Integron Diversity in Heavy-Metal-Contaminated Mine Tailings and Inferences about Integron Evolution

Abstract

Integrons are horizontal gene transfer (HGT) systems containing elements necessary for site-specific recombination and expression of foreign DNA. The overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. This report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. First, using cultureindependent techniques, we explored the diversity of integrons and integron-transferred genes in heavy-metalcontaminated mine tailings. Using degenerate primers, we amplified integron integrase genes from the tailings. We discovered 14 previously undescribed integrase genes, including six novel gene lineages. In addition, we found 11 novel gene cassettes in this sample. One of the gene cassettes that we sequenced is similar to a gene that codes for a step in a pathway for nitroaromatic catabolism, a group of compounds associated with mining activity. This suggests that integrons may be important for gene transfer in response to selective pressures other than the presence of antibiotics. We also investigated the evolution of integrons by statistically comparing the phylogenies of 16S rRNA and integrase genes from the same organisms, using sequences from GenBank and various sequencing projects. We found significant differences between the organismal (16S rRNA) and integrase trees, and we suggest that these differences may be due to HGT.

Antibiotic Resistance in the Environment, with Particular Reference to MRSA

“…Fluit and Schmitz (2004) resistance (Bass et al, 1999;Sorum et al, 2003). A recent study (Nemergut et al, 2004) has shown evidence of a gene cassette encoding nitroaromatic catabolism, a group of compounds associated with mining activity, this highlights the fact that other selective pressures other than antibiotics may also co-select for resistance genes. The process by which a gene becomes a movable cassette is not understood; however, it has been proposed that the 59-base element is added as a transcription terminator to an RNA gene transcript that is subsequently converted into DNA by a hypothetical reverse transcriptase (Recchia and Hall, 1995).…”

The native Pseudomonas stutzeri strain Q chromosomal integron can capture and express cassette-associated genes

“…Under the selective pressure of intensive antibiotic use, class 1 integrons have used the cassette metagenome to engineer the phenotype of multiple antibiotic resistance (Hall & Collis, 1998;Rowe-Magnus et al, 2001). Examination of genome sequence data and targeted environmental surveys have shown that integrons are diverse and present in~5 % of bacterial genomes (Nemergut et al, 2004;Nield et al, 2001;Rowe-Magnus et al, 2001). Given the size of the gene cassette reservoir and the relative frequency of integrons, we might expect that the integron-gene cassette system has also engineered phenotypes other than antibiotic resistance.…”

Occurrence and Characteristics of Class 1 and 2 Integrons in Clinical Bacterial Isolates from Patients in South China

“…There are currently thrity-two unique integron integrase genes available in GeneBank and various sequencing projects, an eight-fold increase in the past 3 years. 8) However only 3 classes of integrons are to date the most extensively studied and clinically significant, defined class 1, 2 and 3 integrons. The gene cassettes found in these integrons are much more variable; more than 60 different gene cassettes have been described, including gene cassettes conferring resistance to aminoglycosides, penicillins, cephalosporins, carbapenems, trimethoprim, chloramphenicol, rifampin, erythromycin, and quaternary ammonium compounds.…”