Dual mode of energy coupling by the oxyanion-translocating ArsB protein

Citrobacter portucalensis Sb-2 contains a metalloid resistance determinant transmitted by Citrobacter phage Chris1

Bacterial adaptation to extreme environments is often mediated by horizontal gene transfer (HGT) via genetic mobile elements. Nevertheless, phage-mediated HGT conferring bacterial arsenic resistance determinants has rarely been investigated. In this study, a highly arsenite and antimonite resistant bacterium, Citrobacter portucalensis strain Sb-2, was isolated, and genome analysis showed that several putative arsenite and antimonite resistance determinants were flanked or embedded in prophages. Furthermore, an active bacteriophage carrying one of the ars clusters (arsRDABC arsR-yraQ/arsP) was obtained and sequenced. These genes encoding putative arsenic resistance determinants were induced by arsenic and antimony as demonstrated by RT-qPCR, and one gene arsP/yraQ of the ars cluster was shown to give resistance to MAs(III) and Rox(III), thereby showing function. Here, we were able to directly show that these phage-mediated arsenic and antimony resistances play a significant role in adapting to As- and Sb-contaminated environments. In addition, we demonstrate that this phage is responsible for conferring arsenic and antimony resistances to C. portucalensis strain Sb-2.

Comparative Analysis of Arsenic Transport and Tolerance Mechanisms: Evolution from Prokaryote to Higher Plants

Arsenic (As) is a toxic metalloid for all living organisms and can cause serious harm to humans. Arsenic is also toxic to plants. To alleviate As toxicity, all living organisms (from prokaryotes to higher plants) have evolved comprehensive mechanisms to reduce cytosolic As concentration through the set of As transporters localized at the plasma and tonoplast membranes, which operate either in arsenite As(III) extrusion out of cells (via ArsB, ACR3, and aquaporins) or by sequestering arsenic into vacuoles (by ABC transporters). In addition, a special arsenate resistance mechanism found in some bacterial systems has evolved in an As hyperaccumulating fern Pteris vittata, which involves transforming arsenate As(V) to an As(V) phosphoglycerate derivative by a glyceraldehyde 3-phosphate dehydrogenase and transporting this complex by an efflux transporter. In the present review, we summarize the evolution of these arsenic resistance mechanisms from prokaryotes to eukaryotes and discuss future approaches that could be utilized to better understand and improve As resistance mechanisms in plants.

Significance of Shewanella Species for the Phytoavailability and Toxicity of Arsenic-A Review

Simple Summary

The availability of some toxic heavy metals, such as arsenic (As), is related to increased human and natural activities. This type of metal availability in the environment is associated with various health and environmental issues. Such problems may arise due to direct contact with or consumption of plant products containing this metal in some of their parts. A microbial approach that employs a group of bacteria (Shewanella species) is proposed to reduce the negative consequences of the availability of this metal (As) in the environment. This innovative strategy can reduce As mobility, its spread, and uptake by plants in the environment. The benefits of this approach include its low cost and the possibility of not exposing other components of the environment to unfavourable consequences.

Abstract

The distribution of arsenic continues due to natural and anthropogenic activities, with varying degrees of impact on plants, animals, and the entire ecosystem. Interactions between iron (Fe) oxides, bacteria, and arsenic are significantly linked to changes in the mobility, toxicity, and availability of arsenic species in aquatic and terrestrial habitats. As a result of these changes, toxic As species become available, posing a range of threats to the entire ecosystem. This review elaborates on arsenic toxicity, the mechanisms of its bioavailability, and selected remediation strategies. The article further describes how the detoxification and methylation mechanisms used by Shewanella species could serve as a potential tool for decreasing phytoavailable As and lessening its contamination in the environment. If taken into account, this approach will provide a globally sustainable and cost-effective strategy for As remediation and more information to the literature on the unique role of this bacterial species in As remediation as opposed to conventional perception of its role as a mobiliser of As.

Silicon's Role in Plant Stress Reduction and Why This Element Is Not Used Routinely for Managing Plant Health

Numerous reviews and hundreds of refereed articles have been published on silicon's effects on abiotic and biotic stress as well as overall plant growth and development. The science for silicon is well-documented and comprehensive. However, even with this robust body of information, silicon is still not routinely used for alleviating plant stress and promoting plant growth and development. What is holding producers and growers back from using silicon? There are several possible reasons, which include: (i) lack of consistent information on which soil orders are low or limited in silicon, (ii) no universally accepted soil test for gauging the amounts of soluble silicon have been calibrated for many agronomic or horticultural crops, (iii) most analytical laboratories do not routinely assay plant tissue for silicon and current standard tissue digestion procedures used would render silicon insoluble, (iv) many scientists still state that plants are either silicon accumulators or non-accumulators when in reality all plants accumulate some silicon in their plant tissues, (v) silicon is not recognized as being necessary for plant development, (vi) lack of economic studies to show the benefits of applying silicon, and (vii) lack of extension outreach to present the positive benefits of silicon to producers and growers. Many of these issues mentioned above will need to be resolved if silicon is to become a standard practice to improve agronomic and horticultural crop production and plant health.

Genome Sequence of Brevundimonas sp., an Arsenic Resistant Soil Bacterium

Brevundimonas sp. is a bacteria able to grow in metal(loid) contaminated soil from Puchuncaví Valley, central Chile. This study has isolated a bacterial strain capable of growth under high doses of arsenic (As) (6000 mg L−1), and a draft genome sequence was generated. Additionally, real-time PCR was performed to examine the effect of As on some genes related to As resistance. Results demonstrated a total of 3275 predicted annotated genes with several genes related to the ars operon, metal(loid) resistance-related genes, metal efflux pumps, and detoxifying enzymes. Real-time PCR showed that the arsB involved in the efflux of As was down-regulated, whereas arsR, arsH, and ACR3 did not show differences with the addition of As. Our study provides novel evidence of diverse As regulating systems in tolerant bacteria that will lead to a better understanding of how microorganisms overcome toxic elements and colonize As contaminated soils and to the possible use of their specific properties in bioremediation.

Unraveling the role of plant growth-promoting rhizobacteria in the alleviation of arsenic phytotoxicity: A review

The toxic metalloid arsenic (As), is a major pollutant of soil and water, imposing severe health concerns on human lives. It enters the food chain mainly through As-contaminated crops. The uptake, translocation and accumulation of As in plant tissue are often controlled by certain soil-inhabiting microbial communities. Among them, indigenous, free-living As-resistant plant growth-promoting rhizobacteria (PGPR) plays a pivotal role in As-immobilization. Besides, the plant's inability to withstand As after a threshold level is actively managed by these PGPR increasing As-tolerance in host plants by a synergistic plant-microbe interaction. The dual functionality of As-resistant PGPR i.e., phytostimulation and minimization of As-induced phytotoxic damages are one of the main focal points of this review article. It is known that such PGPR having the functional arsenic-resistant genes (in ars operon) including As-transporters, As-transforming genes contributed to the As accumulation and detoxification/transformation respectively. Apart from assisting in nutrient acquisition and modulating phytohormone levels, As-resistant PGPR also influences the antioxidative defense system in plants by maneuvering multiple enzymatic and non-enzymatic antioxidants. Furthermore, they are effective in reducing membrane damage and electrolyte leakage in plant cells. As-induced photosynthetic damage is also found to be salvaged by As-resistant PGPR. Briefly, the eco-physiological, biochemical and molecular mechanisms of As-resistant PGPR are thus elaborated here with regard to the As-exposed crops.

Genome and Pangenome Analysis of Lactobacillus hilgardii FLUB-A New Strain Isolated from Mead

The production of mead holds great value for the Polish liquor industry, which is why the bacterium that spoils mead has become an object of concern and scientific interest. This article describes, for the first time, Lactobacillus hilgardii FLUB newly isolated from mead, as a mead spoilage bacteria. Whole genome sequencing of L. hilgardii FLUB revealed a 3 Mbp chromosome and five plasmids, which is the largest reported genome of this species. An extensive phylogenetic analysis and digital DNA-DNA hybridization confirmed the membership of the strain in the L. hilgardii species. The genome of L. hilgardii FLUB encodes 3043 genes, 2871 of which are protein coding sequences, 79 code for RNA, and 93 are pseudogenes. L. hilgardii FLUB possesses three clustered regularly interspaced short palindromic repeats (CRISPR), eight genomic islands (44,155 bp to 6345 bp), and three (two intact and one incomplete) prophage regions. For the first time, the characteristics of the genome of this species were described and a pangenomic analysis was performed. The concept of the pangenome was used not only to establish the genetic repertoire of this species, but primarily to highlight the unique characteristics of L. hilgardii FLUB. The core of the genome of L. hilgardii is centered around genes related to the storage and processing of genetic information, as well as to carbohydrate and amino acid metabolism. Strains with such a genetic constitution can effectively adapt to environmental changes. L. hilgardii FLUB is distinguished by an extensive cluster of metabolic genes, arsenic detoxification genes, and unique surface layer proteins. Variants of MRS broth with ethanol (10-20%), glucose (2-25%), and fructose (2-24%) were prepared to test the strain's growth preferences using Bioscreen C and the PYTHON script. L. hilgardii FLUB was found to be more resistant than a reference strain to high concentrations of alcohol (18%) and sugars (25%). It exhibited greater preference for fructose than glucose, which suggests it has a fructophilic nature. Comparative genomic analysis supported by experimental research imitating the conditions of alcoholic beverages confirmed the niche specialization of L. hilgardii FLUB to the mead environment.

Dependence of arsenic resistance and reduction capacity of Aeromonas hydrophila on carbon substrate

The high toxicity and prevalence of arsenic in the environment have aroused increasing research interest in understanding the mechanisms of microbial arsenic resistance. A wide spectrum of arsenic resistant microbes with ability of arsenic bio-transformation has been isolated from arsenic-contaminated environments. However, arsenic resistance processes and reduction abilities of microbes under various growth conditions remain poorly understood. In this work, a high correlation between the arsenic resistance and reduction ability of Aeromonas hydrophila and the carbon substrate was identified. Genome analysis suggests that the arsenic resistance system is widely present in Aeromonas genus, and the arsenic resistance was associated with the ars operon. The sensitivity of A. hydrophila to As(V) and As(III) depended heavily on the type of carbon substrate. The upregulated expression of arsA, arsB, arsD and/or downregulated expression of glpF might be responsible for the increased microbial tolerance to As(III). The As(V) reduction rate was also affected by the type of carbon substrate. Our results provide new insights into the impacts of carbon substrate on the arsenic biotoxicity as well as arsenic biotransformation processes.

Cadmium transport activity of four mercury transporters (MerC, MerE, MerF and MerT) and effects of the periplasmic mercury-binding protein MerP on Mer-dependent cadmium uptake

Mercury superfamily proteins, i.e. inner membrane-spanning proteins (MerC, MerE, MerF and MerT) and a periplasmic mercury-binding protein (MerP), transport mercury into the cytoplasm. A previous study demonstrated that a Mer transporter homolog exhibits cadmium transport activity; based on this, the present study aimed to evaluate the cadmium transport activity of MerC, MerE, MerF and MerT and the effects of MerP co-expression in Escherichia coli. Bacteria expressing MerC, MerE, MerF or MerT without MerP were more sensitive to cadmium and significantly absorbed more cadmium than did the control strain. Expression of MerP in combination with MerC, MerE, MerF or MerT increased the bacterial sensitivity to cadmium and cadmium accumulation compared to a single expression of MerC, MerE, MerF or MerT. Cadmium uptake mediated by MerC, MerE, MerF or MerT was inhibited under cold or acidic conditions. These findings suggest that MerC, MerE, MerF and MerT are broad-spectrum heavy metal transporters that mediate both mercury and cadmium transport into cells and that MerP accelerates the cadmium transport ability of MerC, MerE, MerF and MerT.

Arsenic efflux in Enterobacter cloacae RSN3 isolated from arsenic-rich soil

In the present study, bacterial isolates were screened for arsenic resistance efficiency. Environmental isolates were isolated from arsenic-rich soil samples (i.e., from Rajnandgaon district of Chhattisgarh state, India). Amplification and sequencing of 16S rRNA gene revealed that the isolates were of Bacillus firmus RSN1, Brevibacterium senegalense RSN2, Enterobacter cloacae RSN3, Stenotrophomonas pavanii RSN6, Achromobacter mucicolens RSN7, and Ochrobactrum intermedium RSN10. Arsenite efflux gene (arsB) was successfully amplified in E. cloacae RSN3. Atomic absorption spectroscopy (AAS) analysis showed an absorption of 32.22% arsenic by the RSN3 strain. Furthermore, results of scanning electron microscopy (SEM) for morphological variations revealed an initial increase in the cell size at 1 mM sodium arsenate; however, it was decreased at 10 mM concentration in comparison to control. This change of the cell size in different metal concentrations was due to the uptake and expulsion of the metal from the cell, which also confirmed the arsenite efflux system.

Marine Microbial Response to Heavy Metals: Mechanism, Implications and Future Prospect

Growing levels of pollution in marine environment has been a matter of serious concern in recent years. Increased levels of heavy metals due to improper waste disposal has led to serious repercussions. This has increased occurrences of heavy metals in marine fauna. Marine microbes are large influencers of nutrient cycling and productivity in oceans. Marine bacteria show altered metabolism as a strategy against metal induced stress. Understanding these strategies used to avoid toxic effects of heavy metals can help in devising novel biotechnological applications for ocean clean-up. Using biological tools for remediation has advantages as it does not involve harmful chemicals and it shows greater flexibility to environmental fluctuations. This review provides a comprehensive insight on marine microbial response to heavy metals and sheds light on existing knowledge about and paves for new avenues in research for bioremediation strategies.

Targeting Acr3 from Ensifer medicae to the plasma membrane or to the tonoplast of tobacco hairy roots allows arsenic extrusion or improved accumulation. Effect of acr3 expression on the root transcriptome

Transgenic tobacco hairy roots expressing the bacterial arsenite efflux pump Acr3 from Ensifer medicae were generated. The gene product was targeted either to the plasma membrane (ACR3 lines) or to the tonoplast by fusing the ACR3 protein to the tonoplast integral protein TIP1.1 (TIP-ACR3 lines). Roots expressing Acr3 at the tonoplast showed greater biomass than those expressing Acr3 at the plasma membrane. Furthermore, higher contents of malondialdehyde (MDA) and RNA degradation in ACR3 lines were indicative of higher oxidative stress. The determination of ROS-scavenging enzymes depicted the transient role of peroxidases in ROS detoxification, followed by the action of superoxide dismutase during both short- and medium-term exposure periods. Regarding As accumulation, ACR3 lines accumulated up to 20-30% less As, whereas TIP-ACR3 achieved a 2-fold increase in As accumulation in comparison to control hairy roots. Strategies that presumably induce As uptake, such as phosphate deprivation or dehydration followed by rehydration in the presence of As, fostered As accumulation up to 10 800 μg g-1. Finally, the effects of the heterologous expression of acr3 on the root transcriptome were assessed. Expression at the plasma membrane induced drastic changes in gene expression, with outstanding overexpression of genes related to electron transport, ATP synthesis and ATPases, suggesting that As efflux is the main detoxification mechanism in these lines. In addition, genes encoding heat shock proteins and those related to proline synthesis and drought tolerance were activated. On the other hand, TIP-ACR3 lines showed a similar gene expression profile to that of control roots, with overexpression of the glutathione and phytochelatin synthesis pathways, together with secondary metabolism pathways as the most important resistance mechanisms in TIP-ACR3, for which As allocation into the vacuole allowed better growth and stress management. Our results suggest that modulation of As accumulation can be achieved by subcellular targeting of Acr3: expression at the tonoplast enhances As accumulation in roots, whereas expression at the plasma membrane could promote As efflux. Thus, both approaches open the possibilities for developing safer crops when grown on As-polluted paddy soils, but expression at the tonoplast leads to better growth and less stressed roots, since the high energy cost of As efflux likely compromises growth in ACR3 lines.

Energy coupling in ABC exporters

Multidrug transporters are important and interesting molecular machines that extrude a wide variety of cytotoxic drugs from target cells. This review summarizes novel insights in the energetics and mechanisms of bacterial ATP-binding cassette multidrug transporters as well as recent advances connecting multidrug transport to ion and lipid translocation processes in other membrane proteins.

Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway

The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern California, which is found there in concentrations up to 3000 μM. Arsenic is a widespread element that can be an environmental issue, as it is highly toxic to most organisms. However, resistance mechanisms in the form of detoxification are widespread and some prokaryotes can even use arsenic as an energy source. We first screened the genomes of 76 Thioalkalivibrio strains for the presence of known arsenic oxidoreductases and found 15 putative ArxA (arsenite oxidase) and two putative ArrA (arsenate reductase). Subsequently, we studied the resistance to arsenite in detail in Thioalkalivibrio jannaschii ALM2^T, and Thioalkalivibrio thiocyanoxidans ARh2^T by comparative genomics and by growing them at different arsenite concentrations followed by arsenic species and transcriptomic analysis. Tv. jannaschii ALM2^T, which has been isolated from Mono Lake, an arsenic-rich soda lake, could resist up to 5 mM arsenite, whereas Tv. thiocyanoxidans ARh2^T, which was isolated from a Kenyan soda lake, could only grow up to 0.1 mM arsenite. Interestingly, both species oxidized arsenite to arsenate under aerobic conditions, although Tv. thiocyanoxidans ARh2^T does not contain any known arsenite oxidases, and in Tv. jannaschii ALM2^T, only arxB2 was clearly upregulated. However, we found the expression of a SoeABC-like gene, which we assume might have been involved in arsenite oxidation. Other arsenite stress responses for both strains were the upregulation of the vitamin B₁₂ synthesis pathway, which can be linked to antioxidant activity, and the up- and downregulation of different DsrE/F-like genes whose roles are still unclear. Moreover, Tv. jannaschii ALM2^T induced the ars gene operon and the Pst system, and Tv. thiocanoxidans ARh2^T upregulated the sox and apr genes as well as different heat shock proteins. Our findings for Thioalkalivibrio confirm previously observed adaptations to arsenic, but also provide new insights into the arsenic stress response and the connection between the arsenic and the sulfur cycle.

Micro-colonization of arsenic-resistant Staphylococcus sp. As-3 on arsenopyrite (FeAsS) drives arsenic mobilization under anoxic sub-surface mimicking conditions

We investigated the subsurface biomatrix of the most abundant As-mineral, arsenopyrite (FeAsS), and meticulously studied a potential biogenic arsenic mobilization phenomenon. An arsenic-resistant [up to 7.5 mM As(III) and 200 mM As(V)] and arsenate-reducing bacterial strain (Staphylococcus sp. As-3) was isolated from a sediment core sample taken from the Budai borehole, on the southwestern coast of Taiwan. Isolate As-3 could reduce 5 mM As(V) to 3.04 mM in 96 h, generating 1.6 mM As(III) under anoxic conditions. Isolate As-3, which adsorbed As(V) up to 19.02 mg g^-1 (cdw) and As(III) up to 0.46 mg g^-1 (cdw), demonstrated effective As-bioaccumulating ability, as corroborated by a TEM-EDS analysis. Under anaerobic batch conditions, isolate As-3 micro-colonies could grow on as well as interact with arsenopyrite (FeAsS), mobilizing arsenic into soluble phase as As(III) and As(V). Using synchrotron radiation-based FTIR micro-spectroscopy, various functional group signatures and critical chemical bonds enabling a direct interaction with arsenopyrite were underpinned, such as a potential P-OFe bond involved in facilitating bacteria-mineral interaction. Using atomic force microscopy, we analyzed the scattered bacterial cell arrangement and structure and measured various biomechanical properties of micro-colonized Staphylococcus sp. As-3 cells on arsenopyrite. We suggest that the release of organic acids from As-3 drives soluble arsenic release in the aqueous phase under anoxic conditions through oxidative dissolution. Furthermore, arsC-encoding putative cytoplasmic arsenic reductase sequencing and transcript characterization indicated that arsC plays a possible role in the reduction of moderately soluble As(V) to highly soluble toxic As(III) under anoxic conditions. Thus, we suggest that firmicutes such as Staphylococcus sp. As-3 may play an important role in microbially-mediated arsenic mobilization, leading to arsenic release in the sub-surface niche.

Genetic mechanisms of arsenic detoxification and metabolism in bacteria

Arsenic, distributed pervasively in the natural environment, is an extremely toxic substance which can severely impair the normal functions of living cells. Research on the genetic mechanisms of arsenic metabolism is of great importance for remediating arsenic-contaminated environments. Many organisms, including bacteria, have developed various strategies to tolerate arsenic, by either detoxifying this harmful element or utilizing it for energy generation. This review summarizes arsenic detoxification as well as arsenic respiratory metabolic pathways in bacteria and discusses novel arsenic resistance pathways in various bacterial strains. This knowledge provides insights into the mechanisms of arsenic biotransformation in bacteria. Multiple detoxification strategies among bacteria imply possible functional relationships among different arsenic detoxification/metabolism pathways. In addition, this review sheds light on the bioremediation of arsenic-contaminated environments and prevention of antibiotic resistance.

Signature Arsenic Detoxification Pathways in Halomonas sp. Strain GFAJ-1

Since the original report that Halomonas sp. strain GFAJ-1 was capable of using arsenic instead of phosphorus to sustain growth, additional studies have been conducted, and GFAJ-1 is now considered a highly arsenic-resistant but phosphorus-dependent bacterium. However, the mechanisms supporting the extreme arsenic resistance of the GFAJ-1 strain remain unknown. In this study, we show that GFAJ-1 has multiple distinct arsenic resistance mechanisms. It lacks the genes to reduce arsenate, which is the essential step in the well-characterized resistance mechanism of arsenate reduction coupled to arsenite extrusion. Instead, GFAJ-1 has two arsenic resistance operons, arsH1-acr3-2-arsH2 and mfs1-mfs2-gapdh, enabling tolerance to high levels of arsenate. mfs2 and gapdh encode proteins homologous to Pseudomonas aeruginosa ArsJ and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), respectively, which constitute the equivalent of an As(V) efflux system to catalyze the transformation of inorganic arsenate to pentavalent organoarsenical 1-arseno-3-phosphoglycerate and its subsequent extrusion. Surprisingly, the arsH1-acr3-2-arsH2 operon seems to consist of typical arsenite resistance genes, but this operon is sufficient to confer both arsenite and arsenate resistance on Escherichia coli AW3110 even in the absence of arsenate reductase, suggesting a novel pathway of arsenic detoxification. The simultaneous occurrence of these two unusual detoxification mechanisms enables the adaptation of strain GFAJ-1 to the particularly arsenic-rich environment of Mono Lake.

Halomonas sp. strain GFAJ-1 was previously reported to use arsenic as a substitute for phosphorus to sustain life under phosphate-limited conditions. Although this claim was later undermined by several groups, how GFAJ-1 can thrive in environments with high arsenic concentrations remains unclear. Here, we determined that this ability can be attributed to the possession of two arsenic detoxification operons, arsH1-acr3-2-arsH2 and mfs1-mfs2-gapdh. mfs2 and gapdh encode proteins homologous to ArsJ and GAPDH in Pseudomonas aeruginosa; these proteins create an arsenate efflux pathway to reduce cellular arsenate accumulation. Interestingly, the combination of acr3-2 with either arsH gene was sufficient to confer resistance to both arsenite and arsenate in E. coli AW3110, even in the absence of arsenate reductase, suggesting a new strategy for bacterial arsenic detoxification. This study concludes that the survival of GFAJ-1 in high arsenic concentrations is attributable to the cooccurrence of these two unusual arsenic detoxification mechanisms.

The Arsenic Detoxification System in Corynebacteria: Basis and Application for Bioremediation and Redox Control

Arsenic (As) is widespread in the environment and highly toxic. It has been released by volcanic and anthropogenic activities and causes serious health problems worldwide. To survive arsenic-rich environments, soil and saprophytic microorganisms have developed molecular detoxification mechanisms to survive arsenic-rich environments, mainly by the enzymatic conversion of inorganic arsenate (As^V) to arsenite (As^III) by arsenate reductases, which is then extruded by arsenite permeases. One of these Gram-positive bacteria, Corynebacterium glutamicum, the workhorse of biotechnological research, is also resistant to arsenic. To sanitize contaminated soils and waters, C. glutamicum strains were modified to work as arsenic "biocontainers." Two chromosomally encoded ars operons (ars1 and ars2) are responsible for As resistance. The genes within these operons encode for metalloregulatory proteins (ArsR1/R2), arsenite permeases (Acr3-1/-2), and arsenate reductases (ArsC1/C2/C1'). ArsC1/C2 arsenate reductases are coupled to the low molecular weight thiol mycothiol (MSH) and to the recently discovered mycoredoxin-1 (Mrx-1) present in most Actinobacteria. This MSH/Mrx-1 redox system protects cells against different forms of stress, including reactive oxygen species (ROS), metals, and antibiotics. ROS can modify functional sulfur cysteines by oxidizing the thiol (-SH) to a sulfenic acid (-SOH). These oxidation-sensitive protein cysteine thiols are redox regulated by the MSH/Mrx-1 couple in Corynebacterium and Mycobacterium. In summary, the molecular mechanisms involved in arsenic resistance system in C. glutamicum have paved the way for understanding the cellular response against oxidative stress in Actinobacteria.

Arsenic mediated modifications in Bacillus aryabhattai and their biotechnological applications for arsenic bioremediation

The present study reports the arsenic (As) tolerance mechanism of bacteria Bacillus aryabhattai (NBRI014). The data explores the intracellular accumulation and volatilization of As from the culture medium after 48 h of exposure to 25,000 mg l^-1 arsenate As(V). The study also provides the evidence of presence of ars operon in bacteria, which may have played an important role in reducing As toxicity. Additionally, we found 7 differentially expressed proteins to be up-regulated in bacterial cells upon As exposure which may have role in reducing As toxicity inside bacterial cells. Furthermore, Fourier transform infrared (FTIR) spectroscopic techniques were useful to describe the structural and compositional alterations in bacterial cells after As treatment. It showed the changes in peak positions of the spectrum pattern when NBRI014 was grown in medium containing As, indicating that these functional groups viz. (amino, alkyl halides and hydroxyl) present on bacterial surface, which may be involved in As binding. The above results signify that biotechnological application of the isolate NBRI014 could be helpful in removal of As from polluted sites.

Genetic identification of arsenate reductase and arsenite oxidase in redox transformations carried out by arsenic metabolising prokaryotes - A comprehensive review

Arsenic (As) contamination in water is a cause of major concern to human population worldwide, especially in Bangladesh and West Bengal, India. Arsenite (As(III)) and arsenate (As(V)) are the two common forms in which arsenic exists in soil and groundwater, the former being more mobile and toxic. A large number of arsenic metabolising microorganisms play a crucial role in microbial transformation of arsenic between its different states, thus playing a key role in remediation of arsenic contaminated water. This review focuses on advances in biochemical, molecular and genomic developments in the field of arsenic metabolising bacteria - covering recent developments in the understanding of structure of arsenate reductase and arsenite oxidase enzymes, their gene and operon structures and their mechanism of action. The genetic and molecular studies of these microbes and their proteins may lead to evolution of successful strategies for effective implementation of bioremediation programs.

Overexpression of rice glutaredoxins (OsGrxs) significantly reduces arsenite accumulation by maintaining glutathione pool and modulating aquaporins in yeast

Arsenic (As) is an acute poison and class I carcinogen, can cause a serious health risk. Staple crops like rice are the primary source of As contamination in human food. Rice grown on As contaminated areas accumulates higher As in their edible parts. Based on our previous transcriptome data, two rice glutaredoxins (OsGrx_C7 and OsGrx_C2.1) were identified that showed up-regulated expression during As stress. Here, we report OsGrx_C7 and OsGrx_C2.1 from rice involved in the regulation of intracellular arsenite (AsIII). To elucidate the mechanism of OsGrx mediated As tolerance, both OsGrxs were cloned and expressed in Escherichia coli (Δars) and Saccharomyces cerevisiae mutant strains (Δycf1, Δacr3). The expression of OsGrxs increased As tolerance in E. coli (Δars) mutant strain (up to 4 mM AsV and up to 0.6 mM AsIII). During AsIII exposure, S. cerevisiae (Δacr3) harboring OsGrx_C7 and OsGrx_C2.1 have lower intracellular AsIII accumulation (up to 30.43% and 24.90%, respectively), compared to vector control. Arsenic accumulation in As-sensitive S. cerevisiae mutant (Δycf1) also reduced significantly on exposure to inorganic As. The expression of OsGrxs in yeast maintained intracellular GSH pool and increased extracellular GSH concentration. Purified OsGrxs displays in vitro GSH-disulfide oxidoreductase, glutathione reductase and arsenate reductase activities. Also, both OsGrxs are involved in AsIII extrusion by altering the Fps1 transcripts in yeast and protect the cell by maintaining cellular GSH pool. Thus, our results strongly suggest that OsGrxs play a crucial role in the maintenance of the intracellular GSH pool and redox status of the cell during both AsV and AsIII stress and might be involved in regulating intracellular AsIII levels by modulation of aquaporin expression and functions.

ATP-dependent substrate transport by the ABC transporter MsbA is proton-coupled

ATP-binding cassette transporters mediate the transbilayer movement of a vast number of substrates in or out of cells in organisms ranging from bacteria to humans. Current alternating access models for ABC exporters including the multidrug and Lipid A transporter MsbA from Escherichia coli suggest a role for nucleotide as the fundamental source of free energy. These models involve cycling between conformations with inward- and outward-facing substrate-binding sites in response to engagement and hydrolysis of ATP at the nucleotide-binding domains. Here we report that MsbA also utilizes another major energy currency in the cell by coupling substrate transport to a transmembrane electrochemical proton gradient. The dependence of ATP-dependent transport on proton coupling, and the stimulation of MsbA-ATPase by the chemical proton gradient highlight the functional integration of both forms of metabolic energy. These findings introduce ion coupling as a new parameter in the mechanism of this homodimeric ABC transporter.

ABC exporters mediate the translocation of cytotoxic compounds to the cell exterior via ATP hydrolysis. Here, the authors show that the bacterial transporter MsbA requires additional energy from the transmembrane electrochemical proton gradient to facilitate drug transport.

Transition Metal Homeostasis

This chapter focuses on transition metals. All transition metal cations are toxic-those that are essential for Escherichia coli and belong to the first transition period of the periodic system of the element and also the "toxic-only" metals with higher atomic numbers. Common themes are visible in the metabolism of these ions. First, there is transport. High-rate but low-affinity uptake systems provide a variety of cations and anions to the cells. Control of the respective systems seems to be mainly through regulation of transport activity (flux control), with control of gene expression playing only a minor role. If these systems do not provide sufficient amounts of a needed ion to the cell, genes for ATP-hydrolyzing high-affinity but low-rate uptake systems are induced, e.g., ABC transport systems or P-type ATPases. On the other hand, if the amount of an ion is in surplus, genes for efflux systems are induced. By combining different kinds of uptake and efflux systems with regulation at the levels of gene expression and transport activity, the concentration of a single ion in the cytoplasm and the composition of the cellular ion "bouquet" can be rapidly adjusted and carefully controlled. The toxicity threshold of an ion is defined by its ability to produce radicals (copper, iron, chromate), to bind to sulfide and thiol groups (copper, zinc, all cations of the second and third transition period), or to interfere with the metabolism of other ions. Iron poses an exceptional metabolic problem due its metabolic importance and the low solubility of Fe(III) compounds, combined with the ability to cause dangerous Fenton reactions. This dilemma for the cells led to the evolution of sophisticated multi-channel iron uptake and storage pathways to prevent the occurrence of unbound iron in the cytoplasm. Toxic metals like Cd2+ bind to thiols and sulfide, preventing assembly of iron complexes and releasing the metal from iron-sulfur clusters. In the unique case of mercury, the cation can be reduced to the volatile metallic form. Interference of nickel and cobalt with iron is prevented by the low abundance of these metals in the cytoplasm and their sequestration by metal chaperones, in the case of nickel, or by B12 and its derivatives, in the case of cobalt. The most dangerous metal, copper, catalyzes Fenton-like reactions, binds to thiol groups, and interferes with iron metabolism. E. coli solves this problem probably by preventing copper uptake, combined with rapid efflux if the metal happens to enter the cytoplasm.

Effects of Arsenite Resistance on the Growth and Functional Gene Expression of Leptospirillum ferriphilum and Acidithiobacillus thiooxidans in Pure Culture and Coculture

The response of iron-oxidizing Leptospirillum ferriphilum YSK and sulfur-oxidizing Acidithiobacillus thiooxidans A01 to arsenite under pure culture and coculture was investigated based on biochemical characterization (concentration of iron ion and pH value) and related gene expression. L. ferriphilum YSK and At. thiooxidans A01 in pure culture could adapt up to 400 mM and 800 mM As(III) after domestication, respectively, although arsenite showed a negative effect on both strains. The coculture showed a stronger sulfur and ferrous ion oxidation activity when exposed to arsenite. In coculture, the pH value showed no significant difference when under 500 mM arsenite stress, and the cell number of At. thiooxidans was higher than that in pure culture benefiting from the interaction with L. ferriphilum. The expression profile showed that the arsenic efflux system in the coculture was more active than that in pure culture, indicating that there is a synergetic interaction between At. thiooxidans A01 and L. ferriphilum YSK. In addition, a model was proposed to illustrate the interaction between arsenite and the ars operon in L. ferriphilum YSK and At. thiooxidans A01. This study will facilitate the effective application of coculture in the bioleaching process by taking advantage of strain-strain communication and coordination.

Bacterial antimicrobial metal ion resistance

Metals such as mercury, arsenic, copper and silver have been used in various forms as antimicrobials for thousands of years with until recently, little understanding of their mode of action. The discovery of antibiotics and new organic antimicrobial compounds during the twentieth century saw a general decline in the clinical use of antimicrobial metal compounds, with the exception of the rediscovery of the use of silver for burns treatments and niche uses for other metal compounds. Antibiotics and new antimicrobials were regarded as being safer for the patient and more effective than the metal-based compounds they supplanted. Bacterial metal ion resistances were first discovered in the second half of the twentieth century. The detailed mechanisms of resistance have now been characterized in a wide range of bacteria. As the use of antimicrobial metals is limited, it is legitimate to ask: are antimicrobial metal resistances in pathogenic and commensal bacteria important now? This review details the new, rediscovered and 'never went away' uses of antimicrobial metals; examines the prevalence and linkage of antimicrobial metal resistance genes to other antimicrobial resistance genes; and examines the evidence for horizontal transfer of these genes between bacteria. Finally, we discuss the possible implications of the widespread dissemination of these resistances on re-emergent uses of antimicrobial metals and how this could impact upon the antibiotic resistance problem.

Metagenomic approach reveals variation of microbes with arsenic and antimony metabolism genes from highly contaminated soil

Microbes have great potential for arsenic (As) and antimony (Sb) bioremediation in heavily contaminated soil because they have the ability to biotransform As and Sb to species that have less toxicity or are more easily removed. In this study, we integrated a metagenomic method with physicochemical characterization to elucidate the composition of microbial community and functional genes (related to As and Sb) in a high As (range from 34.11 to 821.23 mg kg⁻¹) and Sb (range from 226.67 to 3923.07 mg kg⁻¹) contaminated mine field. Metagenomic analysis revealed that microbes from 18 phyla were present in the 5 samples of soil contaminated with high As and Sb. Moreover, redundancy analysis (RDA) of the relationship between the 18 phyla and the concentration of As and Sb demonstrated that 5 phyla of microbes, i.e. Actinobacteria, Firmicutes, Nitrospirae, Tenericutes and Gemmatimonadetes were positively correlated with As and Sb concentration. The distribution, diversity and abundance of functional genes (including arsC, arrA, aioA, arsB and ACR3) were much higher for the samples containing higher As and Sb concentrations. Based on correlation analysis, the results showed a positive relationship between arsC-like (R² = 0.871) and aioA-like (R² = 0.675) gene abundance and As concentration, and indicated that intracellular As(V) reduction and As(III) oxidation could be the dominant As detoxification mechanism enabling the microbes to survive in the environment. This study provides a direct and reliable reference on the diversity of microbial community and functional genes in an extremely high concentration As- and Sb-contaminated environment.

Involvement of the Acr3 and DctA anti-porters in arsenite oxidation in Agrobacterium tumefaciens 5A

Microbial arsenite (AsIII) oxidation forms a critical piece of the arsenic cycle in nature, though our understanding of how and why microorganisms oxidize AsIII remains rudimentary. Our model organism Agrobacterium tumefaciens 5A contains two distinct ars operons (ars1 and ars2) that are similar in their coding region content. The ars1 operon is located nearby the aio operon that is essential for AsIII oxidation. The AsIII/H(+) anti-porters encoded by acr3-1 and acr3-2 are required for maximal AsIII and antimonite (SbIII) resistance, but acr3-1 (negatively regulated by ArsR-1) appears more active in this regard and also required for AsIII oxidation and expression of aioBA. A malate-phosphate anti-porter DctA is regulated by RpoN and AsIII, and is required for normal growth with malate as a sole carbon source. Qualitatively, a ΔdctA mutant was normal for AsIII oxidation and AsIII/SbIII resistance at metalloid concentrations inhibitory to the Δacr3-1 mutant; however, aioBA induction kinetics was significantly phase-shift delayed. Acr3 involvement in AsIII/SbIII resistance is reasonably well understood, but the role of Acr3 and DctA anti-porters in AsIII oxidation and its regulation is unexpected, and suggests that controlled AsIII trafficking across the cytoplasmic membrane is important to a process understood to occur in the periplasm.

The fronds tonoplast quantitative proteomic analysis in arsenic hyperaccumulator Pteris vittata L

Pteris vittata, the first known arsenic hyperaccumulating plant, can accumulate very high concentration arsenic in its aboveground tissues, while low in roots. Previous studies have suggested that arsenic vacuole compartmentalization may play an important role in the arsenic-hyperaccumulation in P. vittata, but the mechanism(s) of arsenic transport to vacuole are largely unknown. We obtained tonoplast isolated from fronds of P. vittata sporophyte grown under minus and 1mM arsenate for 3weeks by iodixanol step gradient centrifugation method, and then used TMPP protein labeling technology followed by liquid chromatography-a linear ion trap-Orbitrap hybrid mass spectrometer analysis for the quantitative detection of proteins. And we designed and used an "artificial" database for database searching. In total, 56 tonoplast proteins were identified; more than 70% of them were transport proteins. Under arsenate treatment, one TDT transporter protein, a member of the TerC family and a PDR-like protein were upregulated differentially. While V-ATPase subunits c, E, and G, and V-PPase, were downregulated. Additionally, the identified tonoplast proteins in our present study provide an informative basis for arsenic carriers or channels and help to clarify the regulation of tonoplast arsenic transport processes in P. vittata.

BIOLOGICAL SIGNIFICANCE

Vacuole compartmentalization is crucial to As hyperaccumulator P. vittata, while there is limited known arsenic transport proteins involved in vacuole compartmentalization. In this paper, we obtained tonoplast of P. vittata fronds by iodixanol step gradient centrifugation method and then used TMPP protein labeling proteome technology for the quantitative detection of fronds tonoplast proteins. Our findings are the first challenge to the tonoplast proteins data mining of P. vittata which provide an informative basis for As carriers or channels. The proteomic approach in our study is suited for detecting alterations tonoplast protein and help to clarify the regulation of tonoplast transport processes. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

Identification of a novel membrane transporter mediating resistance to organic arsenic in Campylobacter jejuni

Although bacterial mechanisms involved in the resistance to inorganic arsenic are well understood, the molecular basis for organic arsenic resistance has not been described. Campylobacter jejuni, a major food-borne pathogen causing gastroenteritis in humans, is highly prevalent in poultry and is reportedly resistant to the arsenic compound roxarsone (4-hydroxy-3-nitrobenzenearsonic acid), which has been used as a feed additive in the poultry industry for growth promotion. In this study, we report the identification of a novel membrane transporter (named ArsP) that contributes to organic arsenic resistance in Campylobacter. ArsP is predicted to be a membrane permease containing eight transmembrane helices, distinct from other known arsenic transporters. Analysis of multiple C. jejuni isolates from various animal species revealed that the presence of an intact arsP gene is associated with elevated resistance to roxarsone. In addition, inactivation of arsP in C. jejuni resulted in 4- and 8-fold reductions in the MICs of roxarsone and nitarsone, respectively, compared to that for the wild-type strain. Furthermore, cloning of arsP into a C. jejuni strain lacking a functional arsP gene led to 16- and 64-fold increases in the MICs of roxarsone and nitarsone, respectively. Neither mutation nor overexpression of arsP affected the MICs of inorganic arsenic, including arsenite and arsenate, in Campylobacter. Moreover, acquisition of arsP in NCTC 11168 led to accumulation of less roxarsone than the wild-type strain lacking arsP. Together, these results indicate that ArsP functions as an efflux transporter specific for extrusion of organic arsenic and contributes to the resistance to these compounds in C. jejuni.

pGIAK1, a heavy metal resistant plasmid from an obligate alkaliphilic and halotolerant bacterium isolated from the Antarctic Concordia station confined environment

pGIAK1 is a 38-kb plasmid originating from the obligate alkaliphilic and halotolerant Bacillaceae strain JMAK1. The strain was originally isolated from the confined environments of the Antarctic Concordia station. Analysis of the pGIAK1 38,362-bp sequence revealed that, in addition to its replication region, this plasmid contains the genetic determinants for cadmium and arsenic resistances, putative methyltransferase, tyrosine recombinase, spore coat protein and potassium transport protein, as well as several hypothetical proteins. Cloning the pGIAK1 cad operon in Bacillus cereus H3081.97 and its ars operon in Bacillus subtilis 1A280 conferred to these hosts cadmium and arsenic resistances, respectively, therefore confirming their bona fide activities. The pGIAK1 replicon region was also shown to be functional in Bacillus thuringiensis, Bacillus subtilis and Staphylococcus aureus, but was only stably maintained in B. subtilis. Finally, using an Escherichia coli - B. thuringiensis shuttle BAC vector, pGIAK1 was shown to display conjugative properties since it was able to transfer the BAC plasmid among B. thuringiensis strains.

Function of arsATorf7orf8 of Bacillus sp. CDB3 in arsenic resistance

Bacillus sp. CDB3 isolated from an arsenic contaminated cattle dip site possesses an uncommon arsenic resistance (ars) operon bearing eight genes in the order of arsRYCDATorf7orf8. We investigated the functions of arsA, arsT, orf7 and orf8 in arsenic resistance using a plasmid-based gene knockout approach in the ars gene deficient Escherichia coli strain AW3110. The CDB3 arsA gene was shown to play a significant role in resistance, suggesting that the encoded ArsA may couple with the arsenite transporter, forming an ArsAY complex that can enhance arsenite extrusion efficiency. The disruption of either arsTor orf7 was not observed to affect arsenic resistance in the heterologous E. coli host, but their involvement in arsenic resistance can not be excluded. The orf8 gene is predicted to encode a putative dual-specificity protein phosphatase which also shares certain homology to arsenate reductases. The function loss of orf8 resulted in a remarkable decrease in resistance to arsenate, though not arsenite. To examine if this effect was due to the reduction of arsenate by orf8, the arsC gene within the 8-gene operon was disrupted. The resulting abolishment of arsenate resistance suggests that the involvement of orf8 in arsenic resistance is not via reductase activity.

Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas

Background

Some Pseudomonas strains function as predominant plant growth-promoting rhizobacteria (PGPR). Within this group, Pseudomonas chlororaphis and Pseudomonas fluorescens are non-pathogenic biocontrol agents, and some Pseudomonas aeruginosa and Pseudomonas stutzeri strains are PGPR. P. chlororaphis GP72 is a plant growth-promoting rhizobacterium with a fully sequenced genome. We conducted a genomic analysis comparing GP72 with three other pseudomonad PGPR: P. fluorescens Pf-5, P. aeruginosa M18, and the nitrogen-fixing strain P. stutzeri A1501. Our aim was to identify the similarities and differences among these strains using a comparative genomic approach to clarify the mechanisms of plant growth-promoting activity.

Results

The genome sizes of GP72, Pf-5, M18, and A1501 ranged from 4.6 to 7.1 M, and the number of protein-coding genes varied among the four species. Clusters of Orthologous Groups (COGs) analysis assigned functions to predicted proteins. The COGs distributions were similar among the four species. However, the percentage of genes encoding transposases and their inactivated derivatives (COG L) was 1.33% of the total genes with COGs classifications in A1501, 0.21% in GP72, 0.02% in Pf-5, and 0.11% in M18. A phylogenetic analysis indicated that GP72 and Pf-5 were the most closely related strains, consistent with the genome alignment results. Comparisons of predicted coding sequences (CDSs) between GP72 and Pf-5 revealed 3544 conserved genes. There were fewer conserved genes when GP72 CDSs were compared with those of A1501 and M18. Comparisons among the four Pseudomonas species revealed 603 conserved genes in GP72, illustrating common plant growth-promoting traits shared among these PGPR. Conserved genes were related to catabolism, transport of plant-derived compounds, stress resistance, and rhizosphere colonization. Some strain-specific CDSs were related to different kinds of biocontrol activities or plant growth promotion. The GP72 genome contained the cus operon (related to heavy metal resistance) and a gene cluster involved in type IV pilus biosynthesis, which confers adhesion ability.

Conclusions

Comparative genomic analysis of four representative PGPR revealed some conserved regions, indicating common characteristics (metabolism of plant-derived compounds, heavy metal resistance, and rhizosphere colonization) among these pseudomonad PGPR. Genomic regions specific to each strain provide clues to its lifestyle, ecological adaptation, and physiological role in the rhizosphere.

Bacterial metabolism of environmental arsenic--mechanisms and biotechnological applications

Arsenic causes threats for environmental and human health in numerous places around the world mainly due to its carcinogenic potential at low doses. Removing arsenic from contaminated sites is hampered by the occurrence of several oxidation states with different physicochemical properties. The actual state of arsenic strongly depends on its environment whereby microorganisms play important roles in its geochemical cycle. Due to its toxicity, nearly all organisms possess metabolic mechanisms to resist its hazardous effects, mainly by active extrusion, but also by extracellular precipitation, chelation, and intracellular sequestration. Some microbes are even able to actively use various arsenic compounds in their metabolism, either as an electron donor or as a terminal electron acceptor for anaerobic respiration. Some microorganisms can also methylate inorganic arsenic, probably as a resistance mechanism, or demethylate organic arsenicals. Bioavailability of arsenic in water and sediments is strongly influenced by such microbial activities. Therefore, understanding microbial reactions to arsenic is of importance for the development of technologies for improved bioremediation of arsenic-contaminated waters and environments. This review gives an overview of the current knowledge on bacterial interactions with arsenic and on biotechnologies for its detoxification and removal.

The contribution of ArsB to arsenic resistance in Campylobacter jejuni

Arsenic, a toxic metalloid, exists in the natural environment and its organic form is approved for use as a feed additive for animal production. As a major foodborne pathogen of animal origin, Campylobacter is exposed to arsenic selection pressure in the food animal production environments. Previous studies showed that Campylobacter isolates from poultry were highly resistant to arsenic compounds and a 4-gene operon (containing arsP, arsR, arsC, and acr3) was associated with arsenic resistance in Campylobacter. However, this 4-gene operon is only present in some Campylobacter isolates and other arsenic resistance mechanisms in C. jejuni have not been characterized. In this study, we determined the role of several putative arsenic resistance genes including arsB, arsC2, and arsR3 in arsenic resistance in C. jejuni and found that arsB, but not the other two genes, contributes to the resistance to arsenite and arsenate. Inactivation of arsB in C. jejuni resulted in 8- and 4-fold reduction in the MICs of arsenite and arsenate, respectively, and complementation of the arsB mutant restored the MIC of arsenite. Additionally, overexpression of arsB in C. jejuni 11168 resulted in a 16-fold increase in the MIC of arsenite. PCR analysis of C. jejuni isolates from different animals hosts indicated that arsB and acr3 (the 4-gene operon) are widely distributed in various C. jejuni strains, suggesting that Campylobacter requires at least one of the two genes for adaptation to arsenic-containing environments. These results identify ArsB as an alternative mechanism for arsenic resistance in C. jejuni and provide new insights into the adaptive mechanisms of Campylobacter in animal food production environments.

Pathways of arsenic uptake and efflux

Arsenic is the most prevalent environmental toxic substance and ranks first on the U.S. Environmental Protection Agency's Superfund List. Arsenic is a carcinogen and a causative agent of numerous human diseases. Paradoxically arsenic is used as a chemotherapeutic agent for treatment of acute promyelocytic leukemia. Inorganic arsenic has two biological important oxidation states: As(V) (arsenate) and As(III) (arsenite). Arsenic uptake is adventitious because the arsenate and arsenite are chemically similar to required nutrients. Arsenate resembles phosphate and is a competitive inhibitor of many phosphate-utilizing enzymes. Arsenate is taken up by phosphate transport systems. In contrast, at physiological pH, the form of arsenite is As(OH)(3), which resembles organic molecules such as glycerol. Consequently, arsenite is taken into cells by aquaglyceroporin channels. Arsenic efflux systems are found in nearly every organism and evolved to rid cells of this toxic metalloid. These efflux systems include members of the multidrug resistance protein family and the bacterial exchangers Acr3 and ArsB. ArsB can also be a subunit of the ArsAB As(III)-translocating ATPase, an ATP-driven efflux pump. The ArsD metallochaperone binds cytosolic As(III) and transfers it to the ArsA subunit of the efflux pump. Knowledge of the pathways and transporters for arsenic uptake and efflux is essential for understanding its toxicity and carcinogenicity and for rational design of cancer chemotherapeutic drugs.

Mechanisms of metal resistance and homeostasis in haloarchaea

Haloarchaea are the predominant microflora of hypersaline econiches such as solar salterns, soda lakes, and estuaries where the salinity ranges from 35 to 400 ppt. Econiches like estuaries and solar crystallizer ponds may contain high concentrations of metals since they serve as ecological sinks for metal pollution and also as effective traps for river borne metals. The availability of metals in these econiches is determined by the type of metal complexes formed and the solubility of the metal species at such high salinity. Haloarchaea have developed specialized mechanisms for the uptake of metals required for various key physiological processes and are not readily available at high salinity, beside evolving resistance mechanisms for metals with high solubility. The present paper seeks to give an overview of the main molecular mechanisms involved in metal tolerance in haloarchaea and focuses on factors such as salinity and metal speciation that affect the bioavailability of metals to haloarchaea. Global transcriptomic analysis during metal stress in these organisms will help in determining the various factors differentially regulated and essential for metal physiology.

Microbial interactions in the arsenic cycle: adoptive strategies and applications in environmental management

Arsenic (As) is a nonessential element that is often present in plants and in other organisms. However, it is one of the most hazardous of toxic elements globally. In many parts of the world, arsenic contamination in groundwater is a serious and continuing threat to human health. Microbes play an important role in regulating the environmental fate of arsenic. Different microbial processes influence the biogeochemical cycling of arsenic in ways that affect the accumulation of different arsenic species in various ecosystem compartments. For example, in soil, there are bacteria that methylate arsenite to trimethylarsine gas, thereby releasing arsenic to the atmosphere.In marine ecosystems, microbes exist that can convert inorganic arsenicals to organic arsenicals (e.g., di- and tri-methylated arsenic derivatives, arsenocholine,arsenobetaine, arsenosugars, arsenolipids). The organo arsenicals are further metabolized to complete the arsenic cycle.Microbes have developed various strategies that enable them to tolerate arsenic and to survive in arsenic-rich environments. Such strategies include As exclusion from cells by establishing permeability barrier, intra- and extracellular sequestration,active efflux pumps, enzymatic reduction, and reduction in the sensitivity of cellular targets. These strategies are used either singly or in combination. In bacteria,the genes for arsenic resistance/detoxification are encoded by the arsenic resistance operons (ars operon).In this review, we have addressed and emphasized the impact of different microbial processes (e.g., arsenite oxidation, cytoplasmic arsenate reduction, respiratory arsenate reduction, arsenite methylation) on the arsenic cycle. Microbes are the only life forms reported to exist in heavy arsenic-contaminated environments. Therefore,an understanding of the strategies adopted by microbes to cope with arsenic stress is important in managing such arsenic-contaminated sites. Further future insights into the different microbial genes/proteins that are involved in arsenic resistance may also be useful for developing arsenic resistant crop plants.

Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure

Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways.

Role of arsenic and its resistance in nature

Contamination of the environment with heavy metals has increased drastically over the last few decades. The heavy metals that are toxic include mercury, cadmium, arsenic, and selenium. Of these heavy metals, arsenic is one of the most important global environmental pollutants and is a persistent bioaccumulative carcinogen. It is a toxic metalloid that exists in two major inorganic forms: arsenate and arsenite. Arsenite disrupts enzymatic functions in cells, while arsenate behaves as a phosphate analog and interferes with phosphate uptake and utilization. Despite its toxicity, arsenic may be actively sequestered in plant and animal tissues. Various microbes interact with this metal and have shown resistance to arsenic exposure, and they appear to possess the ars operon for arsenic resistance consisting of three to five genes, i.e., arsRBC or arsRDABC, organized into a single transcriptional unit; some microbes even use it for respiration. Microbial interactions with metals may have several implications for the environment. Microbes may play a role in cycling of toxic heavy metals and in remediation of metal-contaminated sites. There is a correlation between tolerance to heavy metals and antibiotic resistance, a global problem currently threatening the treatment of infections in plants, animals, and humans. The purpose of this review is to highlight the nature and role of toxic arsenic in bacterial systems and to discuss the various genes responsible for this heavy-metal resistance in nature and the mechanisms to detoxify this element.

The ArsD As(III) metallochaperone

Arsenic, a toxic metalloid widely existing in the environment, causes a variety of health problems. The ars operon encoded by Escherichia coli plasmid R773 has arsD and arsA genes, where ArsA is an ATPase that is the catalytic subunit of the ArsAB As(III) extrusion pump, and ArsD is an arsenic chaperone for ArsA. ArsD transfers As(III) to ArsA and increases the affinity of ArsA for As(III), allowing resistance to environmental concentrations of arsenic. Cys12, Cys13 and Cys18 in ArsD form a three sulfur-coordinated As(III) binding site that is essential for metallochaperone activity. ATP hydrolysis by ArsA is required for transfer of As(III) from ArsD to ArsA, suggesting that transfer occurs with a conformation of ArsA that transiently forms during the catalytic cycle. The 1.4 Å x-ray crystal structure of ArsD shows a core of four β-strands flanked by four α-helices in a thioredoxin fold. Docking of ArsD with ArsA was modeled in silico. Independently ArsD mutants exhibiting either weaker or stronger interaction with ArsA were selected. The locations of the mutations mapped on the surface of ArsD are consistent with the docking model. The results suggest that the interface with ArsA involves one surface of α1 helix and metalloid binding site of ArsD.

A Rhodobacter capsulatus member of a universal permease family imports molybdate and other oxyanions

Molybdenum (Mo) is an important trace element that is toxic at high concentrations. To resolve the mechanisms underlying Mo toxicity, Rhodobacter capsulatus mutants tolerant to high Mo concentrations were isolated by random transposon Tn5 mutagenesis. The insertion sites of six independent isolates mapped within the same gene predicted to code for a permease of unknown function located in the cytoplasmic membrane. During growth under Mo-replete conditions, the wild-type strain accumulated considerably more Mo than the permease mutant. For mutants defective for the permease, the high-affinity molybdate importer ModABC, or both transporters, in vivo Mo-dependent nitrogenase (Mo-nitrogenase) activities at different Mo concentrations suggested that ModABC and the permease import molybdate in nanomolar and micromolar ranges, respectively. Like the permease mutants, a mutant defective for ATP sulfurylase tolerated high Mo concentrations, suggesting that ATP sulfurylase is the main target of Mo inhibition in R. capsulatus. Sulfate-dependent growth of a double mutant defective for the permease and the high-affinity sulfate importer CysTWA was reduced compared to those of the single mutants, implying that the permease plays an important role in sulfate uptake. In addition, permease mutants tolerated higher tungstate and vanadate concentrations than the wild type, suggesting that the permease acts as a general oxyanion importer. We propose to call this permease PerO (for oxyanion permease). It is the first reported bacterial molybdate transporter outside the ABC transporter family.

The extreme C terminus of the ABC protein DrrA contains unique motifs involved in function and assembly of the DrrAB complex

Two novel regulatory motifs, LDEVFL and C-terminal regulatory Glu (E)-rich motif (CREEM), are identified in the extreme C terminus of the ABC protein DrrA, which is involved in direct interaction with the N-terminal cytoplasmic tail of the membrane protein DrrB and in homodimerization of DrrA. Disulfide cross-linking analysis showed that the CREEM and the region immediately upstream of CREEM participate directly in forming an interaction interface with the N terminus of DrrB. A series of mutations created in the LDEVFL and CREEM motifs drastically affected overall function of the DrrAB transporter. Mutations in the LDEVFL motif also significantly impaired interaction between the C terminus of DrrA and the N terminus of DrrB as well as the ability of DrrA and DrrB to co-purify, therefore suggesting that the LDEVFL motif regulates CREEM-mediated interaction between DrrA and DrrB and plays a key role in biogenesis of the DrrAB complex. Modeling analysis indicated that the LDEVFL motif is critical for conformational integrity of the C-terminal domain of DrrA and confirmed that the C terminus of DrrA forms an independent domain. This is the first report which describes the presence of an assembly domain in an ABC protein and uncovers a novel mechanism whereby the ABC component facilitates the assembly of the membrane component. Homology sequence comparisons showed the presence of the LDEVFL and CREEM motifs in close prokaryotic and eukaryotic homologs of DrrA, suggesting that these motifs may play a similar role in other homologous drug and lipid export systems.

Biochemical characterization of a novel ArsA ATPase complex from Alkaliphilus metalliredigens QYMF

The two putative ars operons in Alkaliphilus metalliredigens QYMF are distinctive in that the arsA gene is split in halves, amarsA1 and amarsA2, and, acr3 but not an arsB gene coexists with arsA. Heterologous expression of one of the A. metalliredigensars operons (ars1) conferred arsenite but not antimonite resistance to DeltaarsEscherichia coli. Only the co-expressed AmArsA1 and AmArsA2 displayed arsenite or antimonite stimulated ATPase activity. The results show that AmArsA1-AmArsA2 interaction is needed to form the functional ArsA ATPase. This novel AmArsA1-AmArsA2 complex may provide insight in how it participates with Acr3 in arsenite detoxification.

Archaeal transformation of metals in the environment

We are becoming increasingly aware of the role played by archaea in the biogeochemical cycling of the elements. Metabolism of metals is linked to fundamental metabolic functions, including nitrogen fixation, energy production, and cellular processes based on oxidoreductions. Comparative genomic analyses have shown that genes for metabolism, resistance, and detoxification of metals are widespread throughout the archaeal domain. Archaea share with other organisms strategies allowing them to utilize essential metals and maintain metal ions within a physiological range, although comparative proteomics show, in a few cases, preferences for specific genetic traits related to metals. A more in-depth understanding of the physiology of acidophilic archaea might lead to the development of new strategies for the bioremediation of metal-polluted sites and other applications, such as biomining.

Arsenic-resistant bacteria associated with roots of the wild Cirsium arvense (L.) plant from an arsenic polluted soil, and screening of potential plant growth-promoting characteristics

A rhizobacterial community, associated with the roots of wild thistle Cirsium arvense (L.) growing in an arsenic polluted soil, was studied by fluorescence in situ hybridization (FISH) analysis in conjunction with cultivation-based methods. In the bulk, rhizosphere, and rhizoplane fractions of the soil, the qualitative picture obtained by FISH analysis of the main phylogenetic bacterial groups was similar and was predominantly comprised of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. The arsenic-resistant isolates belonged to 13 genera, the most abundant being those of Bacillus, Achromobacter, Brevundimonas, Microbacterium, and Ochrobactrum. Most bacteria grew in the presence of high arsenic concentrations (over 100mM arsenate and 10mM arsenite). Most strains possessed the ArsC, ArsB and ACR3 genes homologous to arsenate reductase and to the two classes of arsenite efflux pumps, respectively, peculiar to the ars operon of the arsenic detoxification system. ArsB and ACR3 were present simultaneously in highly resistant strains. An inconsistency between 16S rRNA phylogenetic affiliations and the arsenate reductase sequences of the strains was observed, indicating possible horizontal transfer of arsenic resistance genes in the soil bacterial community. Several isolates were able to reduce arsenate and to oxidise arsenite. In particular, Ancylobacter dichloromethanicum strain As3-1b possessed both characteristics, and arsenite oxidation occurred in the strain also under chemoautotrophic conditions. Some rhizobacteria produced siderophores, indole acetic acid and 1-amino-cyclopropane-1-carboxylic acid deaminase, thus possessing potential plant growth-promoting traits.

Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042

BACKGROUND

Escherichia coli can experience a multifaceted life, in some cases acting as a commensal while in other cases causing intestinal and/or extraintestinal disease. Several studies suggest enteroaggregative E. coli are the predominant cause of E. coli-mediated diarrhea in the developed world and are second only to Campylobacter sp. as a cause of bacterial-mediated diarrhea. Furthermore, enteroaggregative E. coli are a predominant cause of persistent diarrhea in the developing world where infection has been associated with malnourishment and growth retardation.

METHODS

In this study we determined the complete genomic sequence of E. coli 042, the prototypical member of the enteroaggregative E. coli, which has been shown to cause disease in volunteer studies. We performed genomic and phylogenetic comparisons with other E. coli strains revealing previously uncharacterised virulence factors including a variety of secreted proteins and a capsular polysaccharide biosynthetic locus. In addition, by using Biolog Phenotype Microarrays we have provided a full metabolic profiling of E. coli 042 and the non-pathogenic lab strain E. coli K-12. We have highlighted the genetic basis for many of the metabolic differences between E. coli 042 and E. coli K-12.

CONCLUSION

This study provides a genetic context for the vast amount of experimental and epidemiological data published thus far and provides a template for future diagnostic and intervention strategies.

Identification of an arsenic resistance and arsenic-sensing system in Campylobacter jejuni

Arsenic is commonly present in the natural environment and is also used as a feed additive for animal production. Poultry is a major reservoir for Campylobacter jejuni, a major food-borne human pathogen causing gastroenteritis. It has been shown that Campylobacter isolates from poultry are highly resistant to arsenic compounds, but the molecular mechanisms responsible for the resistance have not been determined, and it is unclear if the acquired arsenic resistance affects the susceptibility of Campylobacter spp. to other antimicrobials. In this study, we identified a four-gene operon that contributes to arsenic resistance in Campylobacter. This operon encodes a putative membrane permease (ArsP), a transcriptional repressor (ArsR), an arsenate reductase (ArsC), and an efflux protein (Acr3). PCR analysis of various clinical C. jejuni isolates indicated a significant association of this operon with elevated resistance to arsenite and arsenate. Gene-specific mutagenesis confirmed the role of the ars operon in conferring arsenic resistance. It was further shown that this operon is subject to regulation by ArsR, which directly binds to the ars promoter and inhibits the transcription of the operon. Arsenite inhibits the binding of ArsR to the ars promoter DNA and induces the expression of the ars genes. Mutation of the ars genes did not affect the susceptibility of C. jejuni to commonly used antibiotics. These results identify the ars operon as an important mechanism for arsenic resistance and sensing in Campylobacter.

Diversity of arsenate reductase genes (arsC Genes) from arsenic-resistant environmental isolates of E. coli

A polymerase chain reaction (PCR) approach was used to assess the occurrence and diversity of arsenate reductase gene (arsC gene) in arsenic-resistant environmental E. coli strains. For this purpose, two different sets of primers were designed for the specific amplification of approximately 370-bp fragments from the arsC gene. These primers were used to screen a collection of 25 environmental arsenic-resistant strains isolated from different geographical regions of India, as well as Bangladesh. The PCR results showed that 17 out of the 25 environmental isolates (68%) contained a gene related to the arsC family. Phylogenetic analysis of the protein sequences deduced from the amplicons indicated a prevalence of arsC genes in the isolated strains. A significant divergence in the DNA sequence was found in the arsC genes among As-resistant environmental E. coli strains from this study, and arsenic resistance, a genetic character, arose from a common ancestral background.