Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings

• Published in: PloS one 2021-09, Vol.16 (9), p.e0257800-e0257800
• Main Authors: Cusick, Kathleen, Iturbide, Ane, Gautam, Pratima, Price, Amelia, Polson, Shawn, MacDonald, Madolyn, Erill, Ivan
• Format: Article
• Language: English
• Subjects: Algicides; Alteromonas; Alteromonas - drug effects; Alteromonas - genetics; Alteromonas - growth & development; Alteromonas - isolation & purification; Alteromonas macleodii; Antifouling; Antifouling coatings; Antifouling substances; Aquatic Organisms - microbiology; Bacteria; Bacterial Proteins - genetics; Binding sites; Bioinformatics; Biology and Life Sciences; Chromosomes; Chromosomes, Bacterial - genetics; Clusters; Coastal ecosystems; Coatings; Copper; Copper - pharmacology; Cytoplasm; Detoxification; Drug Resistance, Bacterial; E coli; Enzymes; Escherichia coli; Fouling; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genes; Genetic aspects; Genomic analysis; Genomic islands; Genomics; Gram-negative bacteria; Gram-positive bacteria; Herbicides; Homeostasis; Homology; Marine ecosystems; Markov Chains; Medicine and Health Sciences; Methyltransferase; Plasmids; Plasmids - genetics; Properties; Proteins; Sequence Analysis, RNA; Ship hulls; Ships; Signal transduction; Species; Strains (organisms); Transcription; Whole Genome Sequencing
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0257800

Copper is prevalent in coastal ecosystems due to its use as an algaecide and as an anti-fouling agent on ship hulls. Alteromonas spp. have previously been shown to be some of the early colonizers of copper-based anti-fouling paint but little is known about the mechanisms they use to overcome this initial copper challenge. The main models of copper resistance include the Escherichia coli chromosome-based Cue and Cus systems; the plasmid-based E. coli Pco system; and the plasmid-based Pseudomonas syringae Cop system. These were all elucidated from strains isolated from copper-rich environments of agricultural and/or enteric origin. In this work, copper resistance assays demonstrated the ability of Alteromonas macleodii strains CUKW and KCC02 to grow at levels lethal to other marine bacterial species. A custom database of Hidden Markov Models was designed based on proteins from the Cue, Cus, and Cop/Pco systems and used to identify potential copper resistance genes in CUKW and KCC02. Comparative genomic analyses with marine bacterial species and bacterial species isolated from copper-rich environments demonstrated that CUKW and KCC02 possess genetic elements of all systems, oftentimes with multiple copies, distributed throughout the chromosome and mega-plasmids. In particular, two copies of copA (the key player in cytoplasmic detoxification), each with its own apparent MerR-like transcriptional regulator, occur on a mega-plasmid, along with multiple copies of Pco homologs. Genes from both systems were induced upon exposure to elevated copper levels (100 μM- 3 mM). Genomic analysis identified one of the merR-copA clusters occurs on a genomic island (GI) within the plasmid, and comparative genomic analysis found that either of the merR-copA clusters, which also includes genes coding for a cupredoxin domain-containing protein and an isoprenylcysteine methyltransferase, occurs on a GI across diverse bacterial species. These genomic findings combined with the ability of CUKW and KCC02 to grow in copper-challenged conditions are couched within the context of the genome flexibility of the Alteromonas genus.