SRL pathogenicity island contributes to the metabolism of D-aspartate via an aspartate racemase in Shigella flexneri YSH6000

PLoS One. 2020 Jan 24;15(1):e0228178. doi: 10.1371/journal.pone.0228178. eCollection 2020.

Abstract

In recent years, multidrug resistance of Shigella strains associated with genetic elements like pathogenicity islands, have become a public health problem. The Shigella resistance locus pathogenicity island (SRL PAI) of S. flexneri 2a harbors a 16Kbp region that contributes to the multidrug resistance phenotype. However, there is not much information about other functions such as metabolic, physiologic or ecological ones. For that, wild type S. flexneri YSH6000 strain, and its spontaneous SRL PAI mutant, 1363, were used to study the contribution of the island in different growth conditions. Interestingly, when both strains were compared by the Phenotype Microarrays, the ability to metabolize D-aspartic acid as a carbon source was detected in the wild type strain but not in the mutant. When D-aspartate was added to minimal medium with other carbon sources such as mannose or mannitol, the SRL PAI-positive strain was able to metabolize it, while the SRL PAI-negative strain did not. In order to identify the genetic elements responsible for this phenotype, a bioinformatic analysis was performed and two genes belonging to SRL PAI were found: orf8, coding for a putative aspartate racemase, and orf9, coding for a transporter. Thus, it was possible to measure, by an indirect analysis of racemization activity in minimal medium supplemented only with D-aspartate, that YSH6000 strain was able to transform the D-form into L-, while the mutant was impaired to do it. When the orf8-orf9 region from SRL island was transformed into S. flexneri and S. sonnei SRL PAI-negative strains, the phenotype was restored. Although, when single genes were cloned into plasmids, no complementation was observed. Our results strongly suggest that the aspartate racemase and the transporter encoded in the SRL pathogenicity island are important for bacterial survival in environments rich in D-aspartate.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Isomerases / genetics
  • Amino Acid Isomerases / metabolism*
  • Bacterial Proteins / metabolism
  • D-Aspartic Acid / analysis
  • D-Aspartic Acid / metabolism*
  • Drug Resistance, Multiple, Bacterial / genetics*
  • Genes, Bacterial
  • Genomic Islands*
  • Mannose / metabolism
  • Open Reading Frames / genetics
  • Phenotype
  • Shigella flexneri / enzymology
  • Shigella flexneri / genetics*
  • Shigella flexneri / growth & development
  • Shigella sonnei / genetics

Substances

  • Bacterial Proteins
  • D-Aspartic Acid
  • Amino Acid Isomerases
  • aspartate racemase
  • Mannose

Grants and funding

This work was supported by FONDECYT grant 1130394 to CT and CONICYT Doctoral Scholarship 2012-2016, Uch1304 ‏MECESUP Fellowship for doctoral internship 2015 and Operational expenses for Doctoral thesis, CONICYT (Res. 8994), 2014 to TH. HPLC and MS-LS were funded through Research Funds from MM and AS, Middlesex University London. Publication fees are funded by BioMentoring Program, Faculty of Biology, Ludwig-Maximilians Universität München, Germany 2018-2019. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.