Metagenomic analysis of apple orchard soil reveals antibiotic resistance genes encoding predicted bifunctional proteins.
To gain insight into the diversity and origins of antibiotic resistance genes, we identified resistance genes in the soil in an apple orchard using functional metagenomics, which involves inserting large fragments of foreign DNA into Escherichia coli and assaying the resulting clones for expressed functions. Among 13 antibiotic-resistant clones, we found two genes that encode bifunctional proteins. One predicted bifunctional protein confers resistance to ceftazidime and contains a natural fusion between a predicted transcriptional regulator and a beta-lactamase. Sequence analysis of the entire metagenomic clone encoding the predicted bifunctional beta-lactamase revealed a gene potentially involved in chloramphenicol resistance as well as a predicted transposase. A second clone that encodes a predicted bifunctional protein confers resistance to kanamycin and contains an aminoglycoside acetyltransferase domain fused to a second acetyltransferase domain that, based on nucleotide sequence, was predicted not to be involved in antibiotic resistance. This is the first report of a transcriptional regulator fused to a beta-lactamase and of an aminoglycoside acetyltransferase fused to an acetyltransferase not involved in antibiotic resistance.
Donato
Justin J
JJ
Yale University, Department of Molecular, Cellular, and Developmental Biology, P.O. Box 208103, New Haven, CT 06520-8103, USA.
Moe
Luke A
LA
Converse
Brandon J
BJ
Smart
Keith D
KD
Berklein
Flora C
FC
McManus
Patricia S
PS
Handelsman
Jo
J
D000123:Acetyltransferases / Q000235:genetics / Q000378:metabolism; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D002701:Chloramphenicol / Q000494:pharmacology; D003001:Cloning, Molecular; D004269:DNA, Bacterial / Q000235:genetics*; D004352:Drug Resistance, Microbial / Q000235:genetics*; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D007612:Kanamycin / Q000494:pharmacology; D027845:Malus / Q000254:growth & development*; D056186:Metagenomics / Q000379:methods*; D008826:Microbial Sensitivity Tests; D008969:Molecular Sequence Data; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D012987:Soil / Q000032:analysis*; D019895:Transposases / Q000235:genetics / Q000378:metabolism; D001618:beta-Lactamases / Q000235:genetics / Q000378:metabolism
D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D011506:Proteins; D012987:Soil; D007612:Kanamycin; D002701:Chloramphenicol; D000123:Acetyltransferases; C019681:aminoglycoside acetyltransferase; D019895:Transposases; D001618:beta-Lactamases
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