A metagenomic analysis of soil bacteria extends the diversity of quorum‐quenching lactonases

Abstract

A metagenomic library of 10,121 clones, generated from bacteria inhabiting a pasture soil from France, was screened for the presence of fosmids conferring either N-acylhomoserine lactone (NAHL) synthesis or NAHL degradation ability upon their Escherichia coli host. No clone producing NAHLs was identified whereas one, containing a 31 972 bp insert in fosmid p2H8, allowed NAHL degradation. This led to the cloning and identification of a gene, qlcA, encoding an NAHL-lactonase activity, as judged by lactone-ring closure and HPLC/MS analyses of NAHL degradation products. The qlcA gene efficiently quenched quorum-sensing regulated pathogenic functions when expressed in Pectobacterium carotovorum. The QlcA peptide belongs to the family of zinc-dependent metallohydrolases and appears to be distantly related to other NAHL-lactonases discovered in Agrobacterium, Bacillus, Photorhabdus and Rhizobium. In-silico analysis of the metagenomic insert revealed the occurrence of 20 orf, with a constant GC% and codon usage, suggesting a unique bacterial origin. Nine out of these 20 orf were homologous to genes encoding biosynthesis of arginine; they were clustered with an unusual succession argFJADBCRGH. The fosmid p2H8 is able to complement the argA, argB and argC mutants in E. coli. Phylogenetic analysis showed that 9 orf out of 20 were related to sequences from members of the Acidobacteria, supporting the hypothesis that the analysed insert might be originated from an organism related to this phylum.

Exploiting Quorum Sensing To Confuse Bacterial Pathogens

“…Despite their differences in DNA sequence and metal ion dependence ( Table 2), all of these enzymes were confirmed to function as lactonases following biochemical analysis of reaction products. Additionally, in vitro and in vivo studies have confirmed the overall value of these lactonases in quorum quenching and disease prevention against E. carotovora (62,68,71,72), akin to what was originally shown with AiiA.…”

“…Metagenomic analyses faciliated the discovery of QlcA, BipB01, BipB04, BipB05, and BipB07 (68,74,75), and screens for AHL-degrading bacteria led to the identification of QsdA of Rhodococcus erythropolis strain W2 (70), AiiM of Microbacterium testaceum (71), AidH of Ochrobactrium sp. strain T63 (72), and QsdH of Pseudoalteromonas byunsanensis strain 1A01261 (73).…”

Degradation of N-Acylhomoserine Lactone Quorum Sensing Signaling Molecules by Potato Root Surface-Associated Chryseobacterium Strains

“…Genes encoding AHL-acylase, which hydrolyzes the amide bond of AHL, have been cloned from Ralstonia spp., Anabaena spp., Streptomyces spp., Shewanella spp., and Pseudomonas aeruginosa. Novel AHLdegrading genes have been isolated from metagenomic libraries constructed from soil samples (19,22). Recently, it was reported that some members of the α/β hydrolase family have AHL-lactonase activity (11,30).…”

AiiM, a Novel Class of N -Acylhomoserine Lactonase from the Leaf-Associated Bacterium Microbacterium testaceum

“…Human and murine paraoxonase degrades AHL by hydrolyzing its lactone ring (21). Novel AHL lactonase genes have been isolated from a metagenomic library which was constructed from environmental soil samples (24,27). AHL-degrading genes have also been utilized in the biocontrol of plant diseases.…”