Unraveling the genetic basis of microbial metal resistance: Shift from mendelian to systems biology

Microbial metal resistance, a trait that enables microorganisms to withstand high levels of toxic metals, has been studied for over a century. The significance of uncovering these mechanisms goes beyond basic science as they have implications for human health through their connection to microbial pathogenesis, metal bioremediation, and biomining. Recent advances in analytical chemistry and molecular biology have accelerated the discovery and understanding of genetic mechanisms underlying microbial metal resistance, identifying specific metal resistance genes and their operons. The emergence of omics tools has further propelled research towards a comprehensive understanding of how cells respond to metal stress at the systemic level, revealing the complex regulatory networks and evolutionary dynamics that drive microbial adaptation to metal-rich environments. In this article, we present a historical overview of the evolving understanding of the genetic determinants of metal resistance in microbes. Through multiple narrative threads, we illustrate how our knowledge of microbial metal resistance and genetics has interacted with genetic tools and concept development. This review also discusses how our understanding of microbial metal resistance has progressed from the Mendelian perspective to the current systems biology viewpoint, particularly as omics approaches have considerably enhanced our understanding. This system-level understanding has opened new possibilities for genetically engineered microorganisms to regulate metal homeostasis.

ZntR is a critical regulator for zinc homeostasis and involved in pathogenicity in Riemerella anatipestifer

Zinc (Zn2+) is essential for all bacteria, but excessive Zn2+ levels are toxic. Bacteria maintain zinc homeostasis through regulators, such as Zur, AdcR, and ZntR. Riemerella anatipestifer is a significant Flavobacteriales pathogen causing acute serositis in ducks and other birds. In this study, we identified a homolog of ZntR, a regulator for zinc homeostasis, and demonstrated its contribution to the pathogenicity of R. anatipestifer. Deletion of zntR makes the bacteria hypersensitive to excess Zn2+ but not to other metals like manganese (Mn2+), copper (Cu2+), cobalt (Co2+), and nickel (Ni2+). Deletion of zntR also leads to intracellular zinc accumulation but not of other metals. Additionally, compared to the wild type, the deletion of zntR increases resistance to oxidants hydrogen peroxide (H2O2) and sodium hypochlorite (NaOCl), respectively. The deletion of zntR causes significant changes in transcriptional and protein expression levels, revealing 35 genes with potential zinc metabolism functions. Among them, zupT, which is inhibited by ZntR, is required for zinc transport and resistance to oxidative stress. Finally, deletion of zntR leads to attenuation of colonization in ducklings. In summary, ZntR is a crucial regulator for zinc homeostasis and contributes to the pathogenicity of R. anatipestifer.IMPORTANCEZinc homeostasis plays a critical role in the environmental adaptability of bacteria. Riemerella anatipestifer is a significant pathogen in poultry with the potential to encounter zinc-deficient or zinc-excess environment. The mechanism of zinc homeostasis in this bacterium remains largely unexplored. In this study, we showed that the transcriptional regulator ZntR of R. anatipestifer is critical for zinc homeostasis by altering the transcription and expression of a number of genes. Importantly, ZntR inhibits the transcription of zinc transporter ZupT and contributes to colonization in R. anatipestifer. The results are significant for understanding zinc homeostasis and the pathogenic mechanisms in R. anatipestifer.

Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking

Transition metals function as structural and catalytic cofactors for a large diversity of proteins and enzymes that collectively comprise the metalloproteome. Metallostasis considers all cellular processes, notably metal sensing, metalloproteome remodeling, and trafficking (or allocation) of metals that collectively ensure the functional integrity and adaptability of the metalloproteome. Bacteria employ both protein and RNA-based mechanisms that sense intracellular transition metal bioavailability and orchestrate systems-level outputs that maintain metallostasis. In this review, we contextualize metallostasis by briefly discussing the metalloproteome and specialized roles that metals play in biology. We then offer a comprehensive perspective on the diversity of metalloregulatory proteins and metal-sensing riboswitches, defining general principles within each sensor superfamily that capture how specificity is encoded in the sequence, and how selectivity can be leveraged in downstream synthetic biology and biotechnology applications. This is followed by a discussion of recent work that highlights selected metalloregulatory outputs, including metalloproteome remodeling and metal allocation by metallochaperones to both client proteins and compartments. We close by briefly discussing places where more work is needed to fill in gaps in our understanding of metallostasis.

Characterization of three predicted zinc exporters in Brucella ovis identifies ZntR-ZntA as a powerful zinc and cadmium efflux system not required for virulence and unveils pathogenic Brucellae heterogeneity in zinc homeostasis

Brucella ovis causes non-zoonotic ovine brucellosis of worldwide distribution and is responsible for important economic losses mainly derived from male genital lesions and reproductive fails. Studies about the virulence mechanisms of this rough species (lacking lipopolysaccharide O-chains) are underrepresented when compared to the main zoonotic Brucella species that are smooth (with O-chains). Zinc intoxication constitutes a defense mechanism of the host against bacterial pathogens, which have developed efflux systems to counterbalance toxicity. In this study, we have characterized three potential B. ovis zinc exporters, including the ZntA ortholog previously studied in B. abortus. Despite an in-frame deletion removing 100 amino acids from B. ovis ZntA, the protein retained strong zinc efflux properties. Only indirect evidence suggested a higher exporter activity for B. abortus ZntA, which, together with differences in ZntR-mediated regulation of zntA expression between B. ovis and B. abortus, could contribute to explaining why the ΔzntR mutant of B. abortus is attenuated while that of B. ovis is virulent. Additionally, B. ovis ZntA was revealed as a powerful cadmium exporter contributing to cobalt, copper, and nickel detoxification, properties not previously described for the B. abortus ortholog. Deletion mutants for BOV_0501 and BOV_A1100, also identified as potential zinc exporters and pseudogenes in B. abortus, behaved as the B. ovis parental strain in all tests performed. However, their overexpression in the ΔzntA mutant allowed the detection of discrete zinc and cobalt efflux activity for BOV_0501 and BOV_A1100, respectively. Nevertheless, considering their low expression levels and the stronger activity of ZntA as a zinc and cobalt exporter, the biological role of BOV_0501 and BOV_A1100 is questionable. Results presented in this study evidence heterogeneity among pathogenic Brucellae regarding zinc export and, considering the virulence of B. ovis ΔzntA, suggest that host-mediated zinc intoxication is not a relevant mechanism to control B. ovis infection.

ZntA maintains zinc and cadmium homeostasis and promotes oxidative stress resistance and virulence in Vibrio parahaemolyticus

Although metals are essential for life, they are toxic to bacteria in excessive amounts. Therefore, the maintenance of metal homeostasis is critical for bacterial physiology and pathogenesis. Vibrio parahaemolyticus is a significant food-borne pathogen that mainly causes acute gastroenteritis in humans and acute hepatopancreatic necrosis disease in shrimp. Herein, we report that ZntA functions as a zinc (Zn) and cadmium (Cd) homeostasis mechanism and contributes to oxidative stress resistance and virulence in V. parahaemolyticus. zntA is remarkably induced by Zn, copper, cobalt, nickel (Ni), and Cd, while ZntA promotes V. parahaemolyticus growth under excess Zn/Ni and Cd conditions via maintaining Zn and Cd homeostasis, respectively. The growth of ΔzntA was inhibited under iron (Fe)-restricted conditions, and the inhibition was associated with Zn homeostasis disturbance. Ferrous iron supplementation improved the growth of ΔzntA under excess Zn, Ni or Cd conditions. The resistance of ΔzntA to H2O2-induced oxidative stress also decreased, and its virulence was attenuated in zebrafish models. Quantitative real-time PCR, mutagenesis, and β-galactosidase activity assays revealed that ZntR positively regulates zntA expression by binding to its promoter. Collectively, the ZntR-regulated ZntA is crucial for Zn and Cd homeostasis and contributes to oxidative stress resistance and virulence in V. parahaemolyticus.

New insights into bacterial Zn homeostasis and molecular architecture of the metal resistome in soil polluted with nano zinc oxide

Accumulation of nano ZnO (nZnO) in soils could be toxic to bacterial communities through disruption of Zn homeostasis. Under such conditions, bacterial communities strive to maintain cellular Zn levels by accentuation of appropriate cellular machinery. In this study, soil was exposed to a gradient (50-1000 mg Zn kg-1) of nZnO for evaluating their effects on genes involved in Zn homeostasis (ZHG). The responses were compared with similar levels of its bulk counterpart (bZnO). It was observed that ZnO (as nZnO or bZnO) induced a plethora of influx and efflux transporters as well as metallothioneins (MTs) and metallochaperones mediated by an array of Zn sensitive regulatory proteins. Major influx system identified was the ZnuABC transporter, while important efflux transporters identified were CzcCBA, ZntA, YiiP and the major regulator was Zur. The response of communities was dose- dependent at lower concentrations (<500 mg Zn kg-1 as nZnO or bZnO). However, at 1000 mg Zn kg-1, a size-dependent threshold of gene/gene family abundances was evident. Under nZnO, a poor adaptation to toxicity induced anaerobic conditions due to deployment of major influx and secondary detoxifying systems as well as poor chelation of free Zn ions was evident. Moreover, Zn homeostasis related link with biofilm formation and virulence were accentuated under nZnO than bZnO. While these findings were verified by PCoA and Procrustes analysis, Network analysis and taxa vs ZHG associations also substantiated that a stronger Zn shunting mechanism was induced under nZnO due to higher toxicity. Molecular crosstalks with systems governing Cu and Fe homeostasis were also evident. Expression analysis of important resistance genes by qRT-PCR showed good alignment with the predictive metagenome data, thereby validating our findings. From the study it was evident that the induction of detoxifying and resistant genes was greatly lowered under nZnO, which markedly hampered Zn homeostasis among the soil bacterial communities.

Nano-zinc and plant growth-promoting bacteria is a sustainable alternative for improving productivity and agronomic biofortification of common bean

Background and aims

Nano-zinc (Zn) fertilizer is an easily adaptable and environmentally safe alternative option that can effectively improve growth, yield and biofortification of common bean. Plant growth-promoting bacteria (PGPBs) could promote plant growth and nutrients availability in sustainable manner. Therefore, this study aimed to investigate the influence of foliar nano-Zn application in association with seed co-inoculations of PGPBs on growth, yield, biofortification and Zn use efficiencies in common bean cultivation. Two field experiments were performed with seven co-inoculations of PGPBs and three foliar nano-Zn doses applied 50% at R5 and 50% at R8 stages of common bean to determine plant height, shoot dry matter, grain yield, Zn concentration and uptake in shoot and grains, Zn partitioning index, daily Zn intake and Zn use efficiencies for agronomic biofortification.

Results

The combined foliar nano-Zn application and co-inoculation of R. tropici + B. subtilis enhance grain yield, leaf chlorophyll index, total protein content, grain Zn concentration and uptake, daily Zn intake, Zn use efficiency, applied Zn recovery and Zn utilization efficiency in common beans in 2019 and 2020 cropping seasons. Foliar nano-Zn application at a dose of 1.5 kg ha−1 increased plant height, shoot dry matter, shoot Zn uptake, Zn partitioning and agro-physiological efficiency under co-inoculation with R. tropici + B. subtilis in both cropping years.

Conclusions

The treatments with foliar nano-Zn application at a dose of 1.5 ha−1 and co-inoculation with R. tropici + B. subtilis improved performance, chlorophyll index, protein content, grain yield, and Zn efficiencies that can lead to better biofortification of common bean in tropical savannah. Therefore, it is recommended that applying nano-Zn via foliar along with co-inoculation of PGPBs could be the better option for productivity and biofortification of common bean.

Graphical Abstract

Integrated use of plant growth-promoting bacteria and nano-zinc foliar spray is a sustainable approach for wheat biofortification, yield, and zinc use efficiency

INTRODUCTION AND AIMS

The intensive cropping system and imbalance use of chemical fertilizers to pursue high grain production and feed the fast-growing global population has disturbed agricultural sustainability and nutritional security. Understanding micronutrient fertilizer management especially zinc (Zn) through foliar application is a crucial agronomic approach that could improve agronomic biofortification of staple grain crops. The use of plant growth-promoting bacteria (PGPBs) is considered as one of the sustainable and safe strategies that could improve nutrient acquisition and uptake in edible tissues of wheat to combat Zn malnutrition and hidden hunger in humans. Therefore, the objective of this study was to evaluate the best-performing PGPB inoculants in combination with nano-Zn foliar application on the growth, grain yield, and concentration of Zn in shoots and grains, Zn use efficiencies, and estimated Zn intake under wheat cultivation in the tropical savannah of Brazil.

METHODS

The treatments consisted of four PGPB inoculations (without inoculation, Azospirillum brasilense, Bacillus subtilis, and Pseudomonas fluorescens, applied by seeds) and five Zn doses (0, 0.75, 1.5, 3, and 6 kg ha-1, applied from nano ZnO in two splits by leaf).

RESULTS

Inoculation of B. subtilis and P. fluorescens in combination with 1.5 kg ha-1 foliar nano-Zn fertilization increased the concentration of Zn, nitrogen, and phosphorus in the shoot and grain of wheat in the 2019 and 2020 cropping seasons. Shoot dry matter was increased by 5.3% and 5.4% with the inoculation of P. fluorescens, which was statistically not different from the treatments with inoculation of B. subtilis as compared to control. The grain yield of wheat was increased with increasing nano-Zn foliar application up to 5 kg Zn ha-1 with the inoculation of A. brasilense in 2019, and foliar nano-Zn up to a dose of 1.5 kg ha-1 along with the inoculation of P. fluorescens in the 2020 cropping season. The zinc partitioning index was increased with increasing nano Zn application up to 3 kg ha-1 along with the inoculation of P. fluorescens. Zinc use efficiency and applied Zn recovery were improved at low doses of nano-Zn application in combination with the inoculation of A. brasilense, B. subtilis, and P. fluorescens, respectively, as compared to control.

DISCUSSION

Therefore, inoculation with B. subtilis and P. fluorescens along with foliar nano-Zn application is considered a sustainable and environmentally safe strategy to increase nutrition, growth, productivity, and Zn biofortification of wheat in tropical savannah.

Nanozinc and plant growth-promoting bacteria improve biochemical and metabolic attributes of maize in tropical Cerrado

INTRODUCTION

Plant growth-promoting bacteria (PGPBs) could be developed as a sustainable strategy to promote plant growth and yield to feed the ever-growing global population with nutritious food. Foliar application of nano-zinc oxide (ZnO) is an environmentally safe strategy that alleviates zinc (Zn) malnutrition by improving biochemical attributes and storage proteins of grain.

METHODS

In this context, the current study aimed to investigate the combined effect of seed inoculation with PGPBs and foliar nano-ZnO application on the growth, biochemical attributes, nutrient metabolism, and yield of maize in the tropical savannah of Brazil. The treatments consisted of four PGPB inoculations [i.e., without inoculation, Azospirillum brasilense (A. brasilense), Bacillus subtilis (B. subtilis), Pseudomonas fluorescens (P. fluorescens), which was applied on the seeds] and two doses of Zn (i.e., 0 and 3 kg ha-1, applied from nano-ZnO in two splits on the leaf).

RESULTS

Inoculation of B. subtilis with foliar ZnO application increased shoot dry matter (7.3 and 9.8%) and grain yield (17.1 and 16.7%) in 2019-20 and 2020-2021 crop seasons respectively. Inoculation with A. brasilense increased 100-grains weight by 9.5% in both crop seasons. Shoot Zn accumulation was improved by 30 and 51% with inoculation of P. fluorescens in 2019-20 and 2020-2021 crop seasons. Whereas grain Zn accumulation was improved by 49 and 50.7% with inoculation of B. subtilis and P. fluorescens respectively. In addition, biochemical attributes (chlorophyll a, b and total, carotenoids, total soluble sugar and amino acids) were improved with inoculation of B. subtilis along with foliar nano ZnO application as compared to other treatments. Co-application of P. fluorescens with foliar ZnO improved concentration of grains albumin (20 and 13%) and globulin (39 and 30%). Also, co-application of B. subtilis and foliar ZnO improved concentration of grains glutelin (8.8 and 8.7%) and prolamin (15 and 21%) in first and second seasons.

DISCUSSION

Therefore, inoculation of B. subtilis and P. fluorescens with foliar nano-ZnO application is considered a sustainable and environmentally safe strategy for improving the biochemical, metabolic, nutritional, and productivity attributes of maize in tropical Savannah regions.

Genomic Insights Into Cadmium Resistance of a Newly Isolated, Plasmid-Free Cellulomonas sp. Strain Y8

Our current knowledge on bacterial cadmium (Cd) resistance is mainly based on the functional exploration of specific Cd-resistance genes. In this study, we carried out a genomic study on Cd resistance of a newly isolated Cellulomonas strain with a MIC of 5 mM Cd. Full genome of the strain, with a genome size of 4.47 M bp and GC-content of 75.35%, was obtained through high-quality sequencing. Genome-wide annotations identified 54 heavy metal-related genes. Four potential Cd-resistance genes, namely zntAY8, copAY8, HMTY8, and czcDY8, were subjected to functional exploration. Quantitative PCR determination of in vivo expression showed that zntAY8, copAY8, and HMTY8 were strongly Cd-inducible. Expression of the three inducible genes against time and Cd concentrations were further quantified. It is found that zntAY8 responded more strongly to higher Cd concentrations, while expression of copAY8 and HMTY8 increased over time at lower Cd concentrations. Heterologous expression of the four genes in Cd-sensitive Escherichia coli led to different impacts on hosts’ Cd sorption, with an 87% reduction by zntAY8 and a 3.7-fold increase by HMTY8. In conclusion, a Cd-resistant Cellulomonas sp. strain was isolated, whose genome harbors a diverse panel of metal-resistance genes. Cd resistance in the strain is not controlled by a dedicated gene alone, but by several gene systems collectively whose roles are probably time- and dose-dependent. The plasmid-free, high-GC strain Y8 may provide a platform for exploring heavy metal genomics of the Cellulomonas genus.

An overview of Salmonella enterica metal homeostasis pathways during infection

Nutritional immunity is a powerful strategy at the core of the battlefield between host survival and pathogen proliferation. A host can prevent pathogens from accessing biological metals such as Mg, Fe, Zn, Mn, Cu, Co or Ni, or actively intoxicate them with metal overload. While the importance of metal homeostasis for the enteric pathogen Salmonella enterica Typhimurium was demonstrated many decades ago, inconsistent results across various mouse models, diverse Salmonella genotypes, and differing infection routes challenge aspects of our understanding of this phenomenon. With expanding access to CRISPR-Cas9 for host genome manipulation, it is now pertinent to re-visit past results in the context of specific mouse models, identify gaps and incongruities in current knowledge landscape of Salmonella homeostasis, and recommend a straight path forward towards a more universal understanding of this historic host-microbe relationship.

Isolation and genomic characterization of a pathogenic Providencia rettgeri strain G0519 in turtle Trachemys scripta

Providencia rettgeri infection has occurred occasionally in aquaculture, but is rare in turtles. Here, a pathogenic P. rettgeri strain G0519 was isolated from a diseased slider turtle (Trachemys scripta) in China, and qPCR assay was established for the RTX toxin (rtxD) gene. Histopathological examination showed that many inflammatory cells were infiltrated into heart, liver and intestine, as well as the necrosis of liver, kidney and spleen. The genome consisted of one circular chromosome (4.493 Mb) and one plasmid (18.8 kb), and predicted to contain 4170 and 19 protein-coding genes, respectively. Multiple pathogenic and virulence factors (e.g., fimbria, adhesion, invasion, toxin, hemolysin, chemotaxis, secretion system), multidrug-resistant genes (e.g., ampC, per-1, oxa-1, sul1, tetR) and a novel genomic resistance island PRI519 were identified. Comparative genome analysis revealed the closest relationship was with P. rettgeri, and with P. heimbachae closer than with other Providencia spp. To our knowledge, this was first report on genomic characterization of multidrug-resistant pathogenic P. rettgeri in cultured turtles.

Resistance to Metals Used in Agricultural Production

Metals and metalloids have been used alongside antibiotics in livestock production for a long time. The potential and acute negative impact on the environment and human health of these livestock feed supplements has prompted lawmakers to ban or discourage the use of some or all of these supplements. This article provides an overview of current use in the European Union and the United States, detected metal resistance determinants, and the proteins and mechanisms responsible for conferring copper and zinc resistance in bacteria. A detailed description of the most common copper and zinc metal resistance determinants is given to illustrate not only the potential danger of coselecting antibiotic resistance genes but also the potential to generate bacterial strains with an increased potential to be pathogenic to humans. For example, the presence of a 20-gene copper pathogenicity island is highlighted since bacteria containing this gene cluster could be readily isolated from copper-fed pigs, and many pathogenic strains, including Escherichia coli O104:H4, contain this potential virulence factor, suggesting a potential link between copper supplements in livestock and the evolution of pathogens.

Draft Genome Sequence of Bacillus subtilis 2C-9B, a Strain with Biocontrol Potential against Chili Pepper Root Pathogens and Tolerance to Pb and Zn

Bacillus subtilis 2C-9B, obtained from the rhizosphere of wild grass, exhibits inhibition against root rot causal pathogens in Capsicum annuum, Pb and Zn tolerance, and plant growth promotion in medium supplemented with Pb. The genome of B. subtilis 2C-9B was sequenced and the draft genome assembled, with a length of 4,215,855 bp and 4,723 coding genes.

The structural basis of proton driven zinc transport by ZntB

Zinc is an essential microelement to sustain all forms of life. However, excess of zinc is toxic, therefore dedicated import, export and storage proteins for tight regulation of the zinc concentration have evolved. In Enterobacteriaceae, several membrane transporters are involved in zinc homeostasis and linked to virulence. ZntB has been proposed to play a role in the export of zinc, but the transport mechanism of ZntB is poorly understood and based only on experimental characterization of its distant homologue CorA magnesium channel. Here, we report the cryo-electron microscopy structure of full-length ZntB from Escherichia coli together with the results of isothermal titration calorimetry, and radio-ligand uptake and fluorescent transport assays on ZntB reconstituted into liposomes. Our results show that ZntB mediates Zn²⁺ uptake, stimulated by a pH gradient across the membrane, using a transport mechanism that does not resemble the one proposed for homologous CorA channels.

The bacterial zinc transporter ZntB is important for maintaining zinc homeostasis and is mechanistically not well understood. Here, the authors present the cryo-EM structure of ZntB at 4.2 Å resolution, perform transport assays and propose a model for its Zn²⁺ transport mechanism.

Agrobacterium tumefaciens Zur Regulates the High-Affinity Zinc Uptake System TroCBA and the Putative Metal Chaperone YciC, along with ZinT and ZnuABC, for Survival under Zinc-Limiting Conditions

Agrobacterium tumefaciens has a cluster of genes (Atu3178, Atu3179, and Atu3180) encoding an ABC-type transporter, here named troA, troB, and troC, respectively, which is shown here to be a zinc-specific uptake system. Reverse transcription (RT)-PCR analysis confirmed that troA, troB, and troC are cotranscribed, with troC as the first gene of the operon. The yciC (Atu3181) gene is transcribed in the opposite orientation to that of the troCBA operon and belongs to a metal-binding GTPase family. Expression of troCBA and yciC was inducible under zinc-limiting conditions and was controlled by the zinc uptake regulator, Zur. Compared to the wild type, the mutant strain lacking troC was hypersensitive to a metal chelator, EDTA, and the phenotype could be rescued by the addition of zinc, while the strain with a single yciC mutation showed no phenotype. However, yciC was important for survival under zinc limitation when either troC or zinT was inactivated. The periplasmic zinc-binding protein, ZinT, could not function when TroC was inactivated, suggesting that ZinT may interact with TroCBA in zinc uptake. Unlike many other bacteria, the ABC-type transporter ZnuABC was not the major zinc uptake system in A. tumefaciens However, the important role of A. tumefaciens ZnuABC was revealed when TroCBA was impaired. The strain containing double mutations in the znuA and troC genes exhibited a growth defect in minimal medium. A. tumefaciens requires cooperation of zinc uptake systems and zinc chaperones, including TroCBA, ZnuABC, ZinT, and YciC, for survival under a wide range of zinc-limiting conditions.

IMPORTANCE

Both host and pathogen battle over access to essential metals, including zinc. In low-zinc environments, physiological responses that make it possible to acquire enough zinc are important for bacterial survival and could determine the outcome of host-pathogen interactions. A. tumefaciens was found to operate a novel pathway for zinc uptake in which ZinT functions in concert with the high-affinity zinc importer TroCBA.