Metabolic engineering of an aerobic sulfate reduction pathway and its application to precipitation of cadmium on the cell surface

The conversion of sulfate to an excess of free sulfide requires stringent reductive conditions. Dissimilatory sulfate reduction is used in nature by sulfate-reducing bacteria for respiration and results in the conversion of sulfate to sulfide. However, this dissimilatory sulfate reduction pathway is inhibited by oxygen and is thus limited to anaerobic environments. As an alternative, we have metabolically engineered a novel aerobic sulfate reduction pathway for the secretion of sulfides. The assimilatory sulfate reduction pathway was redirected to overproduce cysteine, and excess cysteine was converted to sulfide by cysteine desulfhydrase. As a potential application for this pathway, a bacterium was engineered with this pathway and was used to aerobically precipitate cadmium as cadmium sulfide, which was deposited on the cell surface. To maximize sulfide production and cadmium precipitation, the production of cysteine desulfhydrase was modulated to achieve an optimal balance between the production and degradation of cysteine.     

Analysis of an engineered sulfate reduction pathway and cadmium precipitation on the cell surface

We previously have genetically engineered an aerobic sulfate reduction pathway in Escherichia coli for the generation of hydrogen sulfide and demonstrated the pathway's utility in the precipitation of cadmium. To engineer the pathway, the assimilatory sulfate reduction pathway was modified so that cysteine was overproduced. Excess cysteine was then converted by cysteine desulfhydrase to an abundance of hydrogen sulfide, which then reacted with aqueous cadmium to form cadmium sulfide. In this study, observations of various E. coli clones were combined with an analysis of kinetic and transport phenomena. This analysis revealed that cysteine production is the rate-limiting step in the engineered pathway and provided an explanation for the phenomenon of cell surface precipitation. An analytical model showed that cadmium sulfide must form at the cell surface because the rate of cadmium sulfide formation is extremely fast and the rate of sulfide transport is relatively slow.     

Aerobic sulfide production and cadmium precipitation by Escherichia coli expressing the Treponema denticola cysteine desulfhydrase gene

The cysteine desulfhydrase gene of Treponema denticola was over-expressed in Escherichia coli to produce sulfide under aerobic conditions and to precipitate metal sulfide complexes on the cell wall. When grown in a defined salts medium supplemented with cadmium and cysteine, E. coli producing cysteine desulfhydrase secreted sulfide and removed nearly all of the cadmium from solution after 48 h. A control strain produced significantly less sulfide and removed significantly less cadmium. Measurement of acid-labile sulfide and energy dispersive X-ray spectroscopy indicated that cadmium was precipitated as cadmium sulfide. Without supplemental cysteine, both the E. coli producing cysteine desulfhydrase and the control E. coli demonstrated minimal cadmium removal.     

Co-expression of Arabidopsis thaliana phytochelatin synthase and Treponema denticola cysteine desulfhydrase for enhanced arsenic accumulation

Arsenic is one of the most hazardous pollutants found in aqueous environments and has been shown to be a carcinogen. Phytochelatins (PCs), which are cysteine-rich and thio-reactive peptides, have high binding affinities for various metals including arsenic. Previously, we demonstrated that genetically engineered Saccharomyces cerevisiae strains expressing phytochelatin synthase (AtPCS) produced PCs and accumulated arsenic. In an effort to further improve the overall accumulation of arsenic, cysteine desulfhydrase, an aminotransferase that converts cysteine into hydrogen sulfide under aerobic condition, was co-expressed in order to promote the formation of larger AsS complexes. Yeast cells producing both AtPCS and cysteine desulfhydrase showed a higher level of arsenic accumulation than a simple cumulative effect of expressing both enzymes, confirming the coordinated action of hydrogen sulfide and PCs in the overall bioaccumulation of arsenic.     

Aerobic transformation of zinc into metal sulfide by photosynthetic microorganisms

Industrial activity over the last two centuries has increased heavy metal contamination worldwide, leading to greater human exposure. Zinc is particularly common in industrial effluents and although an essential nutrient, it is highly toxic at elevated concentrations. Photoautotrophic microbes hold promise for heavy metal bioremediation applications because of their ease of culture and their ability to produce sulfide through metabolic processes that in turn are known to complex with the metal ion, Hg(II). The green alga Chlamydomonas reinhardtii, the red alga Cyanidioschyzon merolae, and the cyanobacterium Synechococcus leopoliensis were all able to synthesize sulfide and form zinc sulfide when exposed to Zn(II). Supplementation of their respective media with sulfite and cysteine had deleterious effects on growth, although ZnS still formed in Cyanidioschyzon cells to the same extent as in unsupplemented cells. The simultaneous addition of sulfate and Zn(II) had similar effects to that of Zn(II) alone in all three species, whereas supplying sulfate prior to exposure to Zn(II) enhanced metal sulfide production. The coupled activities of serine acetyltransferase and O-acetylserine(thiol)lyase (SAT/OASTL) did not increase significantly in response to conditions in which enhanced ZnS formation occurred; sulfate added prior to and simultaneously with Zn(II). However, even low activity could provide sufficient sulfate assimilation over this relatively long-term study. Because the extractable activity of cysteine desulfhydrase was elevated in cells that produced higher amounts of zinc sulfide, cysteine is the probable source of the sulfide in this aerobic process.     

Bioremediation of cadmium by growing Rhodobacter sphaeroides: kinetic characteristic and mechanism studies

The removal kinetic characteristic and mechanism of cadmium by growing Rhodobacter sphaeroides were investigated. The removal data were fitted to the second-order equation, with a correlation coefficient, R2=0.9790-0.9916. Furthermore, it was found that the removal mechanism of cadmium was predominantly governed by bioprecipitation as cadmium sulfide with biosorption contributing to a minor extent. Also, the results revealed that the activities of cysteine desulfhydrase in strains grown in the presence of 10 and 20 mg/l of cadmium were higher than in the control, while the activities in the presence of 30 and 40 mg/l of cadmium were lower than in the control. Content analysis of subcellular fractionation showed that cadmium was mostly removed and transformed by precipitation on the cell wall.     

Functional demonstration of reverse transsulfuration in the Mycobacterium tuberculosis complex reveals that methionine is the preferred sulfur source for pathogenic Mycobacteria

Methionine can be used as the sole sulfur source by the Mycobacterium tuberculosis complex although it is not obvious from examination of the genome annotation how these bacteria utilize methionine. Given that genome annotation is a largely predictive process, key challenges are to validate these predictions and to fill in gaps for known functions for which genes have not been annotated. We have addressed these issues by functional analysis of methionine metabolism. Transport, followed by metabolism of (35)S methionine into the cysteine adduct mycothiol, demonstrated the conversion of exogenous methionine to cysteine. Mutational analysis and cloning of the Rv1079 gene showed it to encode the key enzyme required for this conversion, cystathionine gamma-lyase (CGL). Rv1079, annotated metB, was predicted to encode cystathionine gamma-synthase (CGS), but demonstration of a gamma-elimination reaction with cystathionine as well as the gamma-replacement reaction yielding cystathionine showed it encodes a bifunctional CGL/CGS enzyme. Consistent with this, a Rv1079 mutant could not incorporate sulfur from methionine into cysteine, while a cysA mutant lacking sulfate transport and a methionine auxotroph was hypersensitive to the CGL inhibitor propargylglycine. Thus, reverse transsulfuration alone, without any sulfur recycling reactions, allows M. tuberculosis to use methionine as the sole sulfur source. Intracellular cysteine was undetectable so only the CGL reaction occurs in intact mycobacteria. Cysteine desulfhydrase, an activity we showed to be separable from CGL/CGS, may have a role in removing excess cysteine and could explain the ability of M. tuberculosis to recycle sulfur from cysteine, but not methionine.     

Mechanisms of h(2)s production from cysteine and cystine by microorganisms isolated from soil by selective enrichment

Hydrogen sulfide (H(2)S) is a major component of biogenic gaseous sulfur emissions from terrestrial environments. However, little is known concerning the pathways for H(2)S production from the likely substrates, cysteine and cystine. A mixed microbial culture obtained from cystine-enriched soils was used in assays (50 min, 37 degrees C) with 0.05 M Tris-HCl (pH 8.5), 25 mumol of l-cysteine, 25 mumol of l-cystine, and 0.04 mumol of pyridoxal 5'-phosphate. Sulfide was trapped in a center well containing zinc acetate, while pyruvate was measured by derivatization with 2,4-dinitrophenylhydrazine. Sulfide and total pyruvate production were 17.6 and 17.2 nmol mg of protein min, respectively. Dithiothreitol did not alter reaction stoichiometry or the amount of H(2)S and total pyruvate, whereas N-ethylmaleimide reduced both H(2)S and total pyruvate production equally. The amount of H(2)S produced was reduced by 96% when only l-cystine was included as the substrate in the assay and by 15% with the addition of propargylglycine, a specific suicide inhibitor of cystathionine gamma-lyase. These data indicate that the substrate for the reaction was cysteine and the enzyme responsible for H(2)S and pyruvate production was cysteine desulfhydrase (EC 4.4.1.1). The enzyme had a K(m) of 1.32 mM and was inactivated by temperatures greater than 60 degrees C. Because cysteine is present in soil and cysteine desulfhydrase is an inducible enzyme, the potential for H(2)S production by this mechanism exists in terrestrial environments. The relative importance of this mechanism compared with other processes involved in H(2)S production from soil is unknown.     

Precipitation of cadmium by Clostridium thermoaceticum.

Cadmium at an initial concentration of 1 mM was completely precipitated by cultures of Clostridium thermoaceticum in complex medium. The precipitation was energy dependent and required cysteine, although cysteine alone did not act as a growth substrate. Electron microscopic analysis revealed localized areas of precipitation at the surfaces of nonstarved cells as well as precipitate in the surrounding medium. The addition of cadmium had no apparent effect on growth or acetogenesis. However, nickel and cadmium were synergistically toxic at a concentration (1 mM) at which neither alone was toxic. The amount of protein extracted from cadmium-treated cultures was twofold higher than that in control extracts, and the amount of total sulfide was fourfold higher in cultures containing cadmium than in control cultures. Comparable levels of cysteine desulfhydrase activity were observed in extracts of both cadmium-treated and control cultures, but the enzyme activity was expressed maximally about 24 h earlier in the cadmium-treated cultures than in the untreated controls.     

Thiol Accumulation and Cysteine Desulfhydrase Activity in H2S-Fumigated Leaves and Leaf Homogenates of Cucurbit Plants

Fumigation of both, cucurbit plants and cucurbit leaf homogenateswith hydrogen sulfide (H₂S) resulted in an increase in solublethiol, mainly glutathione and cysteine. In leaf homogenatesthis increase was counteracted or prevented by the additionat 1 mM of inhibitors of pyridoxalphosphate dependent enzymesor of products of the cysteine desulfhydrase reaction. Thesecompounds inhibited cysteine desulfhydrase activity, but didnot severely affect O-acetylserine sulfhydrylase activity atthis concentration. These results provide circumstantial evidencethat cysteine desulfhydrase in its reverse reaction, but notO-acetylserine sulfhydrylase participates in the assimilationof atmospheric H₂S. (Received February 4, 1991; Accepted April 30, 1991)     

Complete assimilation of cysteine by a newly isolated non-sulfur purple bacterium resembling Rhodovulum sulfidophilum (Rhodobacter sulfidophilus)

A rod-shaped, motile, phototrophic bacterium, strain SiCys, was enriched and isolated from a marine microbial mat, with cysteine as sole substrate. During phototrophic anaerobic growth with cysteine, sulfide was produced as an intermediate, which was subsequently oxidized to sulfate. The molar growth yield with cysteine was 103 g mol^–1, in accordance with complete assimilation of electrons from the carbon and the sulfur moiety into cell material. Growth yields with alanine and serine were proportionally lower. Thiosulfate, sulfide, hydrogen, and several organic compounds were used as electron donors in the light, whereas cystine, sulfite, or elemental sulfur did not support phototrophic anaerobic growth. Aerobic growth in the dark was possible with fructose as substrate. Cultures of strain SiCys were yellowish-brown in color and contained bacteriochlorophyll a, spheroidene, spheroidenone, and OH-spheroidene as major photosynthetic pigments. Taking the morphology, photosynthetic pigments, aerobic growth in the dark, and utilization of sulfide for phototrophic growth into account, strain SiCys was assigned to the genus Rhodovulum (formerly Rhodobacter) and tentatively classified as a strain of R. sulfidophilum. In cell-free extracts in the presence of pyridoxal phosphate, cysteine was converted to pyruvate and sulfide, which is characteristic for cysteine desulfhydrase activity (l-cystathionine γ-lyase, EC 4.4.1.1). Received: 15 December 1995 / Accepted: 1 April 1996     

Methionine-to-cysteine recycling in Klebsiella aerogenes

In the enteric bacteria Escherichia coli and Salmonella enterica, sulfate is reduced to sulfide and assimilated into the amino acid cysteine; in turn, cysteine provides the sulfur atom for other sulfur-bearing molecules in the cell, including methionine. These organisms cannot use methionine as a sole source of sulfur. Here we report that this constraint is not shared by many other enteric bacteria, which can use either cysteine or methionine as the sole source of sulfur. The enteric bacterium Klebsiella aerogenes appears to use at least two pathways to allow the reduced sulfur of methionine to be recycled into cysteine. In addition, the ability to recycle methionine on solid media, where cys mutants cannot use methionine as a sulfur source, appears to be different from that in liquid media, where they can. One pathway likely uses a cystathionine intermediate to convert homocysteine to cysteine and is induced under conditions of sulfur starvation, which is likely sensed by low levels of the sulfate reduction intermediate adenosine-5'-phosphosulfate. The CysB regulatory proteins appear to control activation of this pathway. A second pathway may use a methanesulfonate intermediate to convert methionine-derived methanethiol to sulfite. While the transsulfurylation pathway may be directed to recovery of methionine, the methanethiol pathway likely represents a general salvage mechanism for recovery of alkane sulfide and alkane sulfonates. Therefore, the relatively distinct biosyntheses of cysteine and methionine in E. coli and Salmonella appear to be more intertwined in Klebsiella.     

Hydrogen sulfide is a novel potential virulence factor of Mycoplasma pneumoniae: characterization of the unusual cysteine desulfurase/desulfhydrase HapE

Mycoplasma pneumoniae is a human pathogen causing atypical pneumonia with a minimalized and highly streamlined genome. So far, hydrogen peroxide production, cytadherence, and the ADP‐ribosylating CARDS toxin have been identified as pathogenicity determinants. We have studied haemolysis caused by M. pneumoniae, and discovered that hydrogen peroxide is responsible for the oxidation of heme, but not for lysis of erythrocytes. This feature could be attributed to hydrogen sulfide, a compound that has previously not been identified as virulence factor in lung pathogens. Indeed, we observed hydrogen sulfide production by M. pneumoniae. The search for a hydrogen sulfide‐producing enzyme identified HapE, a protein with similarity to cysteine desulfurases. In contrast to typical cysteine desulfurases, HapE is a bifunctional enzyme: it has both the cysteine desulfurase activity to produce alanine and the cysteine desulfhydrase activity to produce pyruvate and hydrogen sulfide. Experiments with purified HapE showed that the enzymatic activity of the protein is responsible for haemolysis, demonstrating that HapE is a novel potential virulence factor of M. pneumoniae.     

A kinetic study on bacterial sulfate reduction

The activity of anaerobic sulfate reduction was studied using sulfate-reducing bacteria isolated from the water produced from a Brazilian oil reservoir. The effects of the initial sulfate concentration on the anaerobic sulfate reduction and sulfide generation kinetics were investigated. The redox potential, the biomass solution content, and the sulfate and the sulfide solution content were measured. The results indicate that the sulfate conversion and the sulfide generation are both first-order processes for the initial sulfate concentration of 823, 1,282, and 1,790 mg/L. The results for the kinetic constants for the sulfate conversion indicate an inhibition with the enhancement of the initial sulfate solution content. The kinetic constants for the sulfide generation indicate that this reaction is almost independent of the initial sulfate solution content due to the presence of at least two in-series processes that are faster than the microbial conversion of the sulfate. The kinetic test using the water from an onshore oil field, with an initial sulfide content of 228 mg/L and sulfate content of 947 mg/L, shows a sulfate conversion of 50 % in 528 h. The kinetic modeling for the net content of sulfate and sulfide indicates that the sulfate conversion is slower for this water than for the deionized water tests; however, the sulfide formation has almost the same conversion velocity. The reactions are first order in both cases.     

Effect of hydraulic residence time on microbial sulfide production in an upflow sludge blanket denitrification reactor fed with methanol

Summary In the combined ion exchange/biological denitrification process for nitrate removal from ground water anion exchange resins are regenerated in a closed circuit by way of an upflow sludge blanket denitrification reactor. The regenerant (a concentrated sodium bicarbonate solution) is recirculated through the ion exchanger in the r generation mode and the denitrification reactor. In the closed system sulfate accumulates to very high concentrations. For that reason it was examined under what process conditions sulfate reduction occurs in an upflow sludge blanket denitrification reactor, when the influent contains high sulfate concentrations (5.45 g SO ₄ ^2- /l) and high sodium bicarbonate concentrations (19.8 g NaHCO₃/l) in addition to nitrate and methanol. It appeared that at a hydraulic residence time of 5 h sulfide production started, when the nitrate loading rate was 20% of the denitrification reactor capacity and methanol was added in excess. The excess of methanol was converted into acetate after nitrate was depleted. Conversion of methanol into acetate was a function of the hydraulic residence time. At hydraulic residence times above 8 h this conversion was complete. Also in batch experiments it was observed that excess of methanol was converted into acetate, and that sulfate reduction started when nitrate was depleted. From all experiments it is clear that, provided that methanol is added in good relation to the quantity of nitrate that has to be denitrified, acetate will not be produced and sulfate reduction will not occur in the denitrification reactor, even in the presence of very high sulfate concentrations.     

Biochemical Characterization of Sulfur Assimilation by Salmonella pullorum

The biochemical basis for a cysteine requirement in Salmonella pullorum strain MS35 is presented. Before determining the missing biochemical functions, it was established that the assimilatory sulfate-reducing pathway for this species is an inorganic one in which 3'-phosphoadenylylsulfate (PAPS), sulfite, and sulfide are intermediates. A requirement for 2'- and 3'-adenosine monophosphate was found for in vitro synthesis of PAPS, possibly because 2'- and 3'-adenosine monophosphate inhibits endogenous nucleases that destroy PAPS. The cysteine requirement of strain MS35 was attributed to a defect at 37 C in sulfate permeation and temperature sensitivity in sulfite reduction. At 25 C, sulfite was metabolized to sulfide. A novel property of sulfate-utilizing revertants was their unselected ability to assimilate thiosulfate sulfur at 25 C but not at 37 C.     

Distribution of Cysteine Desulfhydrase in Microorganisms

The distribution of cysteine desulfhydrase activity in microorganisms was studied with intact cells. The enzyme activity was found mainly in strains belonging to Enterobacteriaceae, especially to genus Aerobacter (Enterobacter). Aerobacter cloacae IFO 12009 showed markedly high activity.

l-Cysteine was essential as an inducer of the enzyme formation, of which 0.2% in the medium is appropriate.

Intact cells of bacteria containing high cysteine desulfhydrase activity, prepared from broth cultured for 19hr, catalyzed the synthesis of l-cysteine from pyruvate, ammonia and hydrogen sulfide.     

Cysteine metabolism in cultured tobacco cells

Transported l-[(35)S]cysteine was rapidly metabolized by cultured tobacco cells when supplied to the cells at 0.02 millimolar or 0.5 millimolar. The internal cysteine pool was expandable to approximately 2400 nmoles per gram fresh weight.The (35)S label derived from cysteine was found in several metabolites. The amount of label in glutathione and sulfate was directly proportional to the internal l-[(35)S]cysteine, while the levels of labeled methionine and protein were apparently independent of internal labeled cysteine. Cysteine was more rapidly metabolized when the external cysteine concentration was low (0.02 millimolar) with up to 90% of the (35)S label present as compounds other than cysteine.The initial step in cysteine degradation yielded pyruvate, sulfide, and presumably NH(4) (+). Stoichiometry studies using extracts prepared from acetone powders of tobacco cells indicated that pyruvate and sulfide were produced in a 1:1 ratio. The catabolic reaction was linear with respect to time and amount of protein and had a pH optimum of 8 in crude extracts. Preliminary kinetic data indicated the K(m) to be approximately 0.2 millimolar. The extractable degradative activity was enhanced 15- to 20-fold by preincubating the cells for 24 hours in 0.5 millimolar cysteine. The extractable specific enzyme activity roughly reflected the growth curve of the cells in culture. Maximal cysteine degradation was observed in extracts prepared from late log phase cultures that were preincubated in cysteine, while little activity was found in similar extracts from stationary phase cultures. These results are consistent with an inducible catabolic enzyme similar to the cysteine desulfhydrase from bacteria.