A metagenomic analysis of soil bacteria extends the diversity of quorum-quenching lactonases.
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.
Riaz
Kashif
K
Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, UPR2355, Gif-sur-Yvette, France.
Elmerich
Claudine
C
Moreira
David
D
Raffoux
Aurélie
A
Dessaux
Yves
Y
Faure
Denis
D
D015107:4-Butyrolactone / Q000031:analogs & derivatives / Q000378:metabolism*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D018407:Bacterial Physiological Phenomena; D002265:Carboxylic Ester Hydrolases / Q000235:genetics* / Q000378:metabolism; D002851:Chromatography, High Pressure Liquid; D003001:Cloning, Molecular; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D014644:Genetic Variation; D015698:Genomic Library; D023281:Genomics; D053038:Quorum Sensing; D012988:Soil Microbiology
D004269:DNA, Bacterial; D002265:Carboxylic Ester Hydrolases; C432003:N-acyl homoserine lactonase; D015107:4-Butyrolactone