Responses to arsenate stress by Comamonas sp. strain CNB-1 at genetic and proteomic levels

Dissimilatory and Cytoplasmic Antimonate Reductions in a Hydrogen-Based Membrane Biofilm Reactor

A hydrogen-based membrane biofilm reactor (H₂-MBfR) was operated to investigate the bioreduction of antimonate [Sb(V)] in terms of Sb(V) removal, the fate of Sb, and the pathways of reduction metabolism. The MBfR achieved up to 80% Sb(V) removal and an Sb(V) removal flux of 0.55 g/m²·day. Sb(V) was reduced to Sb(III), which mainly formed Sb₂O₃ precipitates in the biofilm matrix, although some Sb(III) was retained intracellularly. High Sb(V) loading caused stress that deteriorated performance that was not recovered when the high Sb(V) loading was removed. The biofilm community consisted of DSbRB (dissimilatory Sb-reduction bacteria), SbRB (Sb-resistant bacteria), and DIRB (dissimilatory iron-reducing bacteria). Dissimilatory antimonate reduction, mediated by the respiratory arsenate reductase ArrAB, was the main reduction route, but respiratory reduction coexisted with cytoplasmic Sb(V)-reduction mediated by arsenate reductase ArsC. Increasing Sb(V) loading caused stress that led to increases in the expression of arsC gene and intracellular accumulation of Sb(III). By illuminating the roles of the dissimilatory and cytoplasmic Sb(V) reduction mechanism in the biofilms of the H₂-MBfR, this study reveals that the Sb(V) loading should be controlled to avoid stress that deteriorates Sb(V) reduction.

Arsenic Response of Three Altiplanic Exiguobacterium Strains With Different Tolerance Levels Against the Metalloid Species: A Proteomics Study

Exiguobacterium is a polyextremophile bacterial genus with a physiology that allows it to develop in different adverse environments. The Salar de Huasco is one of these environments due to its altitude, atmospheric pressure, solar radiation, temperature variations, pH, salinity, and the presence of toxic compounds such as arsenic. However, the physiological and/or molecular mechanisms that enable them to prosper in these environments have not yet been described. Our research group has isolated several strains of Exiguobacterium genus from different sites of Salar de Huasco, which show different resistance levels to As(III) and As(V). In this work, we compare the protein expression patterns of the three strains in response to arsenic by a proteomic approach; strains were grown in absence of the metalloid and in presence of As(III) and As(V) sublethal concentrations and the protein separation was carried out in 2D electrophoresis gels (2D-GE). In total, 999 spots were detected, between 77 and 173 of which showed significant changes for As(III) among the three strains, and between 90 and 143 for As(V), respectively, compared to the corresponding control condition. Twenty-seven of those were identified by mass spectrometry (MS). Among these identified proteins, the ArsA [ATPase from the As(III) efflux pump] was found to be up-regulated in response to both arsenic conditions in the three strains, as well as the Co-enzyme A disulfide reductase (Cdr) in the two more resistant strains. Interestingly, in this genus the gene that codifies for Cdr is found within the genic context of the ars operon. We suggest that this protein could be restoring antioxidants molecules, necessary for the As(V) reduction. Additionally, among the proteins that change their expression against As, we found several with functions relevant to stress response, e.g., Hpf, LuxS, GLpX, GlnE, and Fur. This study allowed us to shed light into the physiology necessary for these bacteria to be able to tolerate the toxicity and stress generated by the presence of arsenic in their niche.

Study on the mechanism underlying Al-induced hepatotoxicity based on the identification of the Al-binding proteins in liver

Aluminum (Al) is the most abundant metal element in the earth's crust, and is implicated in the pathogenesis of liver lesions. However, the mechanisms underlying Al³⁺-induced hepatotoxicity are still largely elusive. Based on analysis with native gel electrophoresis, Al³⁺ plus 8-hydroxyquinoline staining and LC-MS/MS, the proteins with high Al³⁺ affinity were identified to be carbamoyl-phosphate synthase, adenosylhomocysteinase, heat shock protein 90-alpha, carbonic anhydrase 3, serum albumin and calreticulin. These proteins are involved in physiological processes such as the urea cycle, redox reactions, apoptosis and so on. Then we established an Al³⁺-treated rat model for biochemical tests, morphology observation and Ca²⁺ homeostasis analysis, in order to evaluate the extent of oxidative damage, hepatic histopathology and specific indicators of Al³⁺-related proteins in liver. Our findings indicated the high-affinity interactions with Al³⁺ perturbed the normal function of the above proteins, which could account for the mechanism underlying Al³⁺-induced hepatotoxicity.

Expression of Genes and Proteins Involved in Arsenic Respiration and Resistance in Dissimilatory Arsenate-Reducing Geobacter sp. Strain OR-1

The reduction of arsenate [As(V)] to arsenite [As(III)] by dissimilatory As(V)-reducing bacteria, such as Geobacter spp., may play a significant role in arsenic release from anaerobic sediments into groundwater. The biochemical and molecular mechanisms by which these bacteria cope with this toxic element remain unclear. In this study, the expression of several genes involved in arsenic respiration (arr) and resistance (ars) was determined using Geobacter sp. strain OR-1, the only cultured Geobacter strain capable of As(V) respiration. In addition, proteins expressed differentially under As(V)-respiring conditions were identified by semiquantitative proteomic analysis. Dissimilatory As(V) reductase (Arr) of strain OR-1 was localized predominantly in the periplasmic space, and the transcription of its gene (arrA) was upregulated under As(V)-respiring conditions. The transcription of the detoxifying As(V) reductase gene (arsC) was also upregulated, but its induction required 500 times higher concentration of As(III) (500 μM) than did the arrA gene. Comparative proteomic analysis revealed that in addition to the Arr and Ars proteins, proteins involved in the following processes were upregulated under As(V)-respiring conditions: (i) protein folding and assembly for rescue of proteins with oxidative damage, (ii) DNA replication and repair for restoration of DNA breaks, (iii) anaplerosis and gluconeogenesis for sustainable energy production and biomass formation, and (iv) protein and nucleotide synthesis for the replacement of damaged proteins and nucleotides. These results suggest that strain OR-1 copes with arsenic stress by orchestrating pleiotropic processes that enable this bacterium to resist and actively metabolize arsenic.IMPORTANCE Dissimilatory As(V)-reducing bacteria, such as Geobacter spp., play significant roles in arsenic release and contamination in groundwater and threaten the health of people worldwide. However, the biochemical and molecular mechanisms by which these bacteria cope with arsenic toxicity remain unclear. In this study, it was found that both respiratory and detoxifying As(V) reductases of a dissimilatory As(V)-reducing bacterium, Geobacter sp. strain OR-1, were upregulated under As(V)-respiring conditions. In addition, various proteins expressed specifically or more abundantly in strain OR-1 under arsenic stress were identified. Strain OR-1 actively metabolizes arsenic while orchestrating various metabolic processes that repair oxidative damage caused by arsenic. Such information is useful in assessing and identifying possible countermeasures for the prevention of microbial arsenic release in nature.

Reprogramming One-Carbon Metabolic Pathways To Decouple l-Serine Catabolism from Cell Growth in Corynebacterium glutamicum

l-Serine, the principal one-carbon source for DNA biosynthesis, is difficult for microorganisms to accumulate due to the coupling of l-serine catabolism and microbial growth. Here, we reprogrammed the one-carbon unit metabolic pathways in Corynebacterium glutamicum to decouple l-serine catabolism from cell growth. In silico model-based simulation showed a negative influence on glyA-encoding serine hydroxymethyltransferase flux with l-serine productivity. Attenuation of glyA transcription resulted in increased l-serine accumulation, and a decrease in purine pools, poor growth and longer cell shapes. The gcvTHP-encoded glycine cleavage (Gcv) system from Escherichia coli was introduced into C. glutamicum, allowing glycine-derived ¹³CH₂ to be assimilated into intracellular purine synthesis, which resulted in an increased amount of one-carbon units. Gcv introduction not only restored cell viability and morphology but also increased l-serine accumulation. Moreover, comparative proteomic analysis indicated that abundance changes of the enzymes involved in one-carbon unit cycles might be responsible for maintaining one-carbon unit homeostasis. Reprogramming of the one-carbon metabolic pathways allowed cells to reach a comparable growth rate to accumulate 13.21 g/L l-serine by fed-batch fermentation in minimal medium. This novel strategy provides new insights into the regulation of cellular properties and essential metabolite accumulation by introducing an extrinsic pathway.

Effects upon metabolic pathways and energy production by Sb(III) and As(III)/Sb(III)-oxidase gene aioA in Agrobacterium tumefaciens GW4

Agrobacterium tumefaciens GW4 is a heterotrophic arsenite [As(III)]/antimonite [Sb(III)]-oxidizing strain. The As(III) oxidase AioAB is responsible for As(III) oxidation in the periplasm and it is also involved in Sb(III) oxidation in Agrobacterium tumefaciens 5A. In addition, Sb(III) oxidase AnoA and cellular H₂O₂ are also responsible for Sb(III) oxidation in strain GW4. However, the deletion of aioA increased the Sb(III) oxidation efficiency in strain GW4. In the present study, we found that the cell mobility to Sb(III), ATP and NADH contents and heat release were also increased by Sb(III) and more significantly in the aioA mutant. Proteomics and transcriptional analyses showed that proteins/genes involved in Sb(III) oxidation and resistance, stress responses, carbon metabolism, cell mobility, phosphonate and phosphinate metabolism, and amino acid and nucleotide metabolism were induced by Sb(III) and were more significantly induced in the aioA mutant. The results suggested that Sb(III) oxidation may produce energy. In addition, without periplasmic AioAB, more Sb(III) would enter bacterial cells, however, the cytoplasmic AnoA and the oxidative stress response proteins were significantly up-regulated, which may contribute to the increased Sb(III) oxidation efficiency. Moreover, the carbon metabolism was also activated to generate more energy against Sb(III) stress. The generated energy may be used in Sb transportation, DNA repair, amino acid synthesis, and cell mobility, and may be released in the form of heat.

Diversity, metal resistance and uranium sequestration abilities of bacteria from uranium ore deposit in deep earth stratum

Metal resistance and uranium (U) sequestration abilities of bacteria residing in subsurface U ore was investigated using 122 pure culture strains isolated through enrichment. The cumulative frequencies of isolates resistant to each metal tested were as follows: As(V), 74%; Zn, 58%; Ni, 53%; Cd, 47%; Cr(VI), 41%; Co, 40%; Cu, 20%; and Hg, 4%. 16S rRNA gene analysis revealed that isolated bacteria belonged to 14 genera with abundance of Arthrobacter, Microbacterium, Acinetobacter and Stenotrophomonas. Cobalt did not interfere with the growth of most of the bacterial isolates belonging to different groups while U allowed growth of four different genera of which Stenotrophomonas and Microbacterium showed high U tolerance. Interestingly, tolerance to Ni, Zn, Cu, and Hg was observed only in Microbacterium, Arthrobacter, Paenibacillus¸ and Acinetobacter, respectively. However, Microbacterium was found to be dominant when isolated from other five different metal enrichments including U. Uranium removal study showed that 84% of the test bacteria could remove more than 50mgUg(-1) dry weight from 80 or 160mgL(-1) U within 48h. In general, Microbacterium, Arthrobacter and Acinetobacter could remove a higher amount of U. High resolution transmission electron microscopy (HRTEM) study of U exposed cells revealed that accumulated U sequestered mostly around the cell periphery. The study highlights that indigenous U ore deposit bacteria have the potential to interact with U, and thus could be applied for bioremediation of U contaminated sites or wastes.

Evidences for Chlorogenic Acid--A Major Endogenous Polyphenol Involved in Regulation of Ripening and Senescence of Apple Fruit

To learn how the endogenous polyphenols may play a role in fruit ripening and senescence, apple pulp discs were used as a model to study the influences of chlorogenic acid (CHA, a major polyphenol in apple pulp) on fruit ripening and senescence. Apple ('Golden Delicious') pulp discs prepared from pre-climacteric fruit were treated with 50 mg L(-1) CHA and incubated in flasks with 10 mM MES buffer (pH 6.0, 11% sorbitol). Compared to the control samples, treatment with CHA significantly reduced ethylene production and respiration rate, and enhanced levels of firmness and soluble solids content of the pulp discs during incubation at 25°C. These results suggested that CHA could retard senescence of the apple pulp discs. Proteomics analysis with sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometry (MALDI-TOF/TOF) revealed that the expressions of several key proteins correlated to fruit ripening and senescence were affected by the treatment with CHA. Further study showed that treating the pulp discs with CHA remarkably reduced levels of lipoxygenase, β-galactosidase, NADP-malic enzyme, and enzymatic activities of lipoxygenase and UDP-glucose pyrophosphorylase, all of which are known as promoters of fruit ripening and senescence. These results could provide new insights into the functions of endogenous phenolic compounds in fruit ripening and senescence.

High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains

BACKGROUND

Members of Comamonas testosteroni are environmental microorganisms that are usually found in polluted environment samples. They utilize steroids and aromatic compounds but rarely sugars, and show resistance to multiple heavy metals and multiple drugs. However, comprehensive genomic analysis among the C. testosteroni strains is lacked.

RESULTS

To understand the genome bases of the features of C. testosteroni, we sequenced 10 strains of this species and analyzed them together with other related published genome sequences. The results revealed that: 1) the strains of C. testosteroni have genome sizes ranging from 5.1 to 6.0 Mb and G + C contents ranging from 61.1% to 61.8%. The pan-genome contained 10,165 gene families and the core genome contained 3,599 gene families. Heap's law analysis indicated that the pan-genome of C. testosteroni may be open (α = 0.639); 2) by analyzing 31 phenotypes of 11 available C. testosteroni strains, 99.4% of the genotypes (putative genes) were found to be correlated to the phenotypes, indicating a high correlation between phenotypes and genotypes; 3) gene clusters for nitrate reduction, steroids degradation and metal and multi-drug resistance were found and were highly conserved among all the genomes of this species; 4) the genome similarity of C. testosteroni may be related to the geographical distances.

CONCLUSIONS

This work provided an overview on the genomes of C. testosteroni and new genome resources that would accelerate the further investigations of this species. Importantly, this work focused on the analysis of potential genetic determinants for the typical characters and found high correlation between the phenotypes and their corresponding genotypes.

Proteomics of arsenic stress in the gram-positive organism Exiguobacterium sp. PS NCIM 5463

The general responses of microorganisms to environmental onslaughts are modulated by altering the gene expression pattern to reduce damage in the cell and produce compensating stress responses. The present study attempts to unravel the response of the Gram-positive Exiguobacterium sp. PS NCIM 5463 in the presence of [As(III)] and arsenate [As(V)] using comparative proteomics via two-dimension gel electrophoresis (2-DE) coupled with identification of proteins using matrix-assisted laser desorption/ionisation (MALDI-TOF/MALDI-TOF/TOF). Out of 926 Coomassie-stained proteins, 45 were differentially expressed (p < 0.05). Considering the resolution and abundance level, 24 spots (peptides) were subjected to MALDI analysis, identified and categorised into several functional categories, viz., nitrogen metabolism, energy and stress regulators, carbohydrate metabolism, protein synthesis components and others. A functional role of each protein is discussed in Exiguobacterium sp. PS 5463 under arsenic stress and validated at their transcript level using a quantitative real-time polymerase chain reaction. Unlike previous reports that unravel the responses toward arsenic stress in Gram-negative organisms, the present study identified new proteins under arsenic stress in a Gram-positive organism, Exiguobacterium sp. PS NCIM 5463, which could elucidate the physiology of organisms under arsenic stress.

Genomic responses to arsenic in the cyanobacterium Synechocystis sp. PCC 6803

Arsenic is a ubiquitous contaminant and a toxic metalloid which presents two main redox states in nature: arsenite [As^III] and arsenate [As^V]. Arsenic resistance in Synechocystis sp. strain PCC 6803 is mediated by the arsBHC operon and two additional arsenate reductases encoded by the arsI1 and arsI2 genes. Here we describe the genome-wide responses to the presence of arsenate and arsenite in wild type and mutants in the arsenic resistance system. Both forms of arsenic produced similar responses in the wild type strain, including induction of several stress related genes and repression of energy generation processes. These responses were transient in the wild type strain but maintained in time in an arsB mutant strain, which lacks the arsenite transporter. In contrast, the responses observed in a strain lacking all arsenate reductases were somewhat different and included lower induction of genes involved in metal homeostasis and Fe-S cluster biogenesis, suggesting that these two processes are targeted by arsenite in the wild type strain. Finally, analysis of the arsR mutant strain revealed that ArsR seems to only control 5 genes in the genome. Furthermore, the arsR mutant strain exhibited hypersentivity to nickel, copper and cadmium and this phenotype was suppressed by mutation in arsB but not in arsC gene suggesting that overexpression of arsB is detrimental in the presence of these metals in the media.

Enhanced Photosynthesis and Carbon Metabolism Favor Arsenic Tolerance in Artemisia annua, a Medicinal Plant as Revealed by Homology-Based Proteomics

This paper provides the first proteomic evidence of arsenic (As) tolerance and interactive regulatory network between primary and secondary metabolism in the medicinal plant, Artemisia annua. While chlorophyll fluorescence and photosynthetic rate depicted mild inhibition, there was a significant enhancement in PSI activity, whole chain, ATP, and NADPH contents in 100 μM As treatments compared to the control plants. However, a decrease in the above variables was recorded under 150 μM treatments. Proteomic decoding of the survival strategy of A. annua under As stress using 2-DE followed by MALDI-MS/MS revealed a total of 46 differentially expressed protein spots. In contrast to other plants where As inhibits photosynthesis, A. annua showed appreciable photosynthetic CO₂ assimilation and allocation of carbon resources at 100 μM As concentration. While an increased accumulation of ATP synthase, ferredoxin-NADP(H) oxidoreductase, and FeS-rieske proteins supported the operation of cyclic electron transport, mdr ABC transporter protein and pcs gene might be involved in As detoxification. The most interesting observation was an increased accumulation of LEAFY like novel protein conceivably responsible for an early onset of flowering in A. annua under As stress. This study not only affirmed the role of energy metabolism proteins but also identified potential candidates responsible for As tolerance in plants.

Benzoate metabolism intermediate benzoyl coenzyme A affects gentisate pathway regulation in Comamonas testosteroni

A previous study showed that benzoate was catabolized via a coenzyme A (CoA)-dependent epoxide pathway in Azoarcus evansii (R. Niemetz, U. Altenschmidt, S. Brucker, and G. Fuchs, Eur. J. Biochem. 227:161-168, 1995), but gentisate 1,2-dioxygenase was induced. Similarly, we found that the Comamonas testosteroni strain CNB-1 degraded benzoate via a CoA-dependent epoxide pathway and that gentisate 1,2-dioxygenase (GenA) was also induced when benzoate or 3-hydroxybenzoate served as a carbon source for growth. Genes encoding the CoA-dependent epoxide (box genes) and gentisate (gen genes) pathways were identified. Genetic disruption revealed that the gen genes were not involved in benzoate and 3-hydroxybenzoate degradation. Hence, we investigated gen gene regulation in the CNB-1 strain. The PgenA promoter, a MarR-type regulator (GenR), and the GenR binding site were identified. We found that GenR took gentisate, 3-hydroxybenzoate, and benzoyl-CoA as effectors and that binding of GenR to its target DNA sequence was prohibited when these effectors were present. In vivo studies showed that the CNB-1 mutant that lost benzoyl-CoA synthesis was not able to activate PgenA promoter, while transcription of genA was upregulated in another CNB-1 mutant that lost the ability to degrade benzoyl-CoA. The finding that benzoyl-CoA (a metabolic intermediate of benzoate degradation) and 3-hydroxybenzoate function as GenR effectors explains why GenA was induced when CNB-1 grew on benzoate or 3-hydroxybenzoate. Regulation of gentisate pathways by MarR-, LysR-, and IclR-type regulators in diverse bacterial groups is discussed in detail.

Permanent draft genome sequence of Comamonas testosteroni KF-1

Comamonas testosteroni KF-1 is a model organism for the elucidation of the novel biochemical degradation pathways for xenobiotic 4-sulfophenylcarboxylates (SPC) formed during biodegradation of synthetic 4-sulfophenylalkane surfactants (linear alkylbenzenesulfonates, LAS) by bacterial communities. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,026,527 bp long chromosome (one sequencing gap) exhibits an average G+C content of 61.79% and is predicted to encode 5,492 protein-coding genes and 114 RNA genes.

Proteomic approach of adaptive response to arsenic stress in Exiguobacterium sp. S17, an extremophile strain isolated from a high-altitude Andean Lake stromatolite

The North-Western part of Argentina is particularly rich in wetlands located in the Puna in an altitude between 3,600 and 4,600 m above sea level. Most of these high-altitude Andean lakes are inhospitable areas due to extreme habitat conditions such as high contents of toxic elements, particularly arsenic. Exiguobacterium sp. S17, isolated from stromatolites in Laguna Socompa, exhibited remarkable tolerance to high arsenic concentration, i.e., it tolerated arsenic concentration such as 10 mM of As(III) and 150 mM of As(V). A proteomics approach was conducted to reveal the mechanisms that provide the observed outstanding resistance of Exiguobacterium sp. S17 against arsenic. A comparative analysis of S17, exposed and unexposed to arsenic revealed 25 differentially expressed proteins. Identification of these proteins was performed by MALDI-TOF/MS revealing upregulation of proteins involved in energy metabolism, stress, transport, and in protein synthesis being expressed under arsenic stress. To our knowledge, this work represents the first proteomic study of arsenic tolerance in an Exiguobacterium strain.

Proteomics combines morphological, physiological and biochemical attributes to unravel the survival strategy of Anabaena sp. PCC7120 under arsenic stress

Proteomics in conjunction with morphological, physiological and biochemical variables has been employed for the first time to unravel survival strategies of the diazotrophic cyanobacterium Anabaena sp. PCC7120 under Arsenic (As) stress. Significant reduction in growth, carbon fixation, nitrogenase activity and chlorophyll content after 1 day (1d) and recovery after 15 days (15d) of As exposure indicates the acclimation of the test organism against As stress. The formation of akinete like structures is a novel observation never reported before in Anabaena sp. PCC7120. Proteomic characterization using 2-DE showed average 537, 422 and 439 spots in control, 1 and 15d treatment respectively. MALDI-TOF and LC-MS of As-treated Anabaena revealed a total of 45 differentially expressed proteins, of which 13 were novel (hypothetical) ones. Down-regulation of phosphoglycerate kinase (PGK), fructose bisphosphate aldolase II (FBA II), fructose 1,6 bisphosphatase (FBPase), transketolase (TK), and ATP synthase on day 1 and their significant recovery on the 15th day presumably maintained the glycolysis, pentose phosphate pathway (PPP) and turnover rate of Calvin cycle, hence survival of the test organism. Up-regulation of catalase (CAT), peroxiredoxin (Prx), thioredoxin (Trx) and oxidoreductase appears to protect the cells from oxidative stress. Appreciable induction in phytochelatin content (2.4 fold), GST activity (2.3 fold), and transcripts of phytochelatin synthase (5.0 fold), arsenate reductase (8.5 fold) and arsenite efflux genes - asr1102 (5.0 fold), alr1097 (4.7 fold) reiterates their role in As sequestration and shielding of the organism from As toxicity. While up-regulated metabolic and antioxidative defense proteins, phytochelatin and GST work synchronously, the ars genes play a central role in detoxification and survival of Anabaena under As stress. The proposed hypothetical model explains the interaction of metabolic proteins associated with the survival of Anabaena sp. PCC7120 under As stress.

Molecular diversity of katG genes in the soil bacteria Comamonas

Three complete katG genes coding for bifunctional catalase-peroxidases (KatGs) from the beta-proteobacterium Comamonas terrigena and two related strains of Comamonas testosteroni have been cloned and sequenced. Catalase-peroxidases are unique bifunctional enzymes known to be expressed in these soil bacteria in response to environmental and/or oxidative stress. The evolutionary and structural diversity of these enzymes is investigated based on multiple sequence alignment and comprehensive phylogenetic analysis. The reconstructed phylogenetic tree and well-known structure-function relationships were applied to inspect the conservation of essential residues. Observed diversity is discussed with respect to the fact that KatGs are distinctive gene-duplicated peroxidases comprising a N-terminal (enzymatically active) and a C-terminal (heme-less) domain. The unique promoter motifs regulating katG transcription in four strains of Comamonas were detected and compared with E. coli katG promoter. The relationship between the promoter sequences and the corresponding expression levels was analyzed. A significant difference in heat shock-inducible catalatic and peroxidatic activities between E. coli K12 and Comamonas terrigena & testosteroni strains was observed. The peculiar variability in gene-coding sequences appears to be more significant for such activity output among Comamonas strains than differences in their promoter regions. The functional role of observed increased diversity in the C-terminal domain is discussed with respect to potential modification of catalytic features at the N-terminal domain that could be relevant for these soil bacteria to cope with stressors.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (doi:10.1007/s00203-009-0541-4) contains supplementary material, which is available to authorized users.

Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes

Background

Thiomonas strains are ubiquitous in arsenic-contaminated environments. Differences between Thiomonas strains in the way they have adapted and respond to arsenic have never been studied in detail. For this purpose, five Thiomonas strains, that are interesting in terms of arsenic metabolism were selected: T. arsenivorans, Thiomonas spp. WJ68 and 3As are able to oxidise As(III), while Thiomonas sp. Ynys1 and T. perometabolis are not. Moreover, T. arsenivorans and 3As present interesting physiological traits, in particular that these strains are able to use As(III) as an electron donor.

Results

The metabolism of carbon and arsenic was compared in the five Thiomonas strains belonging to two distinct phylogenetic groups. Greater physiological differences were found between these strains than might have been suggested by 16S rRNA/rpoA gene phylogeny, especially regarding arsenic metabolism. Physiologically, T. perometabolis and Ynys1 were unable to oxidise As(III) and were less arsenic-resistant than the other strains. Genetically, they appeared to lack the aox arsenic-oxidising genes and carried only a single ars arsenic resistance operon. Thiomonas arsenivorans belonged to a distinct phylogenetic group and increased its autotrophic metabolism when arsenic concentration increased. Differential proteomic analysis revealed that in T. arsenivorans, the rbc/cbb genes involved in the assimilation of inorganic carbon were induced in the presence of arsenic, whereas these genes were repressed in Thiomonas sp. 3As.

Conclusion

Taken together, these results show that these closely related bacteria differ substantially in their response to arsenic, amongst other factors, and suggest different relationships between carbon assimilation and arsenic metabolism.

Proteomic and molecular investigation on the physiological adaptation of Comamonas sp. strain CNB-1 growing on 4-chloronitrobenzene

Comamonas sp. strain CNB-1 can utilize 4-chloronitrobenzene (4CNB) as sole carbon and nitrogen source for growth. Previous studies were focused on 4CNB degradative pathway and have showed that CNB-1 contained a plasmid pCNB1 harboring the genes (cnbABCaCbDEFGH, cnbZ) for the enzymes involving in 4CNB degradation, but only three gene products (CnbCa, CnbCb, and CnbZ) were identified in CNB-1 cells. Comamonas strain CNB-2 that lost pCNB1 was not able to grow on 4CNB. In this study, physiological adaptation to 4CNB by CNB-1 was investigated with proteomic and molecular tools. Comparative proteomes of strains CNB-1 and CNB-2 grown on 4CNB and/or succinate revealed that adaptation to 4CNB by CNB-1 included specific degradative pathway and general physiological responses: (1) Seven gene products (CnbA, CnbCa, CnbCb, CnbD, CnbE, CnbF, and CnbZ) for 4CNB degradation were identified in 4CNB-grown cells, and they were constitutively synthesized in CNB-1. Two genes cnbE and cnbF were cloned and simultaneously expressed in E. coli. The CnbE and CnbF together catalyzed the conversion of 2-oxohex-4-ene-5-chloro-1,6-dioate into 2-oxo-4-hydroxy-5-chloro-valeric acid; (2) Enzymes involving in glycolysis, tricarboxylic acid cycle, and synthesis of glutamate increased their abundances in 4CNB-grown cells.