metagenomic analysis of soil bacteria extends the diversity of quorum-quenching lactonases

• Published in: Environmental microbiology 2008-03, Vol.10 (3), p.560-570
• Main Authors: Riaz, Kashif, Elmerich, Claudine, Moreira, David, Raffoux, Aurélie, Dessaux, Yves, Faure, Denis
• Format: Article
• Language: English
• Subjects: 4-Butyrolactone - analogs & derivatives; 4-Butyrolactone - metabolism; Bacteria - classification; Bacteria - genetics; Bacteria - metabolism; Bacterial Physiological Phenomena; Carboxylic Ester Hydrolases - genetics; Carboxylic Ester Hydrolases - metabolism; Chromatography, High Pressure Liquid; Cloning, Molecular; DNA, Bacterial - genetics; Escherichia coli - genetics; Gene Expression Regulation, Bacterial; Genetic Variation; Genomic Library; Genomics; Quorum Sensing; Soil Microbiology
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/j.1462-2920.2007.01475.x

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.