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Primordial microorganisms are postulated to have emerged in H2-rich alkaline Hadean serpentinite-hosted environments with homoacetogenesis as a core metabolism. However, investigation of two modern serpentinization-active analogues of early Earth reveals that conventional H2-/CO2-dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, “Ca. Lithoacetigenota”, that exclusively inhabits Hadean analogues and harbors genes encoding alternative modes of H2-utilizing lithotrophy. Rather than CO2, these metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein – the glycine reductase. A survey of serpentinite-hosted system microbiomes shows that glycine reductases are diverse and nearly ubiquitous in Hadean analogues. “Ca. Lithoacetigenota” glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation for gaining energy from geogenic H2 even under serpentinization-associated hyperalkaline, CO2-poor conditions. This draws remarkable parallels with ancestral archaeal H2-driven methyl-reducing methanogenesis recently proposed. Unique non-CO2-reducing metabolic strategies presented here may provide a new view into metabolisms that supported primordial life and the diversification of LUCA towards Archaea and Bacteria.

Supplementary informationis available for this paper athttps://doi.org/10.1038/s41467-020-18906-7, Six CO2 fixation pathways are known to operate in photoautotrophic and chemoautotrophic microorganisms. Here, we describe chemolithoautotrophic growth of the sulphate-reducing bacterium Desulfovibrio desulfuricans (strain G11) with hydrogen and sulphate as energy substrates. Genomic, transcriptomic, proteomic and metabolomic analyses reveal that D. desulfuricans assimilates CO2 via the reductive glycine pathway, a seventh CO2 fixation pathway. In this pathway, CO2 is first reduced to formate, which is reduced and condensed with a second CO2 to generate glycine. Glycine is further reduced in D. desulfuricans by glycine reductase to acetyl-P, and then to acetyl-CoA, which is condensed with another CO2 to form pyruvate. Ammonia is involved in the operation of the pathway, which is reflected in the dependence of the autotrophic growth rate on the ammonia concentration. Our study demonstrates microbial autotrophic growth fully supported by this highly ATP-efficient CO2 fixation pathway., We acknowledge Änne-Michaelis and William Newell for assistance with the LC-MS forthe metabolomics experiments and Daniel Amador-Noguez for access to the LC-MS usedfor13C intracellular metabolomic analysis. We thank Ines Cardoso Pereira and John vander Oost for critically reading the manuscript. This research was funded by the Neth-erlands Organisation for Scientific Research (NWO) through SIAM Gravitation Grant024.002.002 and the Innovation Program Microbiology (WUR), NJC acknowledgesfunding from NWO through a Rubicon Grant (019.163LW.035) and a Veni Grant(VI.Veni.192.156)., info:eu-repo/semantics/publishedVersion

International audience; For the human pathogen Clostridioides (also known as Clostridium) difficile, the ability to adapt to nutrient availability is critical for its proliferation and production of toxins during infection. Synthesis of the toxins is regulated by the availability of certain carbon sources, fermentation products and amino acids (e.g. proline, cysteine, isoleucine, leucine and valine). The effect of proline is attributable at least in part to its role as an inducer and substrate of D-proline reductase (PR), a Stickland reaction that regenerates NAD+ from NADH. Many Clostridium spp. use Stickland metabolism (co-fermentation of pairs of amino acids) to generate ATP and NAD+ . Synthesis of PR is activated by PrdR, a proline-responsive regulatory protein. Here we report that PrdR, in the presence of proline, represses other NAD+ -generating pathways, such as the glycine reductase and succinate-acetyl CoA utilization pathways leading to butyrate production, but does so indirectly by affecting the activity of Rex, a global redox-sensing regulator that responds to the NAD+ /NADH ratio. Our results indicate that PR activity is the favored mechanism for NAD+ regeneration and that both Rex and PrdR influence toxin production. Using the hamster model of C. difficile infection, we revealed the importance of PrdR-regulated Stickland metabolism in the virulence of C. difficile.

Studying amino acid catabolism-coupled methanogenesis is the important standpoints to decipher the metabolic behavior of a methanogenic culture. l-Glycine and l-alanine are acted as sole carbon and nitrogen sources for acidogenic bacteria. One amino acid is oxidized and another one is reduced for acetate production via pyruvate by oxidative deamination process in the Stickland reactions. Herein, we have developed a kinetic model for the Stickland reactions-coupled methanogenesis (SRCM) and simulated objectively to maximize the rate of methane production. We collected the metabolic information from enzyme kinetic parameters for amino acid catabolism of Clostridium acetobutylicum ATCC 824 and methanogenesis of Methanosarcina acetivorans C2A. The SRCM model of this study consisted of 18 reactions and 61 metabolites with enzyme kinetic parameters derived experimental data. The internal or external metabolic flux rate of this system found to control the acidogenesis and methanogenesis in a methanogenic culture. Using the SRCM model, flux distributions were calculated for each reaction and metabolite in order to maximize the methane production rate from the glycine–alanine pair. Results of this study, we demonstrated the metabolic behavior, metabolite pairing while mutually interact, and advantages of syntrophic metabolism of amino acid-directed methane production in a methanogenic starter culture. Electronic supplementary material The online version of this article (10.1186/s13568-019-0803-8) contains supplementary material, which is available to authorized users.

Clostridium difficile, a proteolytic Gram-positive anaerobe, has emerged as a significant nosocomial pathogen. Stickland fermentation reactions are thought to be important for growth of C. difficile and appear to influence toxin production. In Stickland reactions, pairs of amino acids donate and accept electrons, generating ATP and reducing power in the process. Reduction of the electron acceptors proline and glycine requires the d-proline reductase (PR) and the glycine reductase (GR) enzyme complexes, respectively. Addition of proline in the medium increases the level of PR protein but decreases the level of GR. We report the identification of PrdR, a protein that activates transcription of the PR-encoding genes in the presence of proline and negatively regulates the GR-encoding genes. The results suggest that PrdR is a central metabolism regulator that controls preferential utilization of proline and glycine to produce energy via the Stickland reactions.

Here, we report the draft genome sequence of Gottschalkia purinilyticum (formerly Clostridium purinilyticum ) WA1, an anaerobic bacterium specialized on degradation of purines (including adenine) and glycine, which uses the selenoprotein glycine reductase for substrate degradation. The genome consists of a single chromosome (3.40 Mb).

Here, we report the draft genome sequence of Clostridium cylindrosporum HC-1, a purine- and glycine-fermenting anaerobe, which uses selenoprotein glycine reductase for substrate degradation. The genome consists of a single chromosome (2.72 Mb) and a circular plasmid (14.4 kb).

Clostridium difficile , a proteolytic strict anaerobe, has emerged as a clinically significant nosocomial pathogen in recent years. Pathogenesis is due to the production of lethal toxins, A and B, members of the large clostridial cytotoxin family. Although it has been established that alterations in the amino acid content of the growth medium affect toxin production, the molecular mechanism for this observed effect is not yet known. Since there is a paucity of information on the amino acid fermentation pathways used by this pathogen, we investigated whether Stickland reactions might be at the heart of its bioenergetic pathways. Growth of C. difficile on Stickland pairs yielded large increases in cell density in a limiting basal medium, demonstrating that these reactions are tied to ATP production. Selenium supplementation was required for this increase in cell yield. Analysis of genome sequence data reveals genes encoding the protein components of two key selenoenzyme reductases, glycine reductase and d -proline reductase (PR). These selenoenzymes were expressed upon the addition of the corresponding Stickland acceptor (glycine, proline, or hydroxyproline). Purification of the selenoenzyme d -proline reductase revealed a mixed complex of PrdA and PrdB (SeCys-containing) proteins. PR utilized only d -proline but not l -hydroxyproline, even in the presence of an expressed and purified proline racemase. PR was found to be independent of divalent cations, and zinc was a potent inhibitor of PR. These results show that Stickland reactions are key to the growth of C. difficile and that the mechanism of PR may differ significantly from that of previously studied PR from nonpathogenic species.

Lipoamide dehydrogenase catalyzes the reversible NAD(+)-dependent oxidation of the dihydrolipoyl cofactors that are covalently attached to the acyltransferase components of the pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase, and glycine reductase multienzyme complexes. It contains two redox centers: a tightly, but noncovalently, bound FAD and an enzymic disulfide, each of which can accommodate two electrons. In the two-electron-reduced enzyme (EH(2)), the disulfide is reduced while the FAD cofactor is oxidized. In the four-electron-reduced enzyme (EH(4)), both redox centers are reduced. Lipoamide dehydrogenase can also catalyze the NADH-dependent reduction of alternative electron acceptors such as 2,6-dichlorophenolindophenol, ferricyanide, quinones, and molecular oxygen (O(2)). To determine the mechanism of these "diaphorase" reactions, we generated the EH(2) and EH(4) forms of Mycobacterium tuberculosis lipoamide dehydrogenase and rapidly mixed these enzyme forms with d,l-lipoylpentanoate, 2,6-dimethyl-1,4-benzoquinone, and O(2), in a stopped-flow spectrophotometer at pH 7.5 and 4 degrees C. EH(2) reduced d,l-lipoylpentanoate >/=100 times faster than EH(4) did. Conversely, EH(4) reduced 2,6-dimethyl-1,4-benzoquinone and molecular oxygen 90 and 40 times faster than EH(2), respectively. Comparison of the rates of reduction of the above substrates by EH(2) and EH(4) with their corresponding steady-state kinetic parameters for kinetic competence leads to the conclusion that reduction of lipoyl substrates occurs with EH(2) while reduction of diaphorase substrates occurs with EH(4).

The occurrence of the amino acid selenocysteine in proteins was first demonstrated for protein A of glycine reductase from Clostridium sticklandii in 1976, and questions were immediately raised on its mechanism of incorporation. At that time, the universality of the 20 proteinogenic amino acids was taken for granted, as was the fact that the 64 codons of the "universal" genetic code are assigned either to code for one of these 20 amino acids or to serve as termination signals. Thus, it seemed unlikely that selenocysteine would be considered as a classical amino acid. In principle, the definition of such a 21st amino acid would require (i) that its incorporation proceeds via a cotranslational mechanism, (ii) that it is directed by a specific codon, and (iii) that a specific tRNA mediates its transport to the ribosome. This chapter illustrates that selenocysteine fulfills these criteria. It first describes the unusual structural properties of tRNASec, and then discusses the unique pathway of selenocysteine insertion that has been worked out for Escherichia coli, which has finally led to the proposal of a model for the co-translational incorporation process at the ribosome. The chapter further compares the pathway established in E. coli with the current knowledge on the mammalian system. Finally, it addresses the interesting question of the evolution of the pathway for the incorporation of selenocysteine that differs from that of the 20 standard amino acids in many respects.

A 2.8-kb HindIII fragment, containing three open reading frames, has been cloned and sequenced from Clostridium litorale. The first gene grdA encoded the selenocysteine-containing protein PA of the glycine reductase complex, a protein of 159 amino acids with a deduced molecular mass of 16.7 kDa. The second gene (grdB) encoded the 47-kDa subunit of the substrate-specific selenoprotein PB glycine that is composed of 437 amino acids. The third gene contained the 5′-region of the gene for thioredoxin reductase, trxB. All gene products shared high similarity with the corresponding proteins from Eubacterium acidaminophilum. In both genes grdA and grdB, the opal termination codon (TGA) was found in-frame, indicating the presence of selenocysteine in both polypeptides. Northern-blot analysis showed that grdA and grdB are organized as one operon. Unlike Escherichia coli, no stable secondary structures of the corresponding mRNA were found immediately downstream of the UGA codons to direct an insertion of selenocysteine into the grdA and grdB transcripts of C. litorale. Instead, a secondary structure was identified in the 3′-untranslated region of grdB.

The complete amino acid sequence of Clostridium sticklandii selenoprotein A, a selenocysteine-containing protein component of the glycine reductase complex, has been established. Both the intact protein and peptide fragments produced by Staphylococcus aureus V8 protease or trypsin were purified by reversed-phase high-performance liquid chromatography and subjected to electrospray ionization mass spectrometric analysis and standard Edman degradation. Selenoprotein A consists of 157 amino acids with a chemical molecular weight of 17,011, in reasonable agreement with the observed molecular weight (17,022.7) determined from its ionization mass spectrum. The sequence of the amino-terminal region of the isolated native protein is Ser-Arg-Phe-Thr-Gly-Lys- Lys-Ile-Val-Ile-Ile-Gly-Asp-Arg-Asp-. An N-terminal methionine residue deduced from the gene sequence was not present. Although selenoprotein A reacted positively in a glycoprotein stain when using either the periodic acid-Schiff reagent procedure or a commercial glycan detection kit, no saccharide was detected by carbohydrate analyses after acid hydrolysis or methanolysis. Identity of the amino acid sequence determined by analysis with that deduced from the gene sequence is further evidence of the absence of bound carbohydrate.

Clostridium acidurici is an anaerobic, homoacetogenic bacterium, which is able to use purines such as uric acid as sole carbon, nitrogen, and energy source. Together with the two other known purinolytic clostridia C. cylindrosporum and C. purinilyticum, C. acidurici serves as a model organism for investigation of purine fermentation. Here, we present the first complete sequence and analysis of a genome derived from a purinolytic Clostridium. The genome of C. acidurici 9a consists of one chromosome (3,105,335 bp) and one small circular plasmid (2,913 bp). The lack of candidate genes encoding glycine reductase indicates that C. acidurici 9a uses the energetically less favorable glycine-serine-pyruvate pathway for glycine degradation. In accordance with the specialized lifestyle and the corresponding narrow substrate spectrum of C. acidurici 9a, the number of genes involved in carbohydrate transport and metabolism is significantly lower than in other clostridia such as C. acetobutylicum, C. saccharolyticum, and C. beijerinckii. The only amino acid that can be degraded by C. acidurici is glycine but growth on glycine only occurs in the presence of a fermentable purine. Nevertheless, the addition of glycine resulted in increased transcription levels of genes encoding enzymes involved in the glycine-serine-pyruvate pathway such as serine hydroxymethyltransferase and acetate kinase, whereas the transcription levels of formate dehydrogenaseencoding genes decreased. Sugars could not be utilized by C. acidurici but the full genetic repertoire for glycolysis was detected. In addition, genes encoding enzymes that mediate resistance against several antimicrobials and metals were identified. High resistance of C. acidurici towards bacitracin, acriflavine and azaleucine was experimentally confirmed. peerReviewed

Some strict anaerobic bacteria catalyze with glycine as substrate an internal Stickland reaction by which glycine serves as electron donor being oxidized by glycine-cleavage system or as electron acceptor being reduced by glycine reductase. In both cases, energy is conserved by substrate level phosphorylation. Except for the different substrate-activating proteins PB, reduction of sarcosine or betaine to acetyl phosphate involves in Eubacterium acidaminophilum the same set of proteins as observed for glycine, e.g. a unique thioredoxin system as electron donor and an acetyl phosphate-forming protein PC interacting with the intermediarily formed Secarboxymethylselenoether bound to protein PA.

The genes encoding thioredoxin reductase (trxB), thioredoxin (trxA), protein PA of glycine reductase (grdA) and the first 23 amino acids of the large subunit of protein PC of glycine reductase (grdC) belonging to the reductive deamination systems present in Eubacterium acidaminophilum were cloned and sequenced. The proteins were products of closely linked genes with 314 codons (thioredoxin reductase), 110 codons (thioredoxin), and 158 codons (protein PA). The protein previously called 'atypically small lipoamide dehydrogenase' or 'electron transferring flavoprotein' could now conclusively be identified as a thioredoxin reductase (subunit mass of 34781 Da) by the alignment with the enzyme of Escherichia coli showing the same typical order of the corresponding domains. The thioredoxin (molecular mass of 11742 Da) deviated considerably from the known consensus sequence, even in the most strongly conserved redox-active segment WCGPC that was now GCVPC. The selenocysteine of protein PA (molecular mass of 16609 Da) was encoded by TGA. The protein was highly similar to those of Clostridium purinolyticum and Clostridium sticklandii involved in glycine reductase. Thioredoxin reductase and thioredoxin of E. acidaminophilum could be successfully expressed in E. coli.

Selenium occurs normally in living things as a highly specific component of certain enzymes and amino acid transfer nucleic acids (tRNAs). In bacteria, biosynthesis of essential selenoenzymes has been shown to be unaffected by wide variations in sulfur levels. The naturally occurring selenoenzymes identified from bacterial sources include glycine reductase, formate dehydrogenases, a hydrogenase, nicotinic acid hydroxylase, xanthine dehydrogenase. The selenoenzyme, glutathione peroxidase, and other selenoproteins of unknown function have been isolated from animals. In certain enzymes, e.g. glycine reductase, formate dehydrogenase, hydrogenase and glutathione peroxidase, the chemical form of selenium has been identified as selenocysteine. A labile, unidentified form of selenium is present in nicotinic acid hydroxylase, and by inference, xanthine dehydrogenase.

The clostridial glycine reductase complex catalyzes the reductive deamination of glycine in an energy-conserving process that results in the esterification of orthophosphate. The complex consists of three protein components: selenoprotein A; protein B, a carbonyl group protein; and protein C, a sulfhydryl protein. The protein C component also catalyzes the arsenate-dependent decomposition of acetyl phosphate. Reaction of protein C with iodoacetate inhibits its ability to decompose acetyl phosphate, but this inactivation of the enzyme by alkylation is prevented in the presence of the substrate indicating the formation of an unreactive enzyme-bound acetylthiol ester. The Se-carboxy-methylselenocysteine residue of the selenoprotein A component of glycine reductase was generated by selective alkylation of the ionized selenol group at pH 6 with [14C]bromoacetate. Using this pure alkylated selenoprotein A as substrate, it was shown that protein C catalyzes the conversion of the [14C]carboxymethyl group, in selenoether linkage to protein A, to [14C]acetate in the presence of arsenate, dithiothreitol, and Mg2+. A procedure using hydrophobic chromatographic matrices was developed for the large scale isolation of protein C, and a number of the properties of the enzyme were determined.

The anaerobe Eubacterium acidaminophilum has been shown to contain an uncharacterized peroxidase, which may serve to protect the sensitive selenoproteins in that organism. We purified this peroxidase and found that it was identical with the substrate-specific "protein B"-complex of glycine reductase. The "protein B"-complex consists of the selenocysteine-containing GrdB subunit and two subunits, which derive from the GrdE proprotein. The specific peroxidase activity was 1.7 U (mg protein)(-1) with DTT and cumene hydroperoxide as substrates. Immunoprecipitation experiments revealed that GrdB was important for DTT- and NADH-dependent peroxidase activities in crude extracts, whereas the selenoperoxiredoxin PrxU could be depleted without affecting these peroxidase activities. GrdB could be heterologously produced in Escherichia coli with coexpression of selB and selC from E. acidaminophilum for selenocysteine insertion. Although GrdB was sensitive to proteolysis, some full-size protein was present which accounted for a peroxidase activity of about 0.5 U (mg protein)(-1) in these extracts. Mutation of the potentially redox-active UxxCxxC motif in GrdB resulted in still significant, but decreased activity. Heterologous GrdB was protected from degradation by full-length GrdE or by GrdE-domains. The GrdB-GrdE interaction was confirmed by copurification of GrdE with Strep-tagged GrdB. The data suggest that GrdE domains serve to stabilise GrdB.

In retrospect, the history of selenium biochemistry does not differ greatly from the study of a number of other trace elements in that it occurred over many years, progressing from periods of little general interest to widespread concern regarding toxicity problems and eventually to recognition of selenium as an essential nutrient for many forms of life. My involvement in studies on selenium metabolism is a classic example of serendipity. I was studying an interesting enzyme from an anaerobic bacterium that utilized glycine as substrate (glycine reductase), but the amounts of pure protein I could isolate were very limited because it seemed to be produced only during the very early stages of bacterial cell growth. The rich culture medium supported continued luxuriant growth of the bacterium, but the level of the desired enzyme in the cells merely underwent dilution during the process. Finally, after testing many known growth stimulatory supplements to no avail, my colleagues and I tried two inorganic nutrients, molybdate and selenite. This approach was prompted by the report that addition of these inorganic compounds to a medium used for anaerobic growth of Escherichia coli supported synthesis of the enzyme formate dehydrogenase [1]. Much to my delight, addition of selenite to our growth medium resulted in greatly increased levels of the glycine reductase enzyme, and synthesis of the protein continued throughout the entire growth period. Thus, a common belief among microbiologists that a so-called rich culture medium high in tryptone and yeast extract content was nutritionally adequate is incorrect if growth of the organism depends on ability to synthesize a selenium-containing enzyme. In our case other amino acids in the medium could support growth even when the trace of selenium was depleted and synthesis of glycine reductase stopped. With this unexpected finding, we had an ideal biological system for unraveling details of the role of selenium in the anaerobic metabolism of glycine.

The ability of some anaerobic bacteria to conserve energy via a soluble substrate level phosphorylation system by reducing glycine to acetyl-phosphate has been an intriguing mechanism for about half a century. The genes implicated in this system have been sequenced and form an operon structure with those of the thioredoxin system. The deduced proteins exhibit high degrees of similarity with glycine reductase from other bacteria. Faster progress in understanding the exact mechanisms is hampered, for example, by some unique reactions involving selenoethers and redox active selenocysteines, which do not allow an easy heterologous formation in Escherichia coli. Further major obstacles are the processing of a substrate-specific pro-protein to a new carbonyl/pyruvoyl group in one of the two peptides formed that stabilize the substrate-binding selenoprotein, which contains an additional rather unstable carbonyl group.

Selenoproteins exist within all three domains of life. It is estimated that one-third of prokaryotes utilize selenium for specific biological purposes, whereas the majority of microorganisms do not use or need selenium. Selenoproteins are unique proteins in which selenocysteine is inserted into the polypeptide chain by highly specialized translational machinery. Alternatively, some selenoproteins in which selenium is incorporated as a labile cofactor have been characterized, and this class of selenoproteins also contains either molybdenum or tungsten. Although several selenoproteins have been well characterized for several decades, the biological functions of these proteins are still being defined. The role of selenoproteins, particularly in human pathogens, has received little attention, yet there is evidence that targeting such proteins could play a major role in drug development. In addition, emerging evidence suggests that many well-known cancer drugs target a specific class of selenoproteins in mammals, lending credence to the notion that selenoproteins may indeed already be substantial drug targets in the clinic. Keywords: selenocysteine; selenoprotein; auranofin; arsenic; thioredoxin reductase; glutathione peroxidase; glycine reductase; d-proline reductase; Stickland reaction

In recent years there have been impressive increases in information concerning selenium biochemistry. After the initial discoveries that bacteria (Pinsent, 1954) and animals (Patterson et al., 1957; Schwarz and Foltz, 1957) require this trace element, almost 20 years elapsed before selenium was demonstrated to be an essential component of a mammalian enzyme, glutathione peroxidase,(Flohe et al., 1973; Rotruck et al., 1973) and a protein component of the Clostridial glycine reductase complex (Turner and Stadtman, 1973). Selenocysteine was determined to be the chemical form of selenium present in glycine reductase (Cone et al., 1976). Other prokaryotic selenoenzymes, several formate dehydrogenases (Stadtman, 1979, 1980a, 1980b, 1990 and 1996), a hydrogenase of Methanococcus vannielii (Yamazaki, 1982) and a clostridial nicotinic acid hydroxylase (Dilworth, 1982) were discovered. Mammalian glutathione peroxidase isoenzymes (Ursini et al., 1995) and selenoprotein P, a glycoprotein of unknown function, were isolated (Hill et al., 1991). Selenoprotein P is unusual in that it contains 10 selenocysteine residues in the polypeptide chain. Selenoprotein W, a 10 kDa muscle protein of unknown function was purified from normal muscle and partially characterized (Vendeland et al., 1993; Vendeland et al., 1995). The function of selenoprotein W is unknown but the occurrence of the selenocysteine residue in a Cys-x-x-Secys motif is suggestive of a redox role. The importance of selenium in mammalian physiology was magnified by the discovery of its occurrence in a 5' deiodinase that converts the prothyroid hormone, tetraiodothyronine, to the active hormone, 3,5,3'-tri-iodothyronine (Berry et al., 1991) and this established a direct role of selenium in eukaryotic developmental processes. Several years after the identification of selenocysteine in selenoproteins this unusual amino acid was shown to be inserted cotranslationally. An in-frame TGA codon was

Porphyromonas gingivalis and Treponema denticola are strongly associated with chronic periodontitis. These bacteria have been co-localized in subgingival plaque and demonstrated to exhibit symbiosis in growth in vitro and synergistic virulence upon co-infection in animal models of disease. Here we show that during continuous co-culture a P. gingivalis:T. denticola cell ratio of 6∶1 was maintained with a respective increase of 54% and 30% in cell numbers when compared with mono-culture. Co-culture caused significant changes in global gene expression in both species with altered expression of 184 T. denticola and 134 P. gingivalis genes. P. gingivalis genes encoding a predicted thiamine biosynthesis pathway were up-regulated whilst genes involved in fatty acid biosynthesis were down-regulated. T. denticola genes encoding virulence factors including dentilisin and glycine catabolic pathways were significantly up-regulated during co-culture. Metabolic labeling using 13C-glycine showed that T. denticola rapidly metabolized this amino acid resulting in the production of acetate and lactate. P. gingivalis may be an important source of free glycine for T. denticola as mono-cultures of P. gingivalis and T. denticola were found to produce and consume free glycine, respectively; free glycine production by P. gingivalis was stimulated by T. denticola conditioned medium and glycine supplementation of T. denticola medium increased final cell density 1.7-fold. Collectively these data show P. gingivalis and T. denticola respond metabolically to the presence of each other with T. denticola displaying responses that help explain enhanced virulence of co-infections., Author Summary Unlike the traditional view that most diseases are caused by infection with a single bacterial species, some chronic diseases including periodontitis result from the perturbation of the natural microbiota and the proliferation of a number of opportunistic pathogens. Both Porphyromonas gingivalis and Treponema denticola have been associated with the progression and severity of chronic periodontitis and have been shown to display synergistic virulence in animal models. However, the underlying mechanisms to these observations are unclear. Here we demonstrate that these two bacteria grow synergistically in continuous co-culture and modify their gene expression. The expression of T. denticola genes encoding known virulence factors and enzymes involved in the uptake and metabolism of the amino acid glycine was up-regulated in co-culture. T. denticola stimulated the proteolytic P. gingivalis to produce free glycine, which T. denticola used as a major carbon source. Our study shows P. gingivalis and T. denticola co-operate metabolically and this helps to explain their synergistic virulence in animal models and their intimate association in vivo.

Assessment of the nutritional requirements of Treponema denticola disclosed a strict growth dependence on selenium. In vivo labeling of cells of this organism with (75)Se and electrophoretic analysis revealed three labeled bands, two of which were selenoproteins correlating in size with subunits A and B of glycine reductase. Antibodies directed against glycine- or betaine-reductase subunits of Eubacterium acidaminophilum specifically also reacted with proteins from cell lysates of T. denticola. Moreover, ORFs within the T. denticola genome sequence were found whose products display high sequence similarity to glycine-reductase subunits. These findings strongly support the notion that T. denticola ferments amino acids via the activity of glycine reductase, an enzyme previously thought to be restricted to gram-positive bacteria.

GrdE and PrdA of Clostridium sticklandii are subunits of glycine reductase and D-proline reductase, respectively, that are processed post-translationally to form a catalytic active pyruvoyl group. The cleavage occurred on the N-terminal side of a cysteine residue, which is thus the precursor of a pyruvoyl moiety. Both proproteins could be over-expressed in Escherichia coli and conditions were developed for in vitro processing. GrdE could be expressed as full-size protein, whereas PrdA had to be truncated N-terminally to achieve successful over-expression. Both proproteins were cleaved at the in vivo observed cleavage site after addition of 200 mM NaBH4 in Tris buffer (pH 7.6) at room temperature as analysed by SDS/PAGE and MS. Cleavage of GrdE was observed with a half-time of approximately 30 min. Cys242, as the precursor of the pyruvoyl group in GrdE, was changed to alanine, serine, or threonine by site-directed mutagenesis. The Cys242--Ser and Cys242--Thr mutant proteins were also cleaved under similar conditions with extended half-times. However, the Cys242--Ala mutant protein was not cleaved indicating a pivotal role of the thiol group of cysteine or hydroxyl group of serine and threonine during the processing of pyruvoyl group-dependent reductases.

A probe based on the sequence of the gene encoding selenoprotein A of glycine reductase of Clostridium sticklandii was used to obtain clones of adjacent DNA that encoded the other components of glycine reductase, proteins B and C, in addition to thioredoxin and thioredoxin reductase. The genes of the thioredoxin system and the glycine reductase were shown to be transcribed together, confirming an operon structure. In addition, a gene (grdX) encoding a 13.7-kDa protein of unknown function seemed to be associated with the reductase genes. Four potential promoters were identified by mapping the 5'-end of the mRNAs. The sequence of promoter P1 was shown to be similar to the sigma70 promoter consensus sequence. The other three promoters were similar to each other, but not to known promoter consensus sequences. The transcripts starting at each of the four promoters were terminated to about 80% at a predicted loop structure downstream of grdB; the remaining transcripts continued through this structure and covered the genes encoding both subunits of protein C and bmpA, a gene that was also expressed monocistronically.

There are two types of bacterial selenoenzymes known at present: those that contain selenium in the form of selenocysteine residues in the polypeptide chains and those that instead contain a catalytically essential selenium in a dissociable cofactor form. Among the latter are the molybdopterin containing enzymes, nicotinic acid hydroxylase, xanthine dehydrogenase and the recently discovered purine hydroxylase. The crystal structure of a related enzyme, carbon monooxide dehydrogenase, has been determined. This enzyme, unlike the other three, is present in various aerobic bacteria. Escherichia coli formate dehydrogenase is a selenium-dependent enzyme that contains selenocysteine, molybdenum, a molybdopterin-guanine dinucleotide and an iron-sulfur center. The crystal structures of the oxidized and reduced enzymes have been reported. This enzyme differs from classical molybdenum hydroxylases in that oxygen from water is not incorporated in the product. Clostridial glycine reductase is a selenocysteine-dependent enzyme that reduces glycine to acetylphosphate and ammonia. The reaction mechanism of this enzyme involves the cleavage of a carbon-nitrogen bond of the Schiff base derivative of the glycine substrate and represents a new role of the ionized selenol group of the selenocysteine residue in metabolism. Selenium-carboxymethylselenocysteine is formed as the enzyme-bound intermediate on the selenoprotein A subunit of the enzyme complex in this reaction. Reductive cleavage of the selenoether, transfer to a cysteine residue of another subunit forming an acetylthioester and reaction with phosphate results in the formation of acetylphosphate.

Electron transfer reactions for the reduction of glycine in Eubacterium acidaminophilum involve many selenocysteine (U)- and thiol-containing proteins, as shown by biochemical and molecular analysis. These include an unusual thioredoxin system (-CXXC-), protein A (-CXXU-) and the substrate-specific protein B of glycine reductase (-UXXCXXC-). Most probably a selenoether is formed at protein B by splitting the C-N-bond after binding of the substrate. The carboxymethyl group is then transferred to the selenocysteine of protein A containing a conserved motif. The latter protein acts as a carbon and electron donor by giving rise to a protein C-bound acetyl-thioester and a mixed selenide-sulfide bond at protein A that will be reduced by the thioredoxin system. The dithiothreitol-dependent D-proline reductase of Clostridium sticklandii exhibits many similarities to protein B of glycine reductase including the motif containing selenocysteine. In both cases proprotein processing at a cysteine residue gives rise to a blocked N-terminus, most probably a pyruvoyl group. Formate dehydrogenase and some other proteins from E. acidaminophilum contain selenocysteine, e.g., a 22 kDa protein showing an extensive homology to peroxiredoxins involved in the detoxification of peroxides.

The substrate-specific selenoprotein B of glycine reductase (PBglycine) from Eubacterium acidaminophilum was purified and characterized. The enzyme consisted of three different subunits with molecular masses of about 22 (alpha), 25 (beta) and 47 kDa (gamma), probably in an alpha 2 beta 2 gamma 2 composition. PBglycine purified from cells grown in the presence of [75Se]selenite was labeled in the 47-kDa subunit. The 22-kDa and 47-kDa subunits both reacted with fluorescein thiosemicarbazide, indicating the presence of a carbonyl compound. This carbonyl residue prevented N-terminal sequencing of the 22-kDa (alpha) subunit, but it could be removed for Edman degradation by incubation with o-phenylenediamine. A DNA fragment was isolated and sequenced which encoded beta and alpha subunits of PBglycine (grdE), followed by a gene encoding selenoprotein A (grdA2) and the gamma subunit of PBglycine (grdB2). The cloned DNA fragment represented a second GrdB-encoding gene slightly different from a previously identified partial grdBl-containing fragment. Both grdB genes contained an in-frame UGA codon which confirmed the observed selenium content of the 47-kDa (gamma) subunit. Peptide sequence analyses suggest that grdE encodes a proprotein which is cleaved into the previously sequenced N-terminal 25-kDa (beta) subunit and a 22-kDa (alpha) subunit of PBglycine. Cleavage most probably occurred at an -Asn-Cys- site concomitantly with the generation of the blocking carbonyl moiety from cysteine at the alpha subunit.

Eubacterium acidaminophilum combines the oxidation of amino acids such as alanine or valine with the reduction of glycine to acetate in a two-substrate fermentation (Stickland reaction). In the absence of glycine, dense cell suspensions oxidized alanine or valine only to a small extent, with limited production of hydrogen and acetate. Experiments with 14C-labeled carbonate revealed that acetate was formed under these conditions by net reduction of CO2/HCO3−; 14C-labeled formate was formed as an intermediate. E. acidaminophilum did not grow with hydrogen plus CO2; dense cell suspensions under H2/CO2 produced only very small amounts (

A strictly anaerobic, Gram-positive, non-spore-forming bacterium was isolated from sewage sludge which grew on creatinine as sole source of carbon and energy. This new isolate, designated strain KRE 4T, totally degraded creatinine via creatine, sarcosine and glycine to the products acetate, monomethylamine, ammonia and carbon dioxide. Growth on creatinine or creatine was selenium-dependent and stimulated by formate, indicating the involvement of a creatine reductase, sarcosine reductase and/or glycine reductase. This was substantiated by the fact that creatine, sarcosine and glycine were reduced by cell-free extracts. Growth on creatinine or creatine was also possible in the absence of formate, but with an increase in doubling time. The new bacterium occurred as rod-shaped cells, which exhibited an angular form (2-6 microns long and 0.7-1.1 microns wide) and showed motility by means of peritrichous flagella. The G+C content of the DNA was 30 mol %. Comparative 16S rRNA sequence analysis demonstrated that strain KRE 4T represents a new subline within the genus Tissierella. Due to its very restricted substrate spectrum and the inability of whole cells to utilize sarcosine and glycine as intermediates of creatine breakdown, this organism can be readily separated from currently described species of Tissierella. Therefore, based on the phenotypic and phylogenetic distinctiveness of the new isolate, it si proposed that the bacterium be classified as a new species of the genus Tissierella, Tissierella creatinophila sp. nov. The type strain is KRE 4 (= DSM 6911T).

Simple complementation assay systems were developed for the substrate-specific proteins PB of glycine reductase, sarcosine reductase, and betaine reductase, in which acetyl phosphate was detected as the product in all three cases. The betaine-specific subunits of protein B (PB betaine) responsible for betaine reductase activity were purified to homogeneity from cells of Eubacterium acidaminophilum. The molecular masses of the two different subunits were 45 kDa and 48 kDa according to SDS/PAGE. The molecular mass of the native protein was about 200 kDa, indicating and alpha 2 beta 2 structure. The glycine-specific protein B (PB glycine) was partially purified and subunits of 47 kDa and 27 kDa were N-terminally sequenced. The latter subunits cross-reacted with antibodies raised against PB betaine and showed high sequence similarity to the 45-kDa and 48-kDa subunits of PB betaine, respectively. [2-14C]Glycine could be covalently coupled to the 47-kDa subunit by treatment with borohydride. By the same procedure, [2-14C]sarcosine labeled a protein of the same size. Like the sarcosine reductase activity, this protein was not present in glycine-grown cells, indicating its specific involvement in sarcosine metabolism. The labile viologen-dependent formate dehydrogenase purified with the respective PB proteins and could be tentatively assigned to a 95-kDa protein.

D-Proline is converted to 5-amino valeric acid by D-proline reductase. This conversion involves the reductive cleavage of the α-carbon-nitrogen bond. We have examined the fate of the carboxyl oxygen atoms during conversion of D-proline to δ-NH2-valeric acid. 18O atoms from the carboxyl group of D-proline are not lost during conversion to product. In contrast, in the conversion of glycine to acetyl phosphate by glycine reductase a carboxyl oxygen atom is lost to solvent. An intermediate acyl-enzyme is found during the reduction of glycine. We conclude that the reduction of proline proceeds without the formation of an acyl enzyme intermediate.