Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes

Abstract

Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length putative copA sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative copA sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected copA sequences detected in the tailings metagenome showed that topology of the copA phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of copA diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore copA (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses.

Real‐time PCR based analysis of metal resistance genes in metal resistant Pseudomonas aeruginosa strain J007

“…In spite of wide distribution and frequent detection of major metal homeostasis genes, amplification or detection of sequences similar to those of previously known genes remained unsuccessful with several environmental isolates or metagenomes . The most plausible explanation attributed to such failures are sequence divergence or intrinsic polymorphism of the known genes or even presence of entirely different determinants encoding proteins that manifest metal resistance by alternative mechanisms . The two metal resistance determinants copA and czcA detected in the test bacterium encode periplasmic metal sequestering protein and RND type efflux transporters, respectively.…”

Metagenomic screening of global microbiomes identifies pathogen-enriched environments

“…Like the previously established Local BLASTN method for antibiotic and metal resistance genes screening [58, 62, 63], the Local BLASTP method using the toxin-centered pathogen database in this study was successful at accurately identifying toxin proteins from the database. For screening of the Clostridium perfringens ATCC 13124 genome, the methods successfully detected the pore-forming genes and multiple copies of the glucosyltransferase (toxB-like) and ADP-ribosyltransferase ( spvB-like ) genes, based on the raw data.…”

“…The Local BLASTP was applied following the procedure used in our previous study [58]. Basically, the gene calling results of each metagenome were searched against the toxin factor database using BLASTP embedded in BioEdit.…”

Expression of pathogenicity and virulence related genes in Pseudomonas syringae pv. syringae under copper stress

“…Based on previous studies, the two reference strains in this group are Cu resistant (MIC > 0.8 mM Cu) and are also able to produce syringomycin and are ice nucleation active (Ravindran et al, 2015). Li et al (2015) hypothesized that the polymorphic Cu resistance gene copA can be divided into two highly conserved groups encoding for multicopper oxidase and P-type ATPase.…”