A Metagenomic Study Highlights Phylogenetic Proximity of Quorum-Quenching and Xenobiotic-Degrading Amidases of the AS-family

PLoS One. 2013 Jun 7;8(6):e65473. doi: 10.1371/journal.pone.0065473. Print 2013.

Abstract

Quorum-sensing (QS) signals of the N-acylhomoserine lactone (NAHL) class are cleaved by quorum-quenching enzymes, collectively named NAHLases. Here, functional metagenomics allowed the discovery of a novel bacterial NAHLase in a rhizosphere that was treated with γ-caprolactone. As revealed by rrs-DGGE and rrs-pyrosequencing, this treatment increased the percentage of the NAHL-degrading bacteria and strongly biased the structure of the bacterial community, among which Azospirillum dominated. Among the 29 760 fosmids of the metagenomic library, a single one was detected that expressed the qsdB gene conferring NAHL-degradation upon E. coli and decreased QS-regulated virulence in Pectobacterium. Phylogenetic analysis of the 34 orfs of the fosmid suggested that it would belong to an unknown Proteobacterium - probably a γ-proteobacterium. qPCR quantification of the NAHLase-encoding genes attM, qsdA, and qsdB revealed their higher abundance in the γ-caprolactone-treated rhizosphere as compared to an untreated control. The purified QsdB enzyme exhibited amidase activity. QsdB is the first amidase signature (AS) family member exhibiting NAHLase-activity. Point mutations in the AS-family catalytic triad K-S-S abolished the NAHLase activity of QsdB. This study extends the diversity of NAHLases and highlights a common phylogenic origin of AS-family enzymes involved in the degradation of natural compounds, such as NAHLs, and xenobiotics, such as nylon and linuron.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acyl-Butyrolactones / metabolism
  • Amidohydrolases / metabolism*
  • Bacteria / drug effects
  • Bacteria / enzymology
  • Bacteria / genetics
  • Biocatalysis / drug effects
  • Biodegradation, Environmental
  • Biodiversity
  • Caproates / pharmacology
  • Carboxylic Ester Hydrolases / metabolism
  • Genes, Bacterial / genetics
  • Lactones / pharmacology
  • Metagenomics*
  • Open Reading Frames / genetics
  • Phylogeny*
  • Physical Chromosome Mapping
  • Quorum Sensing* / drug effects
  • Quorum Sensing* / genetics
  • Xenobiotics / metabolism*

Substances

  • Acyl-Butyrolactones
  • Caproates
  • Lactones
  • Xenobiotics
  • caprolactone
  • Carboxylic Ester Hydrolases
  • N-acyl homoserine lactonase
  • Amidohydrolases

Grant support

MT was supported by a PhD grant from Réseau de Recherche sur le Développement Soutenable (R2DS, Région Ile-de-France), AB-C by a post-doctoral fellowship from Comité Nord Plants de Pommes de Terre (CNPPT, France). YD and DF were funded by Centre de la Recherche Scientifique (CNRS) and program Ecosphère Continentale et Côtière (EC2CO, CNRS); DF received financial support from the French programs Ingénierie Ecologique (CNRS), Projets innovants (Fondation pour la Recherche sur la Biodiversité, FRB), and PESTICIDES (Ministère de l’écologie, du développement durable, des transports et du logement). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.