Phylogenetic analysis of the chromate ion transporter (CHR) superfamily

A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas

Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.

Genome analysis of Shewanella putrefaciens 4H revealing the potential mechanisms for the chromium remediation

Microbial remediation of heavy metal polluted environment is ecofriendly and cost effective. Therefore, in the present study, Shewanella putrefaciens stain 4H was previously isolated by our group from the activated sludge of secondary sedimentation tank in a dyeing wastewater treatment plant. The bacterium was able to reduce chromate effectively. The strains showed significant ability to reduce Cr(VI) in the pH range of 8.0 to 10.0 (optimum pH 9.0) and 25-42 ℃ (optimum 30 ℃) and were able to reduce 300 mg/L of Cr(VI) in 72 h under parthenogenetic anaerobic conditions. In this paper, the complete genome sequence was obtained by Nanopore sequencing technology and analyzed chromium metabolism-related genes by comparative genomics The genomic sequence of S. putrefaciens 4H has a length of 4,631,110 bp with a G + C content of 44.66% and contains 4015 protein-coding genes and 3223,  2414, 2343 genes were correspondingly annotated into the COG, KEGG, and GO databases. The qRT-PCR analysis showed that the expression of chrA, mtrC, and undA genes was up-regulated under Cr(VI) stress. This study explores the Chromium Metabolism-Related Genes of S. putrefaciens 4H and will help to deepen our understanding of the mechanisms of Cr(VI) tolerance and reduction in this strain, thus contributing to the better application of S. putrefaciens 4H in the field of remediation of chromium-contaminated environments.

Implantation of Bacillus pseudomycoides Chromate Transporter Increases Chromate Tolerance in Bacillus subtilis

Chromium of anthropogenic origin contaminates the environment worldwide. The toxicity of chromium, a group I human carcinogen, is greatest when it is in a hexavalent oxidation state, Cr(VI). Cr(VI) is actively transported into the cell, triggering oxidative damage intracellularly. Due to the abundance of unspecific intracellular reductants, any microbial species is capable of bio-transformation of toxic Cr(VI) to innocuous Cr(III), however, this process is often lethal. Only some bacterial species are capable of sustaining the vegetative growth in the presence of a high concentration of Cr(VI) and thus operate as self-sustainable bioremediation agents. One of the successful microbial Cr(VI) detoxification strategies is the activation of chromate efflux pumps. This work describes transplantation of the chromate efflux pump from the potentially pathogenic but highly Cr resistant Bacillus pseudomycoides environmental strain into non-pathogenic but only transiently Cr tolerant Bacillus subtilis strain. In our study, we compared the two Bacillus spp. strains harboring evolutionarily diverged chromate efflux proteins. We have found that individual cells of the Cr-resistant B. pseudomycoides environmental strain accumulate less Cr than the cells of B. subtilis strain. Further, we found that survival of the B. subtilis strain during the Cr stress can be increased by the introduction of the chromate transporter from the Cr resistant environmental strain into its genome. Additionally, the expression of B. pseudomycoides chromate transporter ChrA in B. subtilis seems to be activated by the presence of chromate, hinting at versatility of Cr-efflux proteins. This study outlines the future direction for increasing the Cr-tolerance of non-pathogenic species and safe bioremediation using soil bacteria.

Exploring the Cr(VI) removal mechanism of Sporosarcina saromensis M52 from a genomic perspective

Serious hexavalent chromium [Cr(VI)] pollution has continuously threatened ecological security and public health. Microorganism-assisted remediation technology has strong potential in the treatment of environmental Cr(VI) pollution due to its advantages of high efficiency, low cost, and low secondary pollution. Sporosarcina saromensis M52, a strain with strong Cr(VI) removal ability, isolated from coastal intertidal zone was used in this study. Scanning electron microscopy coupled with energy dispersive X-ray analysis indicated M52 was relatively stable under Cr(VI) stress and trace amount of Cr deposited on the cell surface. X-ray photoelectron spectroscopy and X-ray diffraction analyses exhibited M52 could reduce Cr(VI) into Cr(III). Fourier transform infrared spectroscopy showed the bacterial surface was mainly consisted of polysaccharides, phosphate groups, carboxyl groups, amide II (NH/CN) groups, alkyl groups, and hydroxyl groups, while functional groups involving in Cr(VI) bio-reduction were not detected. According to these characterization analyses, the removal of Cr(VI) was primarily depended on bio-reduction, instead of bio-adsorption by M52. Genome analyses further indicated the probable mechanisms of bio-reduction, including the active efflux of Cr(VI) by chromate transporter ChrA, enzymatic redox reactions mediated by reductases, DNA-repaired proteases ability to minimize the ROS damage, and the formation of specific cell components to minimize the biofilm injuries caused by Cr(VI). These studies provided a theoretical basis which was useful for Cr(VI) remediation, especially in terms of increasing its effectiveness. THE MAIN FINDING OF THE WORK: M52 realized the bioremediation of Cr(VI) majorly through bio-reduction, including Cr(VI) efflux, chromate reduction, DNA repair, and the formation of specific cell components, instead of bio-adsorption.

Mechanism of Cr(VI) reduction by Lysinibacillus sp. HST-98, a newly isolated Cr (VI)-reducing strain

Facing the increasingly severe Cr(VI) pollution, bioreduction has proved to be an eco-friendly remediation method. An isolated strain identified as Lysinibacillus can relatively reduce Cr(VI) well. Even if the concentration of Cr(VI) increased to 250mg/L, the strain HST-98 could also grow and remove Cr(VI) well. After optimization of reaction conditions, the optimal pH, temperature, and electron donor are 8~9, 36°C, and sodium lactate, respectively. Coexisting metal ions such as Cu2+, Co2+, and Mn2+ are beneficial to reduce Cr(VI), while Zn2+, Ni2+, and Cd2+ are just the opposite. What is more, the mechanism of the reduction by the strain HST-98 is chiefly mediated by intracellular enzymes. After gene sequence homology blast and analysis, the genes and enzymes related to chromium metabolism in strain HST-98 have been annotated, which helps us to further understand the reduction mechanism of the strain HST-98. In general, Lysinibacillus sp. HST-98 is a potential candidate to repair the Cr(VI)-contaminated sites.

Draft Genome Sequence of Bacillus cereus TN10, a Chromium-Resistant and -Reducing Strain Isolated from Tannery Effluent

Here, we present the draft genome sequence of Bacillus cereus strain TN10, which exhibited chromium resistance and chromium-reducing ability. The whole-genome sequence analysis of strain TN10 will help us to understand its genetic factors involved in the bioremediation of Cr⁶⁺.

Here, we present the draft genome sequence of Bacillus cereus strain TN10, which exhibited chromium resistance and chromium-reducing ability. The whole-genome sequence analysis of strain TN10 will help us to understand its genetic factors involved in the bioremediation of Cr⁶⁺.

Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil

Background

Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems.

Results

The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424^T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni²⁺ and Zn²⁺ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance.

Conclusions

STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.

Hexavalent chromium stress response, reduction capability and bioremediation potential of Trichoderma sp. isolated from electroplating wastewater

In the present study we are investigating the Cr_(VI) reduction potential of a multi-metal tolerant fungus (isolate CR700); isolated from electroplating wastewater. Based on the ITS region sequencing, the isolate was identified as Trichoderma lixii isolate CR700 and able to tolerate As(2000 mg/L), Ni(1500 mg/L), Zn(1200 mg/L), Cu(1200 mg/L), Cr(1000 mg/L), and 100 mg/L of Pb and Cd evident from tolerance assay. Cr_(VI) reduction experiment was conducted in Erlenmeyer flasks containing different concentration of Cr_(VI) (0-200 mg/L) amended potato dextrose broth medium followed by inoculating with a disk (0.5 cm diameter) of 7 days grown isolate CR700, and achieved a maximum of 99.4% within 120 h at 50 mg/L of Cr_(VI). However, the accumulation of total Cr by isolate CR700 was 2.12 ± 0.15 mg/g of dried biomass at the same concentration after 144 h of exposure. Isolate CR700 showed the capability to reduce Cr_(VI) at different physicochemical stress conditions such as pH, temperature, heavy metals, metabolic inhibitor and also in tannery wastewater. Fungus exhibited multifarious morphological and biochemical response under the exposure of Cr_(VI); the scanning electron microscopic analysis revealed that Cr_(VI) treated mycelia of isolate CR700 comparatively irregular, aggregated and swelled than without treated mycelia which might be due to the tolerance mechanism and vacuolar compartmentation of chromium. Moreover, energy dispersive spectroscopy and x-ray photoelectron spectroscopic analysis exposed the Cr_(III) precipitation on the mycelia surface of isolate CR700 and Fourier-transform infrared spectroscopic analysis suggested the contribution of the protein associated functional group in the complexation of Cr_(VI). The phytotoxicity test of fungal treated 100 mg/L of Cr_(VI) supernatant on Vigna radiata and Cicer arietinum revealed the successful detoxification/remediation of Cr_(VI).

A marine plasmid hitchhiking vast phylogenetic and geographic distances

Horizontal gene transfer (HGT) is the movement of genetic material between organisms other than by reproduction, which plays an important role in bacterial evolution. Often, mobile genetic elements such as plasmids are involved in HGT. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized plasmid that is found with 100% sequence identity in multiple distinct bacterial genera obtained from geographically separated locations. This is the only known instance where actual nucleotide identity and not only high synteny has been described for plasmids in environmental organisms. Furthermore, we provide experimental evidence for the potential of this plasmid to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment.

Horizontal gene transfer (HGT) plays an important role in bacterial evolution and serves as a driving force for bacterial diversity and versatility. HGT events often involve mobile genetic elements like plasmids, which can promote their own dissemination by associating with adaptive traits in the gene pool of the so-called mobilome. Novel traits that evolve through HGT can therefore lead to the exploitation of new ecological niches, prompting an adaptive radiation of bacterial species. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized RepL-type plasmid found in diverse members of the marine Roseobacter group across the globe. Noteworthy, 100% identical plasmids were detected in phylogenetically and geographically distant bacteria, revealing a so-far overlooked, but environmentally highly relevant vector for HGT. The genomic and functional characterization of this plasmid showed a completely conserved backbone dedicated to replication, stability, and mobilization as well as an interchangeable gene cassette with highly diverse, but recurring motifs. The majority of the latter appear to be involved in mechanisms coping with toxins and/or pollutants in the marine environment. Furthermore, we provide experimental evidence that the plasmid has the potential to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment.

Chromate Resistance Mechanisms in Leucobacter chromiiresistens

Chromate is one of the major anthropogenic contaminants on Earth. Leucobacter chromiiresistens is a highly chromate-resistant strain, tolerating chromate concentrations in LB medium of up to 400 mM. In response to chromate stress, L. chromiiresistens forms biofilms, which are held together via extracellular DNA. Inhibition of biofilm formation leads to drastically decreased chromate tolerance. Moreover, chromate is reduced intracellularly to the less-toxic Cr(III). The oxidation status and localization of chromium in cell aggregates were analyzed by energy-dispersive X-ray spectroscopy coupled to scanning transmission electron microscopy and X-ray absorption spectroscopy measurements. Most of the heavy metal is localized as Cr(III) at the cytoplasmic membrane. As a new cellular response to chromate stress, we observed an increased production of the carotenoid lutein. Carotenoid production could increase membrane stability and reduce the concentration of reactive oxygen species. Bioinformatic analysis of the L. chromiiresistens genome revealed several gene clusters that could enable heavy-metal resistance. The extreme chromate tolerance and the unique set of resistance factors suggest the use of L. chromiiresistens as a new model organism to study microbial chromate resistance.IMPORTANCE Chromate is a highly toxic oxyanion. Extensive industrial use and inadequate waste management has caused the toxic pollution of several field sites. Understanding the chromate resistance mechanisms that enable organisms to thrive under these conditions is fundamental to develop (micro)biological strategies and applications aiming at bioremediation of contaminated soils or waters. Potential detoxifying microorganisms are often not sufficient in their resistance characteristics to effectively perform, e.g., chromate reduction or biosorption. In this study, we describe the manifold strategies of L. chromiiresistens to establish an extremely high level of chromate resistance. The multitude of mechanisms conferring it make this organism suitable for consideration as a new model organism to study chromate resistance.

ChrASO, the chromate efflux pump of Shewanella oneidensis, improves chromate survival and reduction

The chromate efflux pump encoding gene chrASO was identified on the chromosome of Shewanella oneidensis MR1. Although chrASO is expressed without chromate, its expression level increases when Cr(VI) is added. When deleted, the resulting mutant ΔchrASO exhibits a chromate sensitive phenotype compared to that of the wild-type strain. Interestingly, heterologous expression of chrASO in E. coli confers resistance to high chromate concentration. Moreover, expression of chrASO in S. oneidensis and E. coli significantly improves Cr(VI) reduction. This effect could result either from extracytoplasmic chromate reduction or from a better cell survival leading to enhanced Cr(VI) reduction.

A topologically diverse family of fluoride channels

Dual-topology proteins are likely evolutionary antecedents to a common motif in membrane protein structures, the inverted repeat. A family of fluoride channels, the Flucs, which protect microorganisms, fungi, and plants against cytoplasmic fluoride accumulation, has representatives of all topologies along this evolutionary trajectory, including dual-topology homodimers, antiparallel heterodimers, and, in eukaryotes, fused two-domain proteins with an inverted repeat motif. Recent high-resolution crystal structures of dual-topology homodimers, coupled with extensive functional information about both the homodimers and two-domain Flucs, provide a case study of the co-evolution of fold and function.

Simultaneous microbial reduction of vanadium (V) and chromium (VI) by Shewanella loihica PV-4

Toxic vanadium (V) and chromium (VI) often co-exist in wastewater from vanadium ore smelting and their reductions by bacterial strain Shewanella loihica PV-4 is realized simultaneously. After 27-d operation, 71.3% of V(V) and 91.2% of Cr(VI) were removed respectively, with citrate as organic carbon source. Enhancement of Cr(VI) bioreduction was observed with the suppressed V(V) reduction. V(IV) and Cr(III), the main reduction products, precipitated inside the organisms and attached on cell surfaces. Both membrane components containing cytochrome c and cytoplasmic fractions containing soluble proteins as well as NADH may contribute to these microbial reductions. Most Cr(VI) were reduced extracellularly and V(V) tended to be reduced through intracellular process, as revealed by mapping the microbial surface and a line scan across the cell, performed by scanning transmission electron microscopy. This study provides an efficient alternative for controlling combined pollution caused by these two metals based on microbial technology.

chr genes from adaptive replicons are responsible for chromate resistance by Burkholderia xenovorans LB400

The chromate ion transporter (CHR) superfamily includes proteins that confer chromate resistance by extruding toxic chromate ions from cytoplasm. Burkholderia xenovorans strain LB400 encodes six CHR homologues in its multireplicon genome and has been reported as highly chromate-resistant. The objective of this work was to analyze the involvement of chr redundant genes in chromate resistance by LB400. It was found that B. xenovorans plant rhizosphere strains lacking the megaplasmid are chromate-sensitive, suggesting that the chr gene present in this replicon is responsible for the chromate-resistance phenotype of the LB400 strain. Transformation of a chromate-sensitive B. xenovorans strain with each of the six cloned LB400 chr genes showed that genes from 'adaptive replicons' (chrA1b and chr1NCb from chromosome 2 and chrA2 from the megaplasmid) conferred higher chromate resistance levels than chr genes from 'central' chromosome 1 (chrA1a, chrA6, and chr1NCa). An LB400 insertion mutant affected in the chrA2 gene displayed a chromate-sensitive phenotype, which was fully reverted by transferring the chrA2 wild-type gene, and partially reverted by chrA1b or chr1NCb genes. These data indicate that chr genes from adaptive replicons, mainly chrA2 from the megaplasmid, are responsible for the B. xenovorans LB400 chromate-resistance phenotype.

Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment

Hexavalent chromium [Cr(VI)] is a soluble carcinogen that has caused widespread contamination of soil and water in many industrial nations. Bacteria have the potential to aid remediation as certain strains can catalyze the reduction of Cr(VI) to insoluble and less toxic Cr(III). Here, we examine Cr(VI) reducing Microbacterium spp. (Cr-K1W, Cr-K20, Cr-K29, and Cr-K32) isolated from contaminated sediment (Seymore, Indiana) and show varying chromate responses despite the isolates' phylogenetic similarity (i.e., identical 16S rRNA gene sequences). Detailed analysis identified differences based on genomic metabolic potential, growth and general metabolic capabilities, and capacity to resist and reduce Cr(VI). Taken together, the discrepancies between the isolates demonstrate the complexity inter-strain variation can have on microbial physiology and related biogeochemical processes.

Characterization and structure prediction of partial length protein sequences of pcoA, pcoR and chrB genes from heavy metal resistant bacteria from the Klip River, South Africa

The Klip River has suffered from severe anthropogenic effects from industrial activities such as mining. Long-term exposure to heavy metal pollution has led to the development of heavy metal resistant strains of Pseudomonas sp. KR23, Lysinibacillus sp. KR25, and E. coli KR29. The objectives of this study were to characterize the genetics of copper and chromate resistance of the isolates. Copper and chromate resistance determinants were cloned and sequenced. Open reading frames (ORFs) related to the genes CopA and CopR were identified in E. coli KR29, PcoA in Lysinibacillus sp. KR25 and none related to chromate resistance were detected. The 3D-models predicted by I-TASSER disclose that the PcoA proteins consist of β-sheets, which form a part of the cupredoxin domain of the CopA copper resistance family of genes. The model for PcoR_29 revealed the presence of a helix turn helix; this forms part of a DNA binding protein, which is part of a heavy metal transcriptional regulator. The bacterial strains were cured using ethidium bromide. The genes encoding for heavy metal resistance and antibiotic resistance were found to be located on the chromosome for both Pseudomonas sp. (KR23) and E. coli (KR29). For Lysinibacillus (KR25) the heavy metal resistance determinants are suspected to be located on a mobile genetic element, which was not detected using gel electrophoresis.

Mechanisms of hexavalent chromium resistance and removal by microorganisms

Chromium has been and is extensively used worldwide in multiple industrial processes and is routinely discharged to the environment from such processes. Therefore, this heavy metal is a potential threat to the environment and to public health, primarily because it is non-biodegradable and environmentally persistent. Chromium exists in several oxidation states, the most stable of which are trivalent Cr(Ill) and hexavalent Cr(VI) species. Each species possesses its own individual chemical characteristics and produces its own biological effects. For example, Cr (Ill) is an essential oligoelement for humans, whereas Cr(VI) is carcinogenic and mutagenic. Several chemical methods are used to remove Cr(VI) from contaminated sites. Each of these methods has advantages and disadvantages. Currently, bioremediation is often the preferred method to deal with Cr contaminated sites, because it is eco-friendly, cost-effective and is a "natural" technology. Many yeast, bacterial and fungal species have been assessed for their suitability to reduce or remove Cr(VI) contamination. The mechanisms by which these microorganisms resist and reduce Cr(VI) are variable and are species dependent. There are several Cr-resistance mechanisms that are displayed by microorganisms. These include active efflux of Cr compounds, metabolic reduction of Cr(VI) to Cr (ill), and either intercellular or extracellular prec1p1tation. Microbial Cr (VI) removal typically involves three stages: binding of chromium to the cell surface, translocation of chromium into the cell, and reduction of Cr(VI) to Cr (ill). Cr(VI) reduction by microorganisms may proceed on the cell surface, outside the cell, or intracellularly, either directly via chromate reductase enzymes, or indirectly via metabolite reduction of Cr(VI). The uptake of chromium ions is a biphasic process. The primary step is known as biosorption, a metabolic energyindependent process. Thereafter, bioaccumulation occurs, but is much slower, and is dependent on cell metabolic activity. Choosing an appropriate bioremediation strategy for Cr is extremely important and must involve investigating and understanding the key mechanisms that are involved in microbial resistance to and removal of Cr(VI).

Bacterial chromate reductase, a potential enzyme for bioremediation of hexavalent chromium: a review

Hexavalent chromium is mobile, highly toxic and considered as a priority environmental pollutant. Chromate reductases, found in chromium resistant bacteria are known to catalyse the reduction of Cr(VI) to Cr(III) and have recently received particular attention for their potential use in bioremediation process. Different chromate reductases such as ChrR, YieF, NemA and LpDH, have been identified from bacterial sources which are located either in soluble fractions (cytoplasm) or bound to the membrane of the bacterial cell. The reducing conditions under which these enzymes are functional can either be aerobic or anaerobic or sometimes both. Enzymatic reduction of Cr(VI) to Cr(III) involves transfer of electrons from electron donors like NAD(P)H to Cr(VI) and simultaneous generation of reactive oxygen species (ROS). Based on the steps involved in electron transfer to Cr(VI) and the subsequent amount of ROS generated, two reaction mechanisms, namely, Class I "tight" and Class II "semi tight" have been proposed. The present review discusses on the types of chromate reductases found in different bacteria, their mode of action and potential applications in bioremediation of hexavalent chromium both under free and immobilize conditions. Besides, techniques used in characterization of the Cr (VI) reduced products were also discussed.

Expression of the six chromate ion transporter homologues of Burkholderia xenovorans LB400

The chromate ion transporter (CHR) superfamily comprises transporters that confer chromate resistance by extruding toxic chromate ions from cytoplasm. Burkholderia xenovorans strain LB400 has been reported to encode six CHR homologues in its multireplicon genome. We found that strain LB400 displays chromate-inducible resistance to chromate. Susceptibility tests of Escherichia coli strains transformed with cloned B. xenovorans chr genes indicated that the six genes confer chromate resistance, although under different growth conditions, and suggested that expression of chr genes is regulated by sulfate. Expression of chr genes was measured by quantitative reverse transcription-PCR (RT-qPCR) from total RNA of B. xenovorans LB400 grown under different concentrations of sulfate and exposed or not to chromate. The chr homologues displayed distinct expression levels, but showed no significant differences in transcription under the various sulfate concentrations tested, indicating that sulfate does not regulate chr gene expression in B. xenovorans. The chrA2 gene, encoded in the megaplasmid, was the only chr gene whose expression was induced by chromate and it was shown to constitute the chromate-responsive chrBACF operon. These data suggest that this determinant is mainly responsible for the B. xenovorans LB400 chromate resistance phenotype.

Bacterial mechanisms for Cr(VI) resistance and reduction: an overview and recent advances

Chromium pollution is increasing incessantly due to continuing industrialization. Of various oxidation states, Cr(6+) is very toxic due to its carcinogenic and mutagenic nature. It also has deleterious effects on different microorganisms as well as on plants. Many species of bacteria thriving in the Cr(6+)-contaminated environments have evolved novel strategies to cope with Cr(6+) toxicity. Generally, decreased uptake or exclusion of Cr(6+) compounds through the membranes, biosorption, and the upregulation of genes associated with oxidative stress response are some of the resistance mechanisms in bacterial cells to overcome the Cr(6+) stress. In addition, bacterial Cr(6+) reduction into Cr(3+) is also a mechanism of specific significance as it transforms toxic and mobile chromium derivatives into reduced species which are innocuous and immobile. Ecologically, the bacterial trait of reductive immobilization of Cr(6+) derivatives is of great advantage in bioremediation. The present review is an effort to underline the bacterial resistance and reducing mechanisms to Cr(6+) compounds with recent development in order to garner a broad perspective.

Molecular mechanisms of Cr(VI) resistance in bacteria and fungi

Hexavalent chromium [Cr(VI)] contamination is one of the main problems of environmental protection because the Cr(VI) is a hazard to human health. The Cr(VI) form is highly toxic, mutagenic, and carcinogenic, and it spreads widely beyond the site of initial contamination because of its mobility. Cr(VI), crossing the cellular membrane via the sulfate uptake pathway, generates active intermediates Cr(V) and/or Cr(IV), free radicals, and Cr(III) as the final product. Cr(III) affects DNA replication, causes mutagenesis, and alters the structure and activity of enzymes, reacting with their carboxyl and thiol groups. To persist in Cr(VI)-contaminated environments, microorganisms must have efficient systems to neutralize the negative effects of this form of chromium. The systems involve detoxification or repair strategies such as Cr(VI) efflux pumps, Cr(VI) reduction to Cr(III), and activation of enzymes involved in the ROS detoxifying processes, repair of DNA lesions, sulfur metabolism, and iron homeostasis. This review provides an overview of the processes involved in bacterial and fungal Cr(VI) resistance that have been identified through 'omics' studies. A comparative analysis of the described molecular mechanisms is offered and compared with the cellular evidences obtained using classical microbiological approaches.

The Neurospora crassa chr-1 gene is up-regulated by chromate and its encoded CHR-1 protein causes chromate sensitivity and chromium accumulation

The ChrA membrane protein belongs to the CHR superfamily of chromate ion transporters, which includes homologues from bacteria, archaea and eukaryotes. Bacterial ChrA homologues confer chromate resistance by exporting chromate ions from the cell's cytoplasm. The Neurospora crassa strain 74-A chr-1 gene encodes a putative CHR-1 protein of 507 amino acid residues, which belongs to the CHR superfamily. RT-PCR assays showed that expression of the chr-1 gene was up-regulated by chromate exposure of N. crassa cultures. Introduction in N. crassa of sense and antisense fragments of the chr-1 gene, as part of a silencing module within the pSilent-1 vector, produced transformants with a phenotype of resistance to chromate and diminished accumulation of chromium, as compared with the control strain containing only the vector. A chromate-resistance phenotype was also observed in N crassa strains deleted in the genomic chr-1 gene, thus confirming that the absence of CHR-1 protein confers chromate resistance to the fungus. The cDNA from N. crassa chr-1 gene (Ncchr-1) was cloned into the pYES2 vector under the control of a GAL promoter and the resulting recombinant plasmid was transferred to the yeast Saccharomyces cerevisiae. Galactose-induced S. cerevisiae transformants expressing Ncchr-1 were more sensitive to chromate and accumulated 2.5 times more chromium than the induced strain containing only the vector. Excess sulfate, a chromate analog, was unable to protect S. cerevisiae chr-1 transformants from chromate toxicity. These data indicate that the N. crassa CHR-1 protein functions as a transporter that takes up chromate; it also appears that this transport occurs in a sulfate-independent fashion. This is the first report assigning a role as a chromate transporter to a nonbacterial CHR protein.

Antiparallel membrane topology of paired short-chain chromate transport proteins in Bacillus subtilis

Short-chain monodomain family comprises pairs of membrane proteins of about 200 amino acid residues each that belong to the chromate ion transporter (CHR) superfamily. The short-chain CHR homologous pair Chr3N/Chr3C from Bacillus subtilis strain 168 confers chromate resistance only when both proteins are expressed. Membrane topology of the Chr3N and Chr3C proteins was determined in Escherichia coli by the analysis of translational fusions with reporter enzymes alkaline phosphatase and β-galactosidase. Each short-chain CHR protein was found to consist of five transmembrane segments with antiparallel orientation between them. The C terminus of Chr3N is located in the cytoplasm, whereas the C terminus of Chr3C is located in the periplasm. In silico analyses suggest that this antiparallel arrangement is shared by all protein members of the short-chain CHR3 subfamily and that the two Chr3N/Chr3C proteins might carry out distinct functions for the transport of chromate.

The ChrA homologue from a sulfur-regulated gene cluster in cyanobacterial plasmid pANL confers chromate resistance

The cyanobacterium Synechococcus elongatus strain PCC 7942 possesses pANL, a plasmid rich in genes related to sulfur metabolism. One of these genes, srpC, encodes the SrpC protein, a homologue of the CHR chromate ion transporter superfamily. The srpC gene was cloned and expressed in Escherichia coli and its role in relation to sulfate and chromate was analyzed. srpC was unable to complement the growth of an E. coli cysA sulfate uptake mutant when sulfate was utilized as a sole sulfur source, suggesting that SrpC is not a sulfate transporter. Expression of srpC in E. coli conferred chromate resistance and caused diminished chromate uptake. These results suggest that the S. elongatus SrpC protein functions as a transporter that extrudes chromate ions from the cell's cytoplasm, and further demonstrate the close relationship between sulfate and chromate metabolism in this organism.

Nucleotide sequence of Pseudomonas aeruginosa conjugative plasmid pUM505 containing virulence and heavy-metal resistance genes

We determined the complete nucleotide sequence of conjugative plasmid pUM505 isolated from a clinical strain of Pseudomonas aeruginosa. The plasmid had a length of 123,322bp and contained 138 complete coding regions, including 46% open reading frames encoding hypothetical proteins. pUM505 can be considered a hybrid plasmid because it presents two well-defined regions. The first region corresponded to a larger DNA segment with homology to a pathogenicity island from virulent Pseudomonas strains; this island in pUM505 was comprised of genes probably involved in virulence and genes encoding proteins implicated in replication, maintenance and plasmid transfer. Sequence analysis identified pil genes encoding a type IV secretion system, establishing pUM505 as a member of the family of IncI1 plasmids. Plasmid pUM505 also contained virB4/virD4 homologues, which are linked to virulence in other plasmids. The second region, smaller in length, contains inorganic mercury and chromate resistance gene clusters both flanked by putative mobile elements. Although no genes for antibiotic resistance were identified, when pUM505 was transferred to a recipient strain of P. aeruginosa it conferred resistance to the fluoroquinolone ciprofloxacin. pUM505 also conferred resistance to the superoxide radical generator paraquat. pUM505 could provide Pseudomonas strains with a wide variety of adaptive traits such as virulence, heavy-metal and antibiotic resistance and oxidative stress tolerance which can be selective factors for the distribution and prevalence of this plasmid in diverse environments, including hospitals and heavy metal contaminated soils.

Characterization and genomic analysis of chromate resistant and reducing Bacillus cereus strain SJ1

BACKGROUND

Chromium is a toxic heavy metal, which primarily exists in two inorganic forms, Cr(VI) and Cr(III). Chromate [Cr(VI)] is carcinogenic, mutational, and teratogenic due to its strong oxidizing nature. Biotransformation of Cr(VI) to less-toxic Cr(III) by chromate-resistant and reducing bacteria has offered an ecological and economical option for chromate detoxification and bioremediation. However, knowledge of the genetic determinants for chromate resistance and reduction has been limited so far. Our main aim was to investigate chromate resistance and reduction by Bacillus cereus SJ1, and to further study the underlying mechanisms at the molecular level using the obtained genome sequence.

RESULTS

Bacillus cereus SJ1 isolated from chromium-contaminated wastewater of a metal electroplating factory displayed high Cr(VI) resistance with a minimal inhibitory concentration (MIC) of 30 mM when induced with Cr(VI). A complete bacterial reduction of 1 mM Cr(VI) was achieved within 57 h. By genome sequence analysis, a putative chromate transport operon, chrIA1, and two additional chrA genes encoding putative chromate transporters that likely confer chromate resistance were identified. Furthermore, we also found an azoreductase gene azoR and four nitroreductase genes nitR possibly involved in chromate reduction. Using reverse transcription PCR (RT-PCR) technology, it was shown that expression of adjacent genes chrA1 and chrI was induced in response to Cr(VI) but expression of the other two chromate transporter genes chrA2 and chrA3 was constitutive. In contrast, chromate reduction was constitutive in both phenotypic and gene expression analyses. The presence of a resolvase gene upstream of chrIA1, an arsenic resistance operon and a gene encoding Tn7-like transposition proteins ABBCCCD downstream of chrIA1 in B. cereus SJ1 implied the possibility of recent horizontal gene transfer.

CONCLUSION

Our results indicate that expression of the chromate transporter gene chrA1 was inducible by Cr(VI) and most likely regulated by the putative transcriptional regulator ChrI. The bacterial Cr(VI)-resistant level was also inducible. The presence of an adjacent arsenic resistance gene cluster nearby the chrIA1 suggested that strong selective pressure by chromium and arsenic could cause bacterial horizontal gene transfer. Such events may favor the survival and increase the resistance level of B. cereus SJ1.

High-level chromate resistance in Arthrobacter sp. strain FB24 requires previously uncharacterized accessory genes

Background

The genome of Arthrobacter sp. strain FB24 contains a chromate resistance determinant (CRD), consisting of a cluster of 8 genes located on a 10.6 kb fragment of a 96 kb plasmid. The CRD includes chrA, which encodes a putative chromate efflux protein, and three genes with amino acid similarities to the amino and carboxy termini of ChrB, a putative regulatory protein. There are also three novel genes that have not been previously associated with chromate resistance in other bacteria; they encode an oxidoreductase (most similar to malate:quinone oxidoreductase), a functionally unknown protein with a WD40 repeat domain and a lipoprotein. To delineate the contribution of the CRD genes to the FB24 chromate [Cr(VI)] response, we evaluated the growth of mutant strains bearing regions of the CRD and transcript expression levels in response to Cr(VI) challenge.

Results

A chromate-sensitive mutant (strain D11) was generated by curing FB24 of its 96-kb plasmid. Elemental analysis indicated that chromate-exposed cells of strain D11 accumulated three times more chromium than strain FB24. Introduction of the CRD into strain D11 conferred chromate resistance comparable to wild-type levels, whereas deletion of specific regions of the CRD led to decreased resistance. Using real-time reverse transcriptase PCR, we show that expression of each gene within the CRD is specifically induced in response to chromate but not by lead, hydrogen peroxide or arsenate. Higher levels of chrA expression were achieved when the chrB orthologs and the WD40 repeat domain genes were present, suggesting their possible regulatory roles.

Conclusion

Our findings indicate that chromate resistance in Arthrobacter sp. strain FB24 is due to chromate efflux through the ChrA transport protein. More importantly, new genes have been identified as having significant roles in chromate resistance. Collectively, the functional predictions of these additional genes suggest the involvement of a signal transduction system in the regulation of chromate efflux and warrants further study.

Short-chain chromate ion transporter proteins from Bacillus subtilis confer chromate resistance in Escherichia coli

Tandem paired genes encoding putative short-chain monodomain protein members of the chromate ion transporter (CHR) superfamily (ywrB and ywrA) were cloned from genomic DNA of Bacillus subtilis strain 168. The transcription of the paired genes, renamed chr3N and chr3C, respectively, was shown to occur via a bicistronic mRNA generated from a promoter upstream of the chr3N gene. The chr3N and chr3C genes conferred chromate resistance when expressed in Escherichia coli strain W3110. The cloned chr3N gene alone did not confer chromate resistance on E. coli, suggesting that both chr3N and chr3C genes are required for function. E. coli cells expressing paired chr3N and chr3C genes demonstrated diminished uptake of chromate compared to that by a vector-only control strain. These results suggest that short-chain CHR proteins form heterodimer transporters which efflux chromate ions from the cytoplasm.