PubMed Health⌕ Search

Biomedical subjects

R S Wolfe

Publications and source records attributed to R S Wolfe.

At least 19 recordsLinked to original sources
PubMed1998

Purification, regulation, and molecular and biochemical characterization of pyruvate carboxylase from Methanobacterium thermoautotrophicum strain deltaH.

We discovered that Methanobacterium thermoautotrophicum strain DeltaH possessed pyruvate carboxylase (PYC), and this biotin prototroph required exogenously supplied biotin to exhibit detectable amounts of PYC activity. The enzyme was highly labile and was stabilized by 10% inositol in buffers to an extent that allowed purification to homogeneity and characterization. The purified enzyme was absolutely dependent on ATP, Mg2+ (or Mn2+ or Co2+), pyruvate, and bicarbonate for activity; phosphoenolpyruvate could not replace pyruvate, and acetyl-CoA was not required. The enzyme was inhibited by ADP and alpha-ketoglutarate but not by aspartate or glutamate. ATP was inhibitory at high concentrations. The enzyme, unlike other PYCs, exhibited nonlinear kinetics with respect to bicarbonate and was inhibited by excess Mg2+, Mn2+, or Co2+. The 540-kDa enzyme of A4B4 composition contained a non-biotinylated 52-kDa subunit (PYCA) and a 75-kDa biotinylated subunit (PYCB). The pycB gene was probably monocistronic and followed by a putative gene of a DNA-binding protein on the opposite strand. The pycA was about 727 kilobase pairs away from pycB on the chromosome and was probably co-transcribed with the biotin ligase gene (birA). PYCA and PYCB showed substantial sequence identities (33-62%) to, respectively, the biotin carboxylase and biotin carboxyl carrier + carboxyltransferase domains or subunits of known biotin-dependent carboxylases/decarboxylases. We discovered that PYCB and probably the equivalent domains or subunits of all biotin-dependent carboxylases harbored the serine/threonine dehydratase types of pyridoxal-phosphate attachment site. Our results and the existence of an alternative oxaloacetate synthesizing enzyme phosphoenolpyruvate carboxylase in M. thermoautotrophicum strain DeltaH (Kenealy, W. R., and Zeikus, J. G. (1982) FEMS Microbiol. Lett. 14, 7-10) raise several questions for future investigations.

Amino Acid Sequence↗
PubMed1998

Molecular genetic analysis of phosphite and hypophosphite oxidation by Pseudomonas stutzeri WM88.

The first molecular and genetic characterization of a biochemical pathway for oxidation of the reduced phosphorus (P) compounds phosphite and hypophosphite is reported. The pathway was identified in Pseudomonas stutzeri WM88, which was chosen for detailed studies from a group of organisms isolated based on their ability to oxidize hypophosphite (+1 valence) and phosphite (+3 valence) to phosphate (+5 valence). The genes required for oxidation of both compounds by P. stutzeri WM88 were cloned on a single ca. 30-kbp DNA fragment by screening for expression in Escherichia coli and Pseudomonas aeruginosa. Two lines of evidence suggest that hypophosphite is oxidized to phosphate via a phosphite intermediate. First, plasmid subclones that conferred oxidation of phosphite, but not hypophosphite, upon heterologous hosts were readily obtained. All plasmid subclones that failed to confer phosphite oxidation also failed to confer hypophosphite oxidation. No subclones that conferred only hypophosphite expression were obtained. Second, various deletion derivatives of the cloned genes were made in vitro and recombined onto the chromosome of P. stutzeri WM88. Two phenotypes were displayed by individual mutants. Mutants with the region encoding phosphite oxidation deleted (based upon the subcloning results) lost the ability to oxidize either phosphite or hypophosphite. Mutants with the region encoding hypophosphite oxidation deleted lost only the ability to oxidize hypophosphite. The phenotypes displayed by these mutants also demonstrate that the cloned genes are responsible for the P oxidation phenotypes displayed by the original P. stutzeri WM88 isolate. The DNA sequences of the minimal regions implicated in oxidation of each compound were determined. The region required for oxidation of phosphite to phosphate putatively encodes a binding-protein-dependent phosphite transporter, an NAD+-dependent phosphite dehydrogenase, and a transcriptional activator of the lysR family. The region required for oxidation of hypophosphite to phosphite putatively encodes a binding-protein-dependent hypophosphite transporter and an alpha-ketoglutarate-dependent hypophosphite dioxygenase. The finding of genes dedicated to oxidation of reduced P compounds provides further evidence that a redox cycle for P may be important in the metabolism of this essential, and often growth-limiting, nutrient.

Base Sequence↗
PubMed1997

A genetic system for Archaea of the genus Methanosarcina: liposome-mediated transformation and construction of shuttle vectors.

New methods that allow, for the first time, genetic analysis in Archaea of the genus Methanosarcina are presented. First, several autonomously replicating plasmid shuttle vectors have been constructed based on the naturally occurring plasmid pC2A from Methanosarcina acetivorans. These vectors replicate in 9 of 11 Methanosarcina strains tested and in Escherichia coli. Second, a highly efficient transformation system based upon introduction of DNA by liposomes has been developed. This method allows transformation frequencies of as high as 2 x 10(8) transformants per microgram of DNA per 10(9) cells or approximately 20% of the recipient population. During the course of this work, the complete 5467-bp DNA sequence of pC2A was determined. The implications of these findings for the future of methanoarchaeal research are also discussed.

Amino Acid Sequence↗
PubMed1996

Molecular, genetic, and biochemical characterization of the serC gene of Methanosarcina barkeri Fusaro.

The Methanosarcina barkeri serC gene, encoding phosphoserine aminotransferase, was cloned by complementation of an Escherichia coli serC mutant, and its nucleotide sequence was determined. The M. barkeri SerC protein shares significant homology with other known SerC proteins. E. coli serC hosts carrying the cloned gene express phosphoserine aminotransferase activity, verifying the function of this gene.

Amino Acid Sequence↗
PubMed1993

Component A2 of methylcoenzyme M reductase system from Methanobacterium thermoautotrophicum delta H: nucleotide sequence and functional expression by Escherichia coli.

The gene for component A2 of the methylcoenzyme M reductase system from Methanobacterium thermoautotrophicum delta H was cloned, and its nucleotide sequence was determined. The gene for A2, designated atwA, encodes an acidic protein of 59,335 Da. Amino acid sequence analysis revealed partial homology of A2 to a number of eucaryotic and bacterial proteins in the ATP-binding cassette (ABC) family of transport systems. Component A2 possesses two ATP-binding domains. A 2.2-kb XmaI-BamHI fragment containing atwA and the surrounding open reading frames was cloned into pGEM-7Zf(+). A cell extract from this strain replaced purified A2 from M. thermoautotrophicum delta H in an in vitro methylreductase assay.

Adenosine Triphosphate↗
PubMed1993

Methyl viologen hydrogenase II, a new member of the hydrogenase family from Methanobacterium thermoautotrophicum delta H.

Two methyl viologen hydrogenase (MVH) enzymes from Methanobacterium thermoautotrophicum delta H have been separated (resolution, Rs at 1.0) on a Mono Q column after chromatography on DEAE-Sephacel and Superose 6 Prep Grade. The newly discovered MVH (MVH II) was eluted at 0.5 M NaCl with a linear gradient of 0.45 to 0.65 M NaCl (100 ml). The previously described MVH (MVH I) eluted in a NaCl gradient at 0.56 M. The specific activities of MVH I and MVH II were 184.8 and 61.3 U/mg of protein, respectively, when enzyme activity was compared at pH 7.5, the optimal pH for MVH II. Gel electrophoresis in nondenaturing systems indicated that MVH I and MVH II had a similar molecular mass of 145 kDa. Denatured MVH II showed four protein bands (alpha, 50 kDa; beta, 44 kDa; gamma, 36 kDa; delta, 15 kDa), similar to MVH I. The N-terminal amino acid sequences of the alpha, gamma, and delta subunits of MVH II were identical with the sequences of the equivalent subunits of MVH I. However, the N-terminal amino acid sequence of the beta subunit of MVH II was totally different from the sequence of the beta subunit of MVH I. Both MVH I and MVH II had the same optimal temperature of 60 degrees C for maximum activity. The pH optima of MVH I and MVH II were 9.0 and 7.5, respectively. Most of the divalent metal ions tested significantly inhibited MVH I activity, but MVH II activity was only partially inhibited by some divalent cations. Both hydrogenases were shown to be stable for over 8 days at --20 degrees C under anaerobic conditions. When exposed to air, 90% of MVH I activity was lost within 2 min; however, MVH II lost only 50% of its activity in 3 h.

Amino Acid Sequence↗
PubMed1992

Structural modifications and kinetic studies of the substrates involved in the final step of methane formation in Methanobacterium thermoautotrophicum.

The 2-(methylthio)ethanesulfonic acid (CH3-S-CoM) reductase catalyzes the final methane-yielding reaction in fastidiously anaerobic methanogenic archaebacteria. This step involves the reductive demethylation of CH3-S-CoM with reducing equivalents from N-7-(mercaptoheptanoyl)-L-threonine O3-phosphate (HS-HTP) to yield methane and the nonsymmetrical disulfide of 2-mercaptoethanesulfonic acid and HS-HTP. We chemically synthesized modified analogs of CH3-S-CoM (which has two carbons in the ethylene bridge) and of HS-HTP (which has seven carbons in the side chain); analog pairs possessed an overall correct number of side chain carbons (i.e., a total of nine in combination). They were simultaneously added to anaerobic cell extracts of Methanobacterium thermoautotrophicum delta H. The ability of the extracts to reductively demethylate the modified substrates was tested by gas chromatography. We also describe here previously unknown inhibitors of methanogenesis, 6-(methylthio)hexanoyl-L-threonine O3-phosphate (a structural analog of HS-HTP) and sodium bromomethanesulfonic acid (a structural analog of CH3-S-CoM). Both analogs were found to be effective competitive inhibitors with respect to HS-HTP. These substrate analogs were also found to inhibit a recently described photoactivation of homogeneous inactive reductase (K. D. Olson, C. W. McMahon, and R. S. Wolfe, Proc. Natl. Acad. Sci. USA 88:4099-4103, 1991). In addition, we probed the mechanism of action of a potent inhibitor of the enzyme, 2-bromoethanesulfonic acid, a structural analog of CH3-S-CoM.

Binding, Competitive↗
PubMed1991

Photoactivation of the 2-(methylthio)ethanesulfonic acid reductase from Methanobacterium.

Inactive 2-(methylthio)ethanesulfonic acid (CH3-S-CoM) reductase was partially activated by exposure to light. This simplified system replaces the complex enzymatic system of protein components A2, A3a, A3b, and ATP, which previously represented the only available means of reactivating the enzyme. Components necessary for light activation include N-(7-mercaptoheptanoyl)-L-threonine O3-phosphate (HS-HTP), CH3-S-CoM, titanium(III) citrate [Ti(III)Cit], and light above 400 nm. Photoactivation was inhibited by known inhibitors of methanogenesis: 2-bromoethanesulfonate (BES), N-(6-mercaptohexanoyl)-L-threonine O3-phosphate, N-(8-mercaptooctanoyl)-L-threonine O3-phosphate, and sodium dithionite. Methanogenesis continued when the light-activated reaction mixture was incubated in the dark. Although the specific activity was low (35 nmol of CH4 per h per mg of protein) the reaction products methane and the unsymmetrical disulfide of 2-mercaptoethanesulfonate (HS-CoM) and HS-HTP were identified. We were unable to photoactivate a reaction mixture containing the isolated prosthetic group, native F430, or its analogues.

Citrates↗
PubMed1991

7-Mercaptoheptanoylthreonine phosphate substitutes for heat-stable factor (mobile factor) for growth of Methanomicrobium mobile.

Methanomicrobium mobile requires a heat-stable factor present in ruminal fluid and in boiled cell extract from Methanobacterium thermoautotrophicum for growth. By comparing the growth of M. mobile with boiled cell extract with that observed with various methanogenic cofactors, we found that 7-mercaptoheptanoylthreonine phosphate (HS-HTP) supported sustained growth of M. mobile, at an optimal concentration of 100 microM. No derivatives or possible biosynthetic precursors of HS-HTP could replace HS-HTP as the sole source of growth factor. Results suggest that the growth requirement might be satisfied by 7-mercaptoheptanoic acid plus a second, unidentified heat-stable factor.

Culture Media↗
PubMed1991

Light sensitivity of methanogenic archaebacteria.

Representatives of four families of methanogenic archaebacteria (archaea), Methanobacterium thermoautotrophicum delta H, Methanobacterium thermoautotrophicum Marburg, Methanosarcina acetivorans, Methanococcus voltae, and Methanomicrobium mobile, were found to be light sensitive. The facultative anaerobic eubacteria Escherichia coli and Salmonella typhimurium, however, were tolerant of light when grown anaerobically under identical light conditions. Interference filters were used to show that growth of the methanogens is inhibited by light in the blue end of the visible spectrum (370 to 430 nm).

Euryarchaeota↗
PubMed1990

The formylmethanofuran:tetrahydromethanopterin formyltransferase from Methanobacterium thermoautotrophicum delta H. Nucleotide sequence and functional expression of the cloned gene.

The formylmethanofuran:tetrahydromethanopterin formyltransferase (FTR) from Methanobacterium thermoautotrophicum delta H was cloned and its sequence was determined. The clone was contained on a 4.8-kilobase BamHI fragment of M. thermoautotrophicum DNA ligated into pBR329. When this fragment was subcloned into the phagemid pTZ18R, a functional enzyme was synthesized under control of the lac promoter. Sequence analysis revealed the presence of a ribosome binding site and a possible terminator structure. The absence of an identifiable promoter lends credibility to the open reading frame which is present 5' to ftr. The ftr gene encodes an acidic protein with a calculated molecular weight of 31,401. The sequence of FTR does not appear to be homologous to any other sequenced proteins, including proteins which use pterin substrates.

Amino Acid Sequence↗
PubMed1990

Formyl-methanofuran synthesis in Methanobacterium thermoautotrophicum.

The initial step of methanogenesis from CO2 is the formation of formyl-methanofuran (formyl-MFR) from methanofuran (MFR), CO2 and H2. The enzymology of this novel type of CO2 fixation reaction has been difficult to study because formyl-MFR synthesis is subject to a complex activation. Recently, however, a number of advances have made questions regarding formyl-MFR synthesis more approachable.

Aldehyde Oxidoreductases↗
PubMed1989

An unusual thiol-driven fumarate reductase in Methanobacterium with the production of the heterodisulfide of coenzyme M and N-(7-mercaptoheptanoyl)threonine-O3-phosphate.

An unusual fumarate reductase was purified from cell extracts of Methanobacterium thermoautotrophicum and partially characterized. Two coenzymes previously isolated from cell extracts, 2-mercaptoethane-sulfonic acid (HS-CoM) and N-(7-mercaptoheptanoyl)threonine-O3-phosphate (HS-HTP), were established as direct electron donors for fumarate reductase. By measuring the consumption of free thiol, we determined that fumarate reductase catalyzed the oxidation of HS-CoM and HS-HTP; by the direct measurement of succinate and the heterodisulfide of HS-CoM and HS-HTP (CoM-S-S-HTP), we established that these compounds were products of the fumarate reductase reaction. A number of thiol-containing compounds did not function as substrates for fumarate reductase, but this enzyme had high specific activity when HS-CoM and HS-HTP were used as electron donors. HS-CoM and HS-HTP were quantitatively oxidized by the fumarate reductase reaction, and results indicated that this reaction was irreversible. Additionally, by measuring formylmethanofuran, we demonstrated that the addition of fumarate to cell extracts activated CO2 fixation for the formation of formylmethanofuran. Results indicated that this activation resulted from the production of CoM-S-S-HTP (a compound known to be involved in the activation of formylmethanofuran synthesis) by the fumarate reductase reaction.

Disulfides↗
PubMed1989

Activation of formylmethanofuran synthesis in cell extracts of Methanobacterium thermoautotrophicum.

In cell extracts of Methanobacterium thermoautotrophicum, formylmethanofuran (formyl-MFR) synthesis (an essential CO2 fixation reaction that is an early step in CO2 reduction to methane) is subject to a complex activation that involves a heterodisulfide of coenzyme M and N-(7-mercaptoheptanoyl)threonine O3-phosphate (CoM-S-S-HTP). In this paper we report that titanium(III) citrate, a low-potential reducing agent, stimulated CO2 reduction to methane and activated formyl-MFR synthesis in cell extracts. Titanium(III) citrate functioned as the sole source of electrons for formyl-MFR synthesis and enabled this reaction to occur independently of CoM-S-S-HTP. In addition, CoM-S-S-HTP was found to activate an unknown electron carrier that reduced metronidazole. The activation of formyl-MFR synthesis by CoM-S-S-HTP may involve the activation of a low-potential electron carrier.

Cell-Free System↗