowship: Recipient: E.G.; and the Institute for Critical Technology and Applied Science and Engineering of the Exposome Center (https://ictas.vt.edu/) at Virginia Polytechnic Institute and State University: Recipient: A.P. In addition to the funding sources noted, colleague Marc A. Edwards contributed discretionary research funding to support the sequencing study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.