Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library.
A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events.
Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France. Electronic address: samuel.jacquiod@bio.ku.dk.
Samuel
S
Jacquiod
Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
Sandrine
S
Demanèche
Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
Laure
L
Franqueville
Department for Food Science and Technology Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
Luka
L
Ausec
Molecular Microbial Ecology Group, Section of Microbiology, København Universitet, København, Denmark.
Zhuofei
Z
Xu
Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
Tom O
TO
Delmont
Division of Soil and Water Management, Department of Earth and Environmental Sciences, University of Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium.
Vincent
V
Dunon
Équipe Environnement et Microbiologie, IBEAS - UFR Sciences et Techniques, Université de Pau et des Pays de l'Adour, 64013 Pau, France.
Christine
C
Cagnon
Department for Food Science and Technology Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
Ines
I
Mandic-Mulec
Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
Timothy M
TM
Vogel
Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France. Electronic address: pascal.simonet@ec-lyon.fr.
Pascal
P
Simonet
D001419:Bacteria / Q000201:enzymology / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D002686:Chitin / Q000378:metabolism; D003001:Cloning, Molecular; D004269:DNA, Bacterial / Q000235:genetics; D015723:Gene Library; D005798:Genes, Bacterial; D019426:Integrases / Q000235:genetics; D042845:Laccase / Q000235:genetics; D056186:Metagenomics / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000235:genetics; D012988:Soil Microbiology
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D002686:Chitin; D042845:Laccase; D019426:Integrases
Bacteria; Catabolic genes; Metagenomic fosmid library; Mobile genetic elements; Soil