MrdH, a novel metal resistance determinant of Pseudomonas putida KT2440, is flanked by metal-inducible mobile genetic elements

Effects of Klebsiella michiganensis LDS17 on Codonopsis pilosula growth, rhizosphere soil enzyme activities, and microflora, and genome-wide analysis of plant growth-promoting genes

Codonopsis pilosula is a perennial herbaceous liana with medicinal value. It is critical to promote Codonopsis pilosula growth through effective and sustainable methods, and the use of plant growth-promoting bacteria (PGPB) is a promising candidate. In this study, we isolated a PGPB, Klebsiella michiganensis LDS17, that produced a highly active 1-aminocyclopropane-1-carboxylate deaminase from the Codonopsis pilosula rhizosphere. The strain exhibited multiple plant growth-promoting properties. The antagonistic activity of strain LDS17 against eight phytopathogenic fungi was investigated, and the results showed that strain LDS17 had obvious antagonistic effects on Rhizoctonia solani, Colletotrichum camelliae, Cytospora chrysosperma, and Phomopsis macrospore with growth inhibition rates of 54.22%, 49.41%, 48.89%, and 41.11%, respectively. Inoculation of strain LDS17 not only significantly increased the growth of Codonopsis pilosula seedlings but also increased the invertase and urease activities, the number of culturable bacteria, actinomycetes, and fungi, as well as the functional diversity of microbial communities in the rhizosphere soil of the seedlings. Heavy metal (HM) resistance tests showed that LDS17 is resistant to copper, zinc, and nickel. Whole-genome analysis of strain LDS17 revealed the genes involved in IAA production, siderophore synthesis, nitrogen fixation, P solubilization, and HM resistance. We further identified a gene (koyR) encoding a plant-responsive LuxR solo in the LDS17 genome. Klebsiella michiganensis LDS17 may therefore be useful in microbial fertilizers for Codonopsis pilosula. The identification of genes related to plant growth and HM resistance provides an important foundation for future analyses of the molecular mechanisms underlying the plant growth promotion and HM resistance of LDS17.

IMPORTANCE

We comprehensively evaluated the plant growth-promoting characteristics and heavy metal (HM) resistance ability of the LDS17 strain, as well as the effects of strain LDS17 inoculation on the Codonopsis pilosula seedling growth and the soil qualities in the Codonopsis pilosula rhizosphere. We conducted whole-genome analysis and identified lots of genes and gene clusters contributing to plant-beneficial functions and HM resistance, which is critical for further elucidating the plant growth-promoting mechanism of strain LDS17 and expanding its application in the development of plant growth-promoting agents used in the environment under HM stress.

Evaluation of Legume-Rhizobial Symbiotic Interactions Beyond Nitrogen Fixation That Help the Host Survival and Diversification in Hostile Environments

Plants often experience unfavorable conditions during their life cycle that impact their growth and sometimes their survival. A temporary phase of such stress, which can result from heavy metals, drought, salinity, or extremes of temperature or pH, can cause mild to enormous damage to the plant depending on its duration and intensity. Besides environmental stress, plants are the target of many microbial pathogens, causing diseases of varying severity. In plants that harbor mutualistic bacteria, stress can affect the symbiotic interaction and its outcome. To achieve the full potential of a symbiotic relationship between the host and rhizobia, it is important that the host plant maintains good growth characteristics and stay healthy under challenging environmental conditions. The host plant cannot provide good accommodation for the symbiont if it is infested with diseases and prone to other predators. Because the bacterium relies on metabolites for survival and multiplication, it is in its best interests to keep the host plant as stress-free as possible and to keep the supply stable. Although plants have developed many mitigation strategies to cope with stress, the symbiotic bacterium has developed the capability to augment the plant's defense mechanisms against environmental stress. They also provide the host with protection against certain diseases. The protective features of rhizobial-host interaction along with nitrogen fixation appear to have played a significant role in legume diversification. When considering a legume-rhizobial symbiosis, extra benefits to the host are sometimes overlooked in favor of the symbionts' nitrogen fixation efficiency. This review examines all of those additional considerations of a symbiotic interaction that enable the host to withstand a wide range of stresses, enabling plant survival under hostile regimes. In addition, the review focuses on the rhizosphere microbiome, which has emerged as a strong pillar of evolutionary reserve to equip the symbiotic interaction in the interests of both the rhizobia and host. The evaluation would draw the researchers' attention to the symbiotic relationship as being advantageous to the host plant as a whole and the role it plays in the plant's adaptation to unfavorable environmental conditions.

A halophilic Chromohalobacter species from estuarine coastal waters as a detoxifier of manganese, as well as a novel bio-catalyst for synthesis of n-butyl acetate

Anthropogenic pollution due to ferro-manganese ore transport by barges through the Mandovi estuary in Goa, India is a major environmental concern. In this study a manganese (Mn) tolerant, moderately halophilic Chromohalobacter sp. belonging to the family Halomonadaceae was isolated from the sediments of a solar saltern adjacent to this Mandovi estuary. Using techniques of Atomic absorption spectroscopy, Scanning electron microscopy-Energy dispersive X-ray spectroscopy, Fourier-transform infrared spectroscopy and Atomic Force Microscopy, the Chromohalobacter sp. was explored for its ability to tolerate and immobilize Mn in amended and unamended media with 20% natural salt concentration (w/v). In aqueous media supplemented with 0.1 mM Mn, the Chromohalobacter sp. was capable of sequestering up to 76% Mn with an average immobilization rate of 8 mg Mn /g /day. Growth rate kinetic analysis using Gompertz mathematical functions was found to model the experimental data well. The model inferred that the maximum growth rate of Chromohalobacter sp. was at 10% natural salt concentration (w/v). The Chromohalobacter sp. was further found to be multimetal tolerant showing high tolerance to Iron (Fe), Nickel (Ni) and Cobalt (Co), (each at 4 mM), and tolerated Manganese (Mn) up to 6 mM. Morphologically, the Chromohalobacter sp. was a non-spore forming, Gram negative motile rod (0.726 μ× 1.33 μ). The adaptative mechanism of Chromohalobacter sp. to elevated Mn concentrations (1 mM) resulted in the reduction of its cell size to 0.339 μ× 0.997 μ and the synthesis of an extracellular slime, immobilizing Mn from the liquid phase forming Manganese oxide, as confirmed by Scanning Electron Microscopy. The expression of Mnx genes for manganese oxidation further substantiated the finding. This bacterial synthesized manganese oxide also displayed catalytic activity (∼50% conversion) for the esterification of butan-1-ol with CH₃COOH to yield n-butyl acetate. This Chromohalobacter sp. being indigenous to marine salterns, has adapted to high concentrations of heavy metals and high salinities and can withstand this extremely stressed environment, and thus holds a tremendous potential as an environmentally friendly "green bioremediator" of Mn from euryhaline environments. The study also adds to the limited knowledge about metal-microbe interactions in extreme environments. Further, since Chromohalobacter sp. exhibits commendable catalytic activity for the synthesis of n-butyl acetate, it would have several potential industrial applications.

The MreA Metal-Binding Sites C40, H65, and C69 Play a Critical Role in the Metal Tolerance of Pseudomonas putida KT2440

Metal-binding proteins occur in the cytosol of most eubacteria. The hypothetical metal responsive protein MreA (PP-2969 gene; NreA) seems responsible for zinc, chromium, cadmium accumulation, and metal ion homeostasis. However, there is a lack of definitive evidence regarding the specific metal-binding sites of MreA protein. The present study aimed to identify putative metal-binding regions for MreA. In silico analysis revealed that amino acids C40, H65, and C69 (CHC region) seem critical for metal-protein interactions. We created site-directed mutants (SDM's) of MreA for interacted amino acids to validate in silico results. The differential scanning fluorimetry (DSF) and atomic absorption spectroscopy (AAS) showed that SDM strains of MreA protein curtailed metal accumulation compared to the wild types indicating C40, H65, and C69 amino acids are critical for metal binding. Thus, we report potential implications for MreA-bioengineered strains of Pseudomonas putida KT2440 for metal ion homeostasis by alleviating metal toxicity in the biological environment.

The Combined Effect of Pseudomonas stutzeri and Biochar on the Growth Dynamics and Tolerance of Lettuce Plants (Lactuca sativa) to Cadmium Stress

Agricultural activities lead to the accumulation of cadmium (Cd) in the soil. It is necessary to identify effective and economical ways to reduce the soil Cd bioavailability. To achieve this, three bacterial strains, Pseudomonas stutzeri, P. koreensis, and P. fluorescens, were tested for tolerance and biosorption of different concentrations of Cd (0, 5, 10, 15, 20, and 25 mg L−1). During the 2020 and 2021 seasons, a pot experiment was conducted using four different soil amendments (control, biochar, P. stutzeri, and a combination) under four levels of Cd (0, 40, 80, and 120 mg kg−1) and assessing the effect on growth parameters, physiological modifications, antioxidant enzymes, and Cd accumulation in lettuce plants (Lactuca sativa cv. Balady). In vitro, the results showed that P. stutzeri was the most tolerant of Cd. Our findings in pot trials showed that T4 (biochar + P. stutzeri) was a more efficient treatment in terms of the growth parameters, with 452.00 g plant−1 was recorded for fresh weight, 40.10 g plant−1 for dry weight, 18.89 cm plant−1 for plant height, 6.03 cm2 for leaf area, and 20.48 for the number of leaves plant−1, while in terms of physiological characteristics, we recorded 1.29 mg g−1 FW, 0.35 μg g−1 FW, and 3.69 μg g−1 FW for total chlorophyll, carotenoids, and total soluble sugar, respectively; this was also reflected in the number of antioxidant enzymes and intensity of soil biological activities in soil treated with 120 mg kg−1 Cd compared with the control and other treatments in the first season. A similar trend was observed in the second season. Additionally, significantly lower Cd was observed in both the root (67%) and shoots (78%). Therefore, a combined application of biochar and P. stutzeri could be used as an alternative to mitigate Cd toxicity.

Diversity of metal and antibiotic resistance genes in Enterococcus spp. from the last century reflects multiple pollution and genetic exchange among phyla from overlapping ecosystems

Arsenic (As), mercury (Hg), and copper (Cu) are among the major historical and contemporary metal pollutants linked to global anthropogenic activities. Enterococcus have been considered indicators of fecal pollution and antibiotic resistance for years, but its largely underexplored metallome precludes understanding their role as metal pollution bioindicators as well. Our goal was to determine the occurrence, diversity, and phenotypes associated with known acquired genes/operons conferring tolerance to As, Hg or Cu among Enterococcus and to identify their genetic context (381 field isolates from diverse epidemiological and genetic backgrounds; 3547 enterococcal genomes available in databases representing a time span during 1900-2019). Genes conferring tolerance to As (arsA), Hg (merA) or Cu (tcrB) were used as biomarkers of widespread metal tolerance operons. Different variants of metal tolerance (MeT) genes (13 arsA, 6 merA, 1 tcrB) were more commonly recovered from the food-chain (arsA, tcrB) or humans (merA), and were shared with 49 other bacterial taxa. Comparative genomics analysis revealed that MeT genes occurred in heterogeneous operons, at least since the 1900s, with an increasing accretion of antibiotic resistance genes since the 1960's, reflecting diverse antimicrobial pollution. Multiple MeT genes were co-located on the chromosome or conjugative plasmids flanked by elements with high potential for recombination, often along with antibiotic resistance genes. Phenotypic analysis of some isolates carrying MeT genes revealed up to 128× fold increase in the minimum inhibitory concentrations to metals. The main distribution of functional MeT genes among Enterococcus faecium and Enterococcus faecalis from different sources, time spans, and clonal lineages, and their ability to acquire diverse genes from multiple taxa bacterial communities places these species as good candidates to be used as model organisms in future projects aiming at the identification and quantification of bioindicators of metal polluted environments by anthropogenic activities.

Rhizospheric Communication through Mobile Genetic Element Transfers for the Regulation of Microbe-Plant Interactions

Simple Summary

Rhizosphere, where microbes and plants coexist, is a hotspot of mobile genetic element (MGE) transfers. It was suggested that ancient MGE transfers drove the evolution of both microbes and plants. On the other hand, recurrent MGE transfers regulate microbe-plant interaction and the adaptation of microbes and plants to the environment. The studies of MGE transfers in the rhizosphere provide useful information for the research on pathogenic/ beneficial microbe-plant interaction. In addition, MGE transfers between microbes and the influence by plant root exudates on such transfers provide useful information for the research on bioremediation.

Abstract

The transfer of mobile genetic elements (MGEs) has been known as a strategy adopted by organisms for survival and adaptation to the environment. The rhizosphere, where microbes and plants coexist, is a hotspot of MGE transfers. In this review, we discuss the classic mechanisms as well as novel mechanisms of MGE transfers in the rhizosphere. Both intra-kingdom and cross-kingdom MGE transfers will be addressed. MGE transfers could be ancient events which drove evolution or recurrent events which regulate adaptations. Recent findings on MGE transfers between plant and its interacting microbes suggest gene regulations brought forth by such transfers for symbiosis or defense mechanisms. In the natural environment, factors such as temperature and soil composition constantly influence the interactions among different parties in the rhizosphere. In this review, we will also address the effects of various environmental factors on MGE transfers in the rhizosphere. Besides environmental factors, plant root exudates also play a role in the regulation of MGE transfer among microbes in the rhizosphere. The potential use of microbes and plants for bioremediation will be discussed.

Antibiotic-Selected Gene Amplification Heightens Metal Resistance

The increasing frequency of antibiotic resistance poses myriad challenges to modern medicine. Environmental survival of multidrug-resistant bacteria in health care facilities, including hospitals, creates reservoirs for transmission of these difficult to treat pathogens. To prevent bacterial colonization, these facilities deploy an array of infection control measures, including bactericidal metals on surfaces, as well as implanted devices. Although antibiotics are routinely used in these health care environments, it is unknown whether and how antibiotic exposure affects metal resistance. We identified a multidrug-resistant Enterobacter clinical isolate that displayed heteroresistance to the antibiotic colistin, where only a minor fraction of cells within the population resist the drug. When this isolate was grown in the presence of colistin, a 9-kb DNA region was duplicated in the surviving resistant subpopulation, but surprisingly, was not required for colistin heteroresistance. Instead, the amplified region included a three-gene locus (ncrABC) that conferred resistance to the bactericidal metal, nickel. ncrABC expression alone was sufficient to confer nickel resistance to E. coli K-12. Due to its selection for the colistin-resistant subpopulation harboring the duplicated 9-kb region that includes ncrABC, colistin treatment led to enhanced nickel resistance. Taken together, these data suggest that the use of antibiotics may inadvertently promote enhanced resistance to antimicrobial metals, with potentially profound implications for bacterial colonization and transmission in the health care environment.

Chromate detoxification potential of Staphylococcus sp. isolates from an estuary

Chromium (Cr) pollution is an emerging environmental problem. The present study was carried out to isolate Cr-resistant bacteria and characterize their Cr detoxification and resistance ability. Bacteria screened by exposure to chromate (Cr⁶⁺) were isolated from Mandovi estuary Goa, India. Two isolates expressed high resistance to Cr⁶⁺ (MIC ≥ 300 µg mL^-1), Cr³⁺ (MIC ≥ 900 µg mL^-1), other toxic heavy metals and displayed a pattern of resistance to cephalosporins and ß-lactams. Biochemical and 16 S rRNA gene sequence analysis indicated that both isolates tested belonged to the Staphylococcus genus and were closely related to S. saprophyticus and S. arlettae. Designated as strains NIOER176 and NIOER324, batch experiments demonstrated that both removed 100% of 20 and 50 µg mL^-1 Cr⁶⁺ within 4 and 10 days, respectively. The rate of reduction in both peaked at 0.260 µg mL^-1 h^-1. ATP-binding cassette (ABC) transporter gene involved in transport of a variety of substrates including efflux of toxicants was present in strain NIOER176. Through SDS-PAGE analysis, whole-cell proteins extracted from both strains indicated chromium-induced specific induction and up-regulation of 24 and 40 kDa proteins. Since bacterial ability to ameliorate Cr⁶⁺ is of practical significance, these findings demonstrate strong potential of some estuarine bacteria to detoxify Cr⁶⁺ even when its concentrations far exceed the concentrations reported from many hazardous effluents and chromium contaminated natural habitats. Such potential of salt tolerant bacteria would help in Cr⁶⁺ bioremediation efforts.

A plasmid-encoded mobile genetic element from Pseudomonas aeruginosa that confers heavy metal resistance and virulence

Mobile plasmid-encoded elements are DNA segments that are transferred for horizontal gene transfer and that confer adaptive proprieties, as well as virulence and antibiotic and heavy metal resistance to bacteria. The conjugative plasmid pUM505, isolated from a clinical strain of Pseudomonas aeruginosa, possesses a putative 31.292 kb mobile element (denominated Mpe: Mobile plasmid- encoded element) that, in addition to possessing chr genes that confer chromate resistance to Pseudomonas, contains two putative mer operons that could confer mercury resistance. Moreover, the Mpe contains genes related previously with the virulence of both P. aeruginosa and Escherichia coli strains. In this work, we determined that Mpe from pUM505 was able to independently move to another DNA molecule, conferring chromate and mercury resistance to P. aeruginosa PAO1 and mercury resistance to E. coli JM101, suggesting that its transference might be beneficial to bacteria under certain environmental conditions. Additionally, the transference of Mpe increased the virulence of P. aeruginosa PAO1 against the nematode Caenorhabditis elegans, suggesting its contribution to the pathogenicity of P. aeruginosa. In this work, we describe a new mobile plasmid-encoded element that possesses the potential to be transferred by horizontal gene transference, which could provide bacteria with a wide variety of adaptive traits such as heavy metal resistance and virulence, which can be selective factors for the distribution and prevalence of this plasmid in diverse environments, including hospitals and heavy metal contaminated soils.

Pb2+ tolerance by Frankia sp. strain EAN1pec involves surface-binding

Several Frankia strains have been shown to be lead-resistant. The mechanism of lead resistance was investigated for Frankia sp. strain EAN1pec. Analysis of the cultures by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDAX) and Fourier transforming infrared spectroscopy (FTIR) demonstrated that Frankia sp. strain EAN1pec undergoes surface modifications and binds high quantities of Pb+2. Both labelled and unlabelled shotgun proteomics approaches were used to determine changes in Frankia sp. strain EAN1pec protein expression in response to lead and zinc. Pb2+ specifically induced changes in exopolysaccharides, the stringent response, and the phosphate (pho) regulon. Two metal transporters (a Cu2+-ATPase and cation diffusion facilitator), as well as several hypothetical transporters, were also upregulated and may be involved in metal export. The exported Pb2+ may be precipitated at the cell surface by an upregulated polyphosphate kinase, undecaprenyl diphosphate synthase and inorganic diphosphatase. A variety of metal chaperones for ensuring correct cofactor placement were also upregulated with both Pb+2 and Zn+2 stress. Thus, this Pb+2 resistance mechanism is similar to other characterized systems. The cumulative interplay of these many mechanisms may explain the extraordinary resilience of Frankia sp. strain EAN1pec to Pb+2. A potential transcription factor (DUF156) binding site was identified in association with several proteins identified as upregulated with heavy metals. This site was also discovered, for the first time, in thousands of other organisms across two kingdoms.

Zinc-Induced Transposition of Insertion Sequence Elements Contributes to Increased Adaptability of Cupriavidus metallidurans

Bacteria can respond to adverse environments by increasing their genomic variability and subsequently facilitating adaptive evolution. To demonstrate this, the contribution of Insertion Sequence (IS) elements to the genetic adaptation of Cupriavidus metallidurans AE126 to toxic zinc concentrations was determined. This derivative of type strain CH34, devoid of its main zinc resistance determinant, is still able to increase its zinc resistance level. Specifically, upon plating on medium supplemented with a toxic zinc concentration, resistant variants arose in which a compromised cnrYX regulatory locus caused derepression of CnrH sigma factor activity and concomitant induction of the corresponding RND-driven cnrCBA efflux system. Late-occurring zinc resistant variants likely arose in response to the selective conditions, as they were enriched in cnrYX disruptions caused by specific IS elements whose transposase expression was found to be zinc-responsive. Interestingly, deletion of cnrH, and consequently the CnrH-dependent adaptation potential, still enabled adaptation by transposition of IS elements (ISRme5 and IS1086) that provided outward-directed promoters driving cnrCBAT transcription. Finally, adaptation to zinc by IS reshuffling can also enhance the adaptation to subsequent environmental challenges. Thus, transposition of IS elements can be induced by stress conditions and play a multifaceted, pivotal role in the adaptation to these and subsequent stress conditions.

Lead resistance in micro-organisms

Lead (Pb) is an element present in the environment that negatively affects all living organisms. To diminish its high toxicity, micro-organisms have developed several mechanisms that allow them to survive exposure to Pb(II). The main mechanisms of lead resistance involve adsorption by extracellular polysaccharides, cell exclusion, sequestration as insoluble phosphates, and ion efflux to the cell exterior. This review describes the various lead resistance mechanisms, and the regulation of their expression by lead binding regulatory proteins. Special attention is given to the Pbr system from Cupriavidus metallidurans CH34, which involves a unique mechanism combining efflux and lead precipitation.

Two RND proteins involved in heavy metal efflux in Caulobacter crescentus belong to separate clusters within proteobacteria

Background

Heavy metal Resistance-Nodulation-Division (HME-RND) efflux systems help Gram-negative bacteria to keep the intracellular homeostasis under high metal concentrations. These proteins constitute the cytoplasmic membrane channel of the tripartite RND transport systems. Caulobacter crescentus NA1000 possess two HME-RND proteins, and the aim of this work was to determine their involvement in the response to cadmium, zinc, cobalt and nickel, and to analyze the phylogenetic distribution and characteristic signatures of orthologs of these two proteins.

Results

Expression assays of the czrCBA operon showed significant induction in the presence of cadmium and zinc, and moderate induction by cobalt and nickel. The nczCBA operon is highly induced in the presence of nickel and cobalt, moderately induced by zinc and not induced by cadmium. Analysis of the resistance phenotype of mutant strains showed that the ΔczrA strain is highly sensitive to cadmium, zinc and cobalt, but resistant to nickel. The ΔnczA strain and the double mutant strain showed reduced growth in the presence of all metals tested. Phylogenetic analysis of the C. crescentus HME-RND proteins showed that CzrA-like proteins, in contrast to those similar to NczA, are almost exclusively found in the Alphaproteobacteria group, and the characteristic protein signatures of each group were highlighted.

Conclusions

The czrCBA efflux system is involved mainly in response to cadmium and zinc with a secondary role in response to cobalt. The nczCBA efflux system is involved mainly in response to nickel and cobalt, with a secondary role in response to cadmium and zinc. CzrA belongs to the HME2 subfamily, which is almost exclusively found in the Alphaproteobacteria group, as shown by phylogenetic analysis. NczA belongs to the HME1 subfamily which is more widespread among diverse Proteobacteria groups. Each of these subfamilies present distinctive amino acid signatures.

Metal accumulation in cell wall: a possible mechanism of cadmium resistance by Pseudomonas stutzeri

A heavy metal resistant strain, Pseudomonas stutzeri (MTCC 101) has been investigated for its cadmium tolerance properties along with its antibiotic resistance. The organism could tolerate cadmium up to 1,200 μg/mL with LD50 value 700 μg/mL. The gene(s) involved in such high resistance appear(s) to be induced in the presence of the metal. Increasing concentrations of cadmium successively prolonged the lag phase of growth with delayed attainment of the stationary phase. Transmission electron microscope and scanning electron microscope-energy dispersive analysis of X-ray spectroscope analysis showed cadmium adsorption on the bacterial surface with morphological distortion. Atomic absorption spectrometric study corroborated this data, showing highest cadmium accumulation in the cell wall fraction of the bacteria. Additionally, the cell wall fraction showed synthesis of new proteins when grown under metal stress.

Recruitment and rearrangement of three different genetic determinants into a conjugative plasmid increase copper resistance in Pseudomonas syringae

We describe the genetic organization of a copper-resistant plasmid containing copG and cusCBA genes in the plant pathogen Pseudomonas syringae. Chromosomal variants of czcCBA and a plasmid variant of cusCBA were present in different P. syringae pathovar strains. Transformation of the copper-sensitive Pseudomonas syringae pv. syringae FF5 strain with copG or cusCBA conferred copper resistance, and quantitative real-time PCR (qRT-PCR) experiments confirmed their induction by copper.

Specific metal recognition in nickel trafficking

Nickel is an essential metal for a number of bacterial species that have developed systems for acquiring, delivering, and incorporating the metal into target enzymes and controlling the levels of nickel in cells to prevent toxic effects. As with other transition metals, these trafficking systems must be able to distinguish between the desired metal and other transition metal ions with similar physical and chemical properties. Because there are few enzymes (targets) that require nickel for activity (e.g., Escherichia coli transports nickel for hydrogenases made under anaerobic conditions, and Helicobacter pylori requires nickel for hydrogenase and urease that are essential for acid viability), the "traffic pattern" for nickel is relatively simple, and nickel trafficking therefore presents an opportunity to examine a system for the mechanisms that are used to distinguish nickel from other metals. In this review, we describe the details known for examples of uptake permeases, metallochaperones and proteins involved in metallocenter assembly, and nickel metalloregulators. We also illustrate a variety of mechanisms, including molecular recognition in the case of NikA protein and examples of allosteric regulation for HypA, NikR, and RcnR, employed to generate specific biological responses to nickel ions.

RcnB is a periplasmic protein essential for maintaining intracellular Ni and Co concentrations in Escherichia coli

Nickel and cobalt are both essential trace elements that are toxic when present in excess. The main resistance mechanism that bacteria use to overcome this toxicity is the efflux of these cations out of the cytoplasm. RND (resistance-nodulation-cell division)- and MFS (major facilitator superfamily)-type efflux systems are known to export either nickel or cobalt. The RcnA efflux pump, which belongs to a unique family, is responsible for the detoxification of Ni and Co in Escherichia coli. In this work, the role of the gene yohN, which is located downstream of rcnA, is investigated. yohN is cotranscribed with rcnA, and its expression is induced by Ni and Co. Surprisingly, in contrast to the effect of deleting rcnA, deletion of yohN conferred enhanced resistance to Ni and Co in E. coli, accompanied by decreased metal accumulation. We show that YohN is localized to the periplasm and does not bind Ni or Co ions directly. Physiological and genetic experiments demonstrate that YohN is not involved in Ni import. YohN is conserved among proteobacteria and belongs to a new family of proteins; consequently, yohN has been renamed rcnB. We show that the enhanced resistance of rcnB mutants to Ni and Co and their decreased Ni and Co intracellular accumulation are linked to the greater efflux of these ions in the absence of rcnB. Taken together, these results suggest that RcnB is required to maintain metal ion homeostasis, in conjunction with the efflux pump RcnA, presumably by modulating RcnA-mediated export of Ni and Co to avoid excess efflux of Ni and Co ions via an unknown novel mechanism.

Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida

Pseudomonas putida is a gram-negative rod-shaped gammaproteobacterium that is found throughout various environments. Members of the species P. putida show a diverse spectrum of metabolic activities, which is indicative of their adaptation to various niches, which includes the ability to live in soils and sediments contaminated with high concentrations of heavy metals and organic contaminants. Pseudomonas putida strains are also found as plant growth-promoting rhizospheric and endophytic bacteria. The genome sequences of several P. putida species have become available and provide a unique tool to study the specific niche adaptation of the various P. putida strains. In this review, we compare the genomes of four P. putida strains: the rhizospheric strain KT2440, the endophytic strain W619, the aromatic hydrocarbon-degrading strain F1 and the manganese-oxidizing strain GB-1. Comparative genomics provided a powerful tool to gain new insights into the adaptation of P. putida to specific lifestyles and environmental niches, and clearly demonstrated that horizontal gene transfer played a key role in this adaptation process, as many of the niche-specific functions were found to be encoded on clearly defined genomic islands.

Identification of the transcriptional regulator NcrB in the nickel resistance determinant of Leptospirillum ferriphilum UBK03

The nickel resistance determinant ncrABCY was identified in Leptospirillum ferriphilum UBK03. Within this operon, ncrA and ncrC encode two membrane proteins that form an efflux system, and ncrB encodes NcrB, which belongs to an uncharacterized family (DUF156) of proteins. How this determinant is regulated remains unknown. Our data indicate that expression of the nickel resistance determinant is induced by nickel. The promoter of ncrA, designated pncrA, was cloned into the promoter probe vector pPR9TT, and co-transformed with either a wild-type or mutant nickel resistance determinant. The results revealed that ncrB encoded a transcriptional regulator that could regulate the expression of ncrA, ncrB, and ncrC. A GC-rich inverted repeat sequence was identified in the promoter pncrA. Electrophoretic mobility shift assays (EMSAs) and footprinting assays showed that purified NcrB could specifically bind to the inverted repeat sequence of pncrA in vitro; this was confirmed by bacterial one-hybrid analysis. Moreover, this binding was inhibited in the presence of nickel ions. Thus, we classified NcrB as a transcriptional regulator that recognizes the inverted repeat sequence binding motif to regulate the expression of the key nickel resistance gene, ncrA.

The Escherichia coli metallo-regulator RcnR represses rcnA and rcnR transcription through binding on a shared operator site: Insights into regulatory specificity towards nickel and cobalt

RcnA is an efflux pump responsible for Ni and Co detoxification in Escherichia coli. The expression of rcnA is induced by Ni and Co via the metallo-regulator RcnR. In the present work, the functioning of the promoter-operator region of rcnR and rcnA was investigated using primer extension and DNAse I footprinting experiments. We show that the promoters of rcnR and rcnA are convergent and that apo-RcnR binds on symmetrically located sequences in this intergenic region. Moreover, RcnR DNA binding is specifically modulated by one Ni or Co equivalent and not by other metals. In addition to rcnA, RcnR controls expression of its own gene in response to Ni and Co, but the two genes are differentially expressed.