Sequence and analysis of a plasmid-encoded mercury resistance operon from Mycobacterium marinum identifies MerH, a new mercuric ion transporter

Genomic Analyses of Longitudinal Mycobacterium abscessus Isolates in a Multicenter Cohort Reveal Parallel Signatures of In-Host Adaptation

BACKGROUND

Nontuberculous mycobacteria (NTM) are ubiquitous in the environment and an increasingly frequent cause of opportunistic infections. Mycobacterium abscessus complex (MABC) is one of the major NTM lung pathogens that disproportionately colonize and infect the lungs of individuals with cystic fibrosis (CF). MABC infection can persist for years, and antimicrobial treatment is frequently ineffective.

METHODS

We sequenced the genomes of 175 isolates longitudinally collected from 30 patients with MABC lung infection. We contextualized our cohort amidst the broader MABC phylogeny and investigated genes undergoing parallel adaptation across patients. Finally, we tested the phenotypic consequences of parallel mutations by conducting antimicrobial resistance and mercury-resistance assays.

RESULTS

We identified highly related isolate pairs across hospital centers with low likelihood of transmission. We further annotated nonrandom parallel mutations in 22 genes and demonstrated altered macrolide susceptibility co-occurring with a nonsynonymous whiB1 mutation. Finally, we highlighted a 23-kb mercury-resistance plasmid whose loss during chronic infection conferred phenotypic susceptibility to organic and nonorganic mercury compounds.

CONCLUSIONS

We characterized parallel genomic processes through which MABC is adapting to promote survival within the host. The within-lineage polymorphisms we observed have phenotypic effects, potentially benefiting fitness in the host at the putative detriment of environmental survival.

Emergence of Inducible Macrolide Resistance in Mycobacterium chelonae Due to Broad-Host-Range Plasmid and Chromosomal Variants of the Novel 23S rRNA Methylase Gene, erm(55)

Macrolides are a mainstay of therapy for infections due to nontuberculous mycobacteria (NTM). Among rapidly growing mycobacteria (RGM), inducible macrolide resistance is associated with four chromosomal 23S rRNA methylase (erm) genes. Beginning in 2018, we detected high-level inducible clarithromycin resistance (MICs of ≥16μg/mL) in clinical isolates of Mycobacterium chelonae, an RGM species not previously known to contain erm genes. Using whole-genome sequencing, we identified a novel plasmid-mediated erm gene. This gene, designated erm(55)P, exhibits <65% amino acid identity to previously described RGM erm genes. Two additional chromosomal erm(55) alleles, with sequence identities of 81% to 86% to erm(55)P, were also identified and designated erm(55)C and erm(55)T. The erm(55)T is part of a transposon. The erm(55)P allele variant is located on a putative 137-kb conjugative plasmid, pMchErm55. Evaluation of 133 consecutive isolates from 2020 to 2022 revealed 5 (3.8%) with erm(55). The erm(55)P gene was also identified in public data sets of two emerging pathogenic pigmented RGM species: Mycobacterium iranicum and Mycobacterium obuense, dating back to 2008. In both species, the gene appeared to be present on plasmids homologous to pMchErm55. Plasmid-mediated macrolide resistance, not described previously for any NTM species, appears to have spread to multiple RGM species. This has important implications for antimicrobial susceptibility guidelines and treatment of RGM infections. Further spread could present serious consequences for treatment of other macrolide-susceptible RGM. Additional studies are needed to determine the transmissibility of pMchErm55 and the distribution of erm(55) among other RGM species.

Transporter drives the biosorption of heavy metals by Stenotrophomonas rhizophila JC1

To better understand the function of transporter in heavy metal detoxification of bacteria, the transporters associated with heavy metal detoxification in S. rhizophila JC1 were analyzed, among which four members were verified by RT-qPCR. In addition, the removal rates of four single metal ions (Cr⁶⁺, Cu²⁺, Zn²⁺, Pb²⁺) and polymetallic ions by strain JC1 were studied, respectively. We also researched the physiological response of strain JC1 to different metal stress via morphological observation, elemental composition, functional group and membrane permeability analysis. The results showed that in the single metal ion solution, removal capacities of Cu²⁺ (120 mg/L) and Cr⁶⁺ (80 mg/L) of S. rhizophila JC1 reached to 79.9% and 89.3%, respectively, while in polymetallic ions solution, the removal capacity of each metal ion all decreased, and in detail, the adsorption capacity was determined Cr⁶+>Cu²⁺>Zn²⁺>Pb²⁺ under the same condition. The physiological response analyses results showed that extracellular adsorption phenomena occurred, and the change of membrane permeability hindered the uptake of metal ions by bacteria. The analysis of transporters in strain JC1 genome illustrated that a total of 323 transporters were predicted. Among them, two, six and five proteins of the cation diffusion facilitator, resistance-nodulation-division efflux and P-type ATPase families were, respectively, predicted. The expression of corresponding genes showed that the synergistic action of correlative transporters played important roles in the process of adsorption. The comparative genomics analysis revealed that S. rhizophila JC1 has long-distance evolutionary relationships with other strains, but the efflux system of S. rhizophila JC1 contained the same types of metal transporters as other metal-resistant bacteria.

Cellular and genetic mechanism of bacterial mercury resistance and their role in biogeochemistry and bioremediation

Mercury (Hg) is a highly toxic element that occurs at low concentrations in nature. However, various anthropogenic and natural sources contribute around 5000 to 8000 metric tons of Hg per year, rapidly deteriorating the environmental conditions. Mercury-resistant bacteria that possess the mer operon system have the potential for Hg bioremediation through volatilization from the contaminated milieus. Thus, bacterial mer operon plays a crucial role in Hg biogeochemistry and bioremediation by converting both reactive inorganic and organic forms of Hg to relatively inert, volatile, and monoatomic forms. Both the broad-spectrum and narrow-spectrum bacteria harbor many genes of mer operon with their unique definitive functions. The presence of mer genes or proteins can regulate the fate of Hg in the biogeochemical cycle in the environment. The efficiency of Hg transformation depends upon the nature and diversity of mer genes present in mercury-resistant bacteria. Additionally, the bacterial cellular mechanism of Hg resistance involves reduced Hg uptake, extracellular sequestration, and bioaccumulation. The presence of unique physiological properties in a specific group of mercury-resistant bacteria enhances their bioremediation capabilities. Many advanced biotechnological tools also can improve the bioremediation efficiency of mercury-resistant bacteria to achieve Hg bioremediation.

Acute Toxicity of Divalent Mercury to Bacteria Explained by the Formation of Dicysteinate and Tetracysteinate Complexes Bound to Proteins in Escherichia coli and Bacillus subtilis

Bacteria are the most abundant organisms on Earth and also the major life form affected by mercury (Hg) poisoning in aquatic and terrestrial food webs. In this study, we applied high energy-resolution X-ray absorption near edge structure (HR-XANES) spectroscopy to bacteria with intracellular concentrations of Hg as low as 0.7 ng/mg (ppm) for identifying the intracellular molecular forms and trafficking pathways of Hg in bacteria at environmentally relevant concentrations. Gram-positive Bacillus subtilis and Gram-negative Escherichia coli were exposed to three Hg species: HgCl₂, Hg-dicysteinate (Hg(Cys)₂), and Hg-dithioglycolate (Hg(TGA)₂). In all cases, Hg was transformed into new two- and four-coordinate cysteinate complexes, interpreted to be bound, respectively, to the consensus metal-binding CXXC motif and zinc finger domains of proteins, with glutathione acting as a transfer ligand. Replacement of zinc cofactors essential to gene regulatory proteins with Hg would inhibit vital functions such as DNA transcription and repair and is suggested to be a main cause of Hg genotoxicity.

The chemical species of mercury accumulated by Pseudomonas idrijaensis, a bacterium from a rock of the Idrija mercury mine, Slovenia

A mercury-resistant bacterial strain has been isolated from a rock of the Idrija mercury mine in Slovenia. The rock had 19 g carbon and 2952 mg mercury (Hg) per kg. Mass spectrometry and DNA sequencing showed that the bacterium belongs to the Pseudomonas genus. It is called Pseudomonas idrijaensis. This bacterial strain is sensitive to methylmercury (MeHg) like the reference P. aeruginosa strain PAO1, and is resistant to divalent mercury (Hg(II)) in contrast to PAO1. This difference could be attributed to the presence of the mer operon yet deprived of the merB gene encoding the organomercurial lyase, on the basis of whole genome sequencing. The P. idrijaensis mer operon displays the RTPCADE organization and is contained in the Tn5041 transposon. This transposon identified here occurs in other Gram-negative Hg-resistant strains isolated from mercury ores, aquatic systems and soils, including Pseudomonas strains from 15,000 to 40,000 years old Siberian permafrost. When P. idrijaensis was exposed to mercury chloride, two intracellular Hg species were identified by high energy-resolution XANES spectroscopy, a dithiolate Hg(SR)₂ and a tetrathiolate Hg(SR)₄ complex. P. idrijaensis had a much higher [Hg(SR)₂]/[Hg(SR)₄] molar ratio than bacteria lacking the mer operon when exposed to 4 μg Hg²⁺/L - resulting in an intracellular accumulation of 4.3 μg Hg/g dw. A higher amount of the Hg(SR)₂ complex provides a chemical signature for the expression of the dicysteinate Mer proteins in response to mercury toxicity.

Microbial Diversity of Mer Operon Genes and Their Potential Rules in Mercury Bioremediation and Resistance

Background:

Mercury is a toxic metal that is present in small amounts in the environment, but its level is rising steadily, due to different human activities, such as industrialization. It can reach humans through the food chain, amalgam fillings, and other sources, causing different neurological disorders, memory loss, vision impairment, and may even lead to death; making its detoxification an urgent task.

Methods:

Various physical and chemical mercury remediation techniques are available, which generally aim at: (i) reducing its mobility or solubility; (ii) causing its vaporization or condensation; (iii) its separation from contaminated soils. Biological remediation techniques, commonly known as bioremediation, are also another possible alternative, which is considered as cheaper than the conventional means and can be accomplished using either (i) organisms harboring themeroperon genes (merB,merA,merR,merP,merT,merD,merF,merC,merE,merHandmerG), or (ii) plants expressing metal-binding proteins. Recently, differentmerdeterminants have been genetically engineered into several organisms, including bacteria and plants, to aid in detoxification of both ionic and organic forms of mercury.

Results:

Bacteria that are resistant to mercury compounds have at least a mercuric reductase enzyme (MerA) that reduces Hg+2to volatile Hg0, a membrane-bound protein (MerT) for Hg+2uptake and an additional enzyme, MerB, that degrades organomercurials by protonolysis. Presence of bothmerA andmerB genes confer broad-spectrum mercury resistance. However,merA alone confers narrow spectrum inorganic mercury resistance.

Conclusion:

To conclude, this review discusses the importance of mercury-resistance genes in mercury bioremediation. Functional analysis ofmeroperon genes and the recent advances in genetic engineering techniques could provide the most environmental friendly, safe, effective and fantastic solution to overcome mercuric toxicity.

Genetic basis and importance of metal resistant genes in bacteria for bioremediation of contaminated environments with toxic metal pollutants

Metal pollution is one of the most persistent and complex environmental issues, causing threat to the ecosystem and human health. On exposure to several toxic metals such as arsenic, cadmium, chromium, copper, lead, and mercury, several bacteria has evolved with many metal-resistant genes as a means of their adaptation. These genes can be further exploited for bioremediation of the metal-contaminated environments. Many operon-clustered metal-resistant genes such as cadB, chrA, copAB, pbrA, merA, and NiCoT have been reported in bacterial systems for cadmium, chromium, copper, lead, mercury, and nickel resistance and detoxification, respectively. The field of environmental bioremediation has been ameliorated by exploiting diverse bacterial detoxification genes. Genetic engineering integrated with bioremediation assists in manipulation of bacterial genome which can enhance toxic metal detoxification that is not usually performed by normal bacteria. These techniques include genetic engineering with single genes or operons, pathway construction, and alternations of the sequences of existing genes. However, numerous facets of bacterial novel metal-resistant genes are yet to be explored for application in microbial bioremediation practices. This review describes the role of bacteria and their adaptive mechanisms for toxic metal detoxification and restoration of contaminated sites.

Analysis for the presence of determinants involved in the transport of mercury across bacterial membrane from polluted water bodies of India

Mercury, which is ubiquitous and recalcitrant to biodegradation processes, threatens human health by escaping to the environment via various natural and anthropogenic activities. Non-biodegradability of mercury pollutants has necessitated the development and implementation of economic alternatives with promising potential to remove metals from the environment. Enhancement of microbial based remediation strategies through genetic engineering approaches provides one such alternative with a promising future. In this study, bacterial isolates inhabiting polluted sites were screened for tolerance to varying concentrations of mercuric chloride. Following identification, several Pseudomonas and Klebsiella species were found to exhibit the highest tolerance to both organic and inorganic mercury. Screened bacterial isolates were examined for their genetic make-up in terms of the presence of genes (merP and merT) involved in the transport of mercury across the membrane either alone or in combination to deal with the toxic mercury. Gene sequence analysis revealed that the merP gene showed 86-99% homology, while the merT gene showed >98% homology with previously reported sequences. By exploring the genes involved in imparting metal resistance to bacteria, this study will serve to highlight the credentials that are particularly advantageous for their practical application to remediation of mercury from the environment.

Role of the horizontal gene exchange in evolution of pathogenic Mycobacteria

BACKGROUND

Mycobacterium tuberculosis is one of the most dangerous human pathogens, the causative agent of tuberculosis. While this pathogen is considered as extremely clonal and resistant to horizontal gene exchange, there are many facts supporting the hypothesis that on the early stages of evolution the development of pathogenicity of ancestral Mtb has started with a horizontal acquisition of virulence factors. Episodes of infections caused by non-tuberculosis Mycobacteria reported worldwide may suggest a potential for new pathogens to appear. If so, what is the role of horizontal gene transfer in this process?

RESULTS

Availing of accessibility of complete genomes sequences of multiple pathogenic, conditionally pathogenic and saprophytic Mycobacteria, a genome comparative study was performed to investigate the distribution of genomic islands among bacteria and identify ontological links between these mobile elements. It was shown that the ancient genomic islands from M. tuberculosis still may be rooted to the pool of mobile genetic vectors distributed among Mycobacteria. A frequent exchange of genes was observed between M. marinum and several saprophytic and conditionally pathogenic species. Among them M. avium was the most promiscuous species acquiring genetic materials from diverse origins.

CONCLUSIONS

Recent activation of genetic vectors circulating among Mycobacteria potentially may lead to emergence of new pathogens from environmental and conditionally pathogenic Mycobacteria. The species which require monitoring are M. marinum and M. avium as they eagerly acquire genes from different sources and may become donors of virulence gene cassettes to other micro-organisms.

Pollution due to hazardous glass waste

Pollution resulting from hazardous glass (HG) is widespread across the globe, both in terms of quantity and associated health risks. In waste cathode ray tube (CRT) and fluorescent lamp glass, mercury and lead are present as the major pollutants. The current review discusses the issues related to quantity and associated risk from the pollutant present in HG and proposes the chemical, biological, thermal, hybrid, and nanotechniques for its management. The hybrid is one of the upcoming research models involving the compatible combination of two or more techniques for better and efficient remediation. Thermal mercury desorption starts at 100 °C but for efficient removal, the temperature should be >460 °C. Involvement of solar energy for this purpose makes the research more viable and ecofriendly. Nanoparticles such as Fe, Se, Cu, Ni, Zn, Ag, and WS2 alone or with its formulation can immobilize heavy metals present in HG by involving a redox mechanism. Straight-line equation from year-wise sale can provide future sale data in comparison with lifespan which gives future pollutant approximation. Waste compact fluorescent lamps units projected for the year 2015 is 9,300,000,000 units and can emit nearly 9,300 kg of mercury. On the other hand, CRT monitors have been continuously replaced by more improved versions like liquid crystal display and plasma display panel resulting in the production of more waste. Worldwide CRT production was 83,300,000 units in 2002 and can approximately release 83,000 metric tons of lead.

Antimicrobial activity of metals: mechanisms, molecular targets and applications

Metals have been used as antimicrobial agents since antiquity, but throughout most of history their modes of action have remained unclear. Recent studies indicate that different metals cause discrete and distinct types of injuries to microbial cells as a result of oxidative stress, protein dysfunction or membrane damage. Here, we describe the chemical and toxicological principles that underlie the antimicrobial activity of metals and discuss the preferences of metal atoms for specific microbial targets. Interdisciplinary research is advancing not only our understanding of metal toxicity but also the design of metal-based compounds for use as antimicrobial agents and alternatives to antibiotics.

Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus

Crenarchaeota include extremely thermoacidophilic organisms that thrive in geothermal environments dominated by sulfidic ores and heavy metals such as mercury. Mercuric ion, Hg(II), inactivates transcription in the crenarchaeote Sulfolobus solfataricus and simultaneously derepresses transcription of a resistance operon, merHAI, through interaction with the MerR transcription factor. While mercuric reductase (MerA) is required for metal resistance, the role of MerH, an adjacent small and predicted product of an ORF, has not been explored. Inactivation of MerH either by nonsense mutation or by in-frame deletion diminished Hg(II) resistance of mutant cells. Promoter mapping studies indicated that Hg(II) sensitivity of the merH nonsense mutant arose through transcriptional polarity, and its metal resistance was restored partially by single copy merH complementation. Since MerH was not required in vitro for MerA-catalysed Hg(II) reduction, MerH may play an alternative role in metal resistance. Inductively coupled plasma-mass spectrometry analysis of the MerH deletion strain following metal challenge indicated that there was prolonged retention of intracellular Hg(II). Finally, a reduced rate of mer operon induction in the merH deletion mutant suggested that the requirement for MerH could result from metal trafficking to the MerR transcription factor.

The mercury resistance (mer) operon in a marine gliding flavobacterium, Tenacibaculum discolor 9A5

Genes conferring mercury resistance have been investigated in a variety of bacteria and archaea but not in bacteria of the phylum Bacteroidetes, despite their importance in many environments. We found, however, that a marine gliding Bacteroidetes species, Tenacibaculum discolor, was the predominant mercury-resistant bacterial taxon cultured from a salt marsh fertilized with mercury-contaminated sewage sludge. Here we report characterization of the mercuric reductase and the narrow-spectrum mercury resistance (mer) operon from one of these strains - T. discolor 9A5. This mer operon, which confers mercury resistance when cloned into Flavobacterium johnsoniae, encodes a novel mercury-responsive ArsR/SmtB family transcriptional regulator that appears to have evolved independently from other mercury-responsive regulators, a novel putative transport protein consisting of a fusion between the integral membrane Hg(II) transporter MerT and the periplasmic Hg(II)-binding protein MerP, an additional MerP protein, and a mercuric reductase that is phylogenetically distinct from other known mercuric reductases.

A thermophilic bacterial origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase

Mercuric reductase (MerA) is central to the mercury (Hg) resistance (mer) system, catalyzing the reduction of ionic Hg to volatile Hg(0). A total of 213 merA homologues were identified in sequence databases, the majority of which belonged to microbial lineages that occupy oxic environments. merA was absent among phototrophs and in lineages that inhabit anoxic environments. Phylogenetic reconstructions of MerA indicate that (i) merA originated in a thermophilic bacterium following the divergence of the Archaea and Bacteria with a subsequent acquisition in Archaea via horizontal gene transfer (HGT), (ii) HGT of merA was rare across phylum boundaries and (iii) MerA from marine bacteria formed distinct and strongly supported lineages. Collectively, these observations suggest that a combination of redox, light and salinity conditions constrain MerA to microbial lineages that occupy environments where the most oxidized and toxic form of Hg, Hg(II), predominates. Further, the taxon-specific distribution of MerA with and without a 70 amino acid N-terminal extension may reflect intracellular levels of thiols. In conclusion, MerA likely evolved following the widespread oxygenation of the biosphere in a thermal environment and its subsequent evolution has been modulated by the interactions of Hg with the intra- and extracellular environment of the organism.