Metal ion cofactors afford proteins virtually unlimited catalytic potential, enable electron transfer reactions and have a great impact on protein stability. Consequently, metalloproteins have key roles in most biological processes, including respiration (iron and copper), photosynthesis (manganese) and drug metabolism (iron). Yet, predicting from genome sequence the numbers and types of metal an organism assimilates from its environment or uses in its metalloproteome is currently impossible because metal coordination sites are diverse and poorly recognized. We present here a robust, metal-based approach to determine all metals an organism assimilates and identify its metalloproteins on a genome-wide scale. This shifts the focus from classical protein-based purification to metal-based identification and purification by liquid chromatography, high-throughput tandem mass spectrometry (HT-MS/MS) and inductively coupled plasma mass spectrometry (ICP-MS) to characterize cytoplasmic metalloproteins from an exemplary microorganism (Pyrococcus furiosus). Of 343 metal peaks in chromatography fractions, 158 did not match any predicted metalloprotein. Unassigned peaks included metals known to be used (cobalt, iron, nickel, tungsten and zinc; 83 peaks) plus metals the organism was not thought to assimilate (lead, manganese, molybdenum, uranium and vanadium; 75 peaks). Purification of eight of 158 unexpected metal peaks yielded four novel nickel- and molybdenum-containing proteins, whereas four purified proteins contained sub-stoichiometric amounts of misincorporated lead and uranium. Analyses of two additional microorganisms (Escherichia coli and Sulfolobus solfataricus) revealed species-specific assimilation of yet more unexpected metals. Metalloproteomes are therefore much more extensive and diverse than previously recognized, and promise to provide key insights for cell biology, microbial growth and toxicity mechanisms.

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Microorganisms can be engineered to produce useful products, including chemicals and fuels from sugars derived from renewable feedstocks, such as plant biomass. An alternative method is to use low potential reducing power from nonbiomass sources, such as hydrogen gas or electricity, to reduce carbon dioxide directly into products. This approach circumvents the overall low efficiency of photosynthesis and the production of sugar intermediates. Although significant advances have been made in manipulating microorganisms to produce useful products from organic substrates, engineering them to use carbon dioxide and hydrogen gas has not been reported. Herein, we describe a unique temperature-dependent approach that confers on a microorganism (the archaeon Pyrococcus furiosus, which grows optimally on carbohydrates at 100°C) the capacity to use carbon dioxide, a reaction that it does not accomplish naturally. This was achieved by the heterologous expression of five genes of the carbon fixation cycle of the archaeon Metallosphaera sedula, which grows autotrophically at 73°C. The engineered P. furiosus strain is able to use hydrogen gas and incorporate carbon dioxide into 3-hydroxypropionic acid, one of the top 12 industrial chemical building blocks. The reaction can be accomplished by cell-free extracts and by whole cells of the recombinant P. furiosus strain. Moreover, it is carried out some 30°C below the optimal growth temperature of the organism in conditions that support only minimal growth but maintain sufficient metabolic activity to sustain the production of 3-hydroxypropionate. The approach described here can be expanded to produce important organic chemicals, all through biological activation of carbon dioxide.

Cobalt is essential for growth of Salmonella enterica and other organisms, yet this metal can be toxic when present in excess. Wild-type Salmonella exhibits several metabolic defects when grown in the presence of cobalt, some of which generate visible growth consequences. Work herein identifies sulfur assimilation, iron homeostasis, and Fe-S cluster metabolism as targets for cobalt toxicity. In each case it is proposed that cobalt exerts its effect by one of two mechanisms: direct competition with iron or indirectly through a mechanism that involves the status of reduced thiols in the cell. Cobalt toxicity results in decreased siroheme production, increased expression of the Fur regulon, and decreased activity of Fe-S cluster proteins. The consequences of reduced sulfite reductase activity in particular are exacerbated by the need for glutathione in cobalt resistance. Significantly, independent metabolic perturbations could be detected at cobalt concentrations below those required to generate a detectable growth defect.Trace metals are necessary for the growth of living organisms, partly because they are cofactors for several essential enzymes. The requirement for these metals is complicated by the fact that they can be toxic at elevated concentrations. Heavy metal toxicity has been described over the years in a variety of organisms. Despite the long-standing recognition of metal toxicity, the mechanism(s) of toxicity is not completely understood. The toxicities of several metals, including iron, copper, cadmium, and nickel, involve interactions with oxygen that result in radical generation (reviewed in reference 45). Cobalt in particular has been shown to (i) generate a spectrum of reactive oxygen species in water (25) and (ii) result in free radicals in circulating rat blood in the presence of ascorbic acid (50). Further, Escherichia coli strains lacking both cytoplasmic superoxide dismutases were found to be more sensitive to cobalt than wild-type strains (16).Other reports have suggested cobalt toxicity is generated by a competition with iron, with which it shares several similarities in atomic properties. For instance, iron-enriched medium decreased induction of the erythropoietin gene by cobalt in human Hep3B cells (20). In Saccharomyces cerevisiae, Aft1 is an iron-binding transcriptional activator of genes involved in iron uptake and homeostasis. Cobalt was found to induce genes that were part of the Aft1 regulon. Significantly, this cobaltinduced phenotype was suppressed by the addition of iron to the growth medium (44). In E. coli, rcnA, which encodes a transporter involved in cobalt and nickel efflux (37), was found to be regulated by the ferric uptake regulator (Fur) (23). Finally, in Salmonella enterica, strains lacking yggX and one of several other genes (apbC, apbE, gshA, and rseC) implicated in Fe-S cluster metabolism were shown to have a cobalt-induced thiamine auxotrophy which could be suppressed by iron (41). In the last case it was hypothesized that cobalt could compete with iron in the proces...

The concentrations of molybdenum (Mo) and 25 other metals were measured in groundwater samples from 80 wells on the Oak Ridge Reservation (ORR) (Oak Ridge, TN), many of which are contaminated with nitrate, as well as uranium and various other metals. The concentrations of nitrate and uranium were in the ranges of 0.1 M to 230 mM and <0.2 nM to 580 M, respectively. Almost all metals examined had significantly greater median concentrations in a subset of wells that were highly contaminated with uranium (>126 nM). They included cadmium, manganese, and cobalt, which were 1,300-to 2,700-fold higher. A notable exception, however, was Mo, which had a lower median concentration in the uranium-contaminated wells. This is significant, because Mo is essential in the dissimilatory nitrate reduction branch of the global nitrogen cycle. It is required at the catalytic site of nitrate reductase, the enzyme that reduces nitrate to nitrite. Moreover, more than 85% of the groundwater samples contained less than 10 nM Mo, whereas concentrations of 10 to 100 nM Mo were required for efficient growth by nitrate reduction for two Pseudomonas strains isolated from ORR wells and by a model denitrifier, Pseudomonas stutzeri RCH2. Higher concentrations of Mo tended to inhibit the growth of these strains due to the accumulation of toxic concentrations of nitrite, and this effect was exacerbated at high nitrate concentrations. The relevance of these results to a Mo-based nitrate removal strategy and the potential community-driving role that Mo plays in contaminated environments are discussed.

Significance The diverse microorganisms contained within the human gut are known to have significant effects on human health. Herein, we show that genes encoding members of the tungsten oxidoreductase (WOR) family of enzymes and a tungstate-specific transporter are prevalent in the human gut microbiome and metagenome. We demonstrate that two model gut microbes assimilate tungsten into multiple WOR enzymes and that some of these enzymes catalyze the conversion of gut aldehydes to the corresponding acid, likely as a detoxification strategy to remove these reactive compounds.

The anaerobic archaeon Pyrococcus furiosus grows by fermenting carbohydrates producing H 2 , CO 2 , and acetate. We show here that it is surprisingly tolerant to oxygen, growing well in the presence of 8% (vol/vol) O 2 . Although cell growth and acetate production were not significantly affected by O 2 , H 2 production was reduced by 50% (using 8% O 2 ). The amount of H 2 produced decreased in a linear manner with increasing concentrations of O 2 over the range 2-12% (vol/vol), and for each mole of O 2 consumed, the amount of H 2 produced decreased by approximately 2 mol. The recycling of H 2 by the two cytoplasmic hydrogenases appeared not to play a role in O 2 resistance because a mutant strain lacking both enzymes was not more sensitive to O 2 than the parent strain. Decreased H 2 production was also not due to inactivation of the H 2 -producing, ferredoxin-dependent membrane-bound hydrogenase because its activity was unaffected by O 2 exposure. Electrons from carbohydrate oxidation must therefore be diverted to relieve O 2 stress at the level of reduced ferredoxin before H 2 production. Deletion strains lacking superoxide reductase (SOR) and putative flavodiiron protein A showed increased sensitivity to O 2 , indicating that these enzymes play primary roles in resisting O 2 . However, a mutant strain lacking the proposed electron donor to SOR, rubredoxin, was unaffected in response to O 2 . Hence, electrons from sugar oxidation normally used to produce H 2 are diverted to O 2 detoxification by SOR and putative flavodiiron protein A, but the electron flow pathway from ferredoxin does not necessarily involve rubredoxin.j T he anaerobic archaeon Pyrococcus furiosus grows optimally near 100°C by fermenting various carbohydrates and peptides to form organic acids, CO 2 , and H 2 , or, in the presence of elemental sulfur (S 0 ), H 2 S (1). In the metabolism of sugars to acetate via a modified Embden-Meyerhof pathway, the two oxidation steps are catalyzed by glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR) and pyruvate ferredoxin oxidoreductase (POR), both of which use oxidized ferredoxin as an electron acceptor rather than nicotinamide-adenine dinucleotide or NADP (2, 3). In the absence of S 0 , the reduced ferredoxin is oxidized by a membrane-bound [NiFe]-hydrogenase (MBH) that conserves energy in the form of an ion gradient that can be used to generate ATP via a membrane-bound ATP synthase (4). It is estimated that for each glucose molecule oxidized, the formation of H 2 by MBH is able to add 1.2 ATP to the energy pool. Substrate level phosphorylation from the conversion of phosphoenolpyruvate to pyruvate and the conversion of acetyl-CoA to acetate is responsible for 2.0 ATP per glucose molecule for a total of 3.2 ATP/glucose (4).In addition to MBH, P. furiosus has two cytoplasmic [NiFe]-hydrogenases termed soluble hydrogenases I and II (SHI and SHII). Both enzymes are extremely active in vitro using H 2 to reduce NADP to NADPH; these are assumed to be the physiological reactions (5). Support for thi...

Enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library from Pseudomonas stutzeri strain RCH2 was grown under denitrifying conditions, using nitrate or nitrite as an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. The dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation.