Characterization of an Fe(2+)-dependent archaeal-specific GTP cyclohydrolase, MptA, from Methanocaldococcus jannaschii

The first step in the biosynthesis of pterins in bacteria and plants is the conversion of GTP to 7,8-dihydro-d-neopterin triphosphate catalyzed by GTP cyclohydrolase I (GTPCHI). Although GTP has been shown to be a precursor of pterins in archaea, homologues of GTPCHI have not been identified in most archaeal genomes. Here we report the identification of a new GTP cyclohydrolase that converts GTP to 7,8-dihydro-d-neopterin 2',3'-cyclic phosphate, the first intermediate in methanopterin biosynthesis in methanogenic archaea. The enzyme from Methanocaldococcus jannaschii is designated MptA to indicate that it catalyzes the first step in the biosynthesis of methanopterin. MptA is the archetype of a new class of GTP cyclohydrolases that catalyzes a series of reactions most similar to that seen with GTPCHI but unique in that the cyclic phosphate is the product. MptA was found to require Fe2+ for activity. Mutation of conserved histidine residues H200N, H293N, and H295N, expected to be involved in Fe2+ binding, resulted in reduced enzymatic activity but no reduction in the amount of bound iron.

A novel function for the N-terminal nucleophile hydrolase fold demonstrated by the structure of an archaeal inosine monophosphate cyclohydrolase

Inosine 5'-monophosphate (IMP) cyclohydrolase catalyzes the cyclization of 5-formaminoimidazole-4-carboxamide ribonucleotide (FAICAR) to IMP in the final step of de novo purine biosynthesis. Two major types of this enzyme have been discovered to date: PurH in Bacteria and Eukarya and PurO in Archaea. The structure of the MTH1020 gene product from Methanothermobacter thermoautotrophicus was previously solved without functional annotation but shows high amino acid sequence similarity to other PurOs. We determined the crystal structure of the MTH1020 gene product in complex with either IMP or 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) at 2.0 and 2.6 A resolution, respectively. On the basis of the sequence analysis, ligand-bound structures, and biochemical data, MTH1020 is confirmed as an archaeal IMP cyclohydrolase, thus designated as MthPurO. MthPurO has a four-layered alphabeta betaalpha core structure, showing an N-terminal nucleophile (NTN) hydrolase fold. The active site is located at the deep pocket between two central beta-sheets and contains residues strictly conserved within PurOs. Comparisons of the two types of IMP cyclohydrolase, PurO and PurH, revealed that there are no similarities in sequence, structure, or the active site architecture, suggesting that they are evolutionarily not related to each other. The MjR31K mutant of PurO from Methanocaldococcus jannaschii showed 76% decreased activity and the MjE102Q mutation completely abolished enzymatic activity, suggesting that these highly conserved residues play critical roles in catalysis. Interestingly, green fluorescent protein (GFP), which has no structural homology to either PurO or PurH but catalyzes a similar intramolecular cyclohydrolase reaction required for chromophore maturation, utilizes Arg96 and Glu222 in a mechanism analogous to that of PurO.

Methylglyoxal is an intermediate in the biosynthesis of 6-deoxy-5-ketofructose-1-phosphate: a precursor for aromatic amino acid biosynthesis in Methanocaldococcus jannaschii

A biosynthetic pathway is proposed for creating 6-deoxy-5-ketofructose-1-phosphate (DKFP), a precursor sugar for aromatic amino acid biosynthesis in Methanocaldococcus jannaschii. First, two possible routes were investigated to determine if a modified, established biosynthetic pathway could be responsible for generating 6-deoxyhexoses in M. jannaschii. Both the nucleoside diphosphate mannose pathway and a pathway involving nucleoside diphosphate derivatives of fructose-1-P, fructose-2-P, or fructose-1,6-bisP were tested and eliminated. The established pathways did not produce the expected intermediates nor did the anticipated enzymes have the predicted enzymatic activities. Because neither anticipated pathway could produce DKFP, M. jannaschii glucose-6-P metabolism was studied in detail to establish exactly how glucose-6-P is converted into DKFP. This detailed analysis showed that methylglyoxal and a fructose-1-P- or fructose-1,6-bisP-derived dihydroxyacetone-P fragment are key intermediates in DKFP production. Glucose-6-P readily converts to fructose-6-P, which in turn converts to fructose-1,6-bisP. Fructose-6-P and fructose-1,6-bisP convert into glyceraldehyde-3-P (Ga-P-3), which converts into methylglyoxal by a 2,3-elimination of phosphate. The MJ1585-derived enzyme catalyzes the condensation of methylglyoxal with a dihydroxyacetone-P fragment, which is derived from fructose-1-P and/or fructose-1,6-bisP, generating DKFP. The elimination of phosphate from Ga-P-3 proceeds by both enzymatic and chemical routes in cell extracts, producing sufficient concentrations of methylglyoxal to support the reaction. This work is the first report of methylglyoxal functioning in central metabolism.

Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis

Methanococcus maripaludis is a strictly anaerobic, methane-producing archaeon and facultative autotroph capable of biosynthesizing all the amino acids and vitamins required for growth. In this work, the novel 6-deoxy-5-ketofructose-1-phosphate (DKFP) pathway for the biosynthesis of aromatic amino acids (AroAAs) and p-aminobenzoic acid (PABA) was demonstrated in M. maripaludis. Moreover, PABA was shown to be derived from an early intermediate in AroAA biosynthesis and not from chorismate. Following metabolic labelling with [U-(13)C]-acetate, the expected enrichments for phenylalanine and arylamine derived from PABA were observed. DKFP pathway activity was reduced following growth with aryl acids, an alternative source of the AroAAs. Lastly, a deletion mutant of aroA', which encodes the first step in the DKFP pathway, required AroAAs and PABA for growth. Complementation of the mutants by an aroA' expression vector restored the wild-type phenotype. In contrast, a deletion of aroB', which encodes the second step in the DKFP pathway, did not require AroAAs or PABA for growth. Presumably, methanococci contain an alternative activity for this step. These results identify the initial reactions of a new pathway for the biosynthesis of PABA in methanococci.

Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate

Archaea have been shown to produce isoprenoids from mevalonate; however, genome analysis has failed to identify several genes in the mevalonate pathway on the basis of sequence similarity. A predicted archaeal kinase, coded for by the MJ0044 gene, was associated with other mevalonate pathway genes in the archaea and was predicted to be the "missing" phosphomevalonate kinase. The MJ0044-derived protein was tested for phosphomevalonate kinase activity and was found not to catalyze this reaction. The MJ0044 gene product was found to phosphorylate isopentenyl phosphate, generating isopentenyl diphosphate. Unlike other known kinases associated with isoprene biosynthesis, Methanocaldococcus jannaschii isopentenyl phosphate kinase is predicted to be a member of the aspartokinase superfamily.

Identification of lactaldehyde dehydrogenase in Methanocaldococcus jannaschii and its involvement in production of lactate for F420 biosynthesis

One of the early steps in the biosynthesis of coenzyme F(420) in Methanocaldococcus jannaschii requires generation of 2-phospho-L-lactate, which is formed by the phosphorylation of L-lactate. Preliminary studies had shown that L-lactate in M. jannaschii is not derived from pyruvate, and thus an alternate pathway(s) for its formation was examined. Here we report that L-lactate is formed by the NAD(+)-dependent oxidation of l-lactaldehyde by the MJ1411 gene product. The lactaldehyde, in turn, was found to be generated either by the NAD(P)H reduction of methylglyoxal or by the aldol cleavage of fuculose-1-phosphate by fuculose-1-phosphate aldolase, the MJ1418 gene product.

Ribose-5-phosphate biosynthesis in Methanocaldococcus jannaschii occurs in the absence of a pentose-phosphate pathway

Recent work has raised a question as to the involvement of erythrose-4-phosphate, a product of the pentose phosphate pathway, in the metabolism of the methanogenic archaea (R. H. White, Biochemistry 43:7618-7627, 2004). To address the possible absence of erythrose-4-phosphate in Methanocaldococcus jannaschii, we have assayed cell extracts of this methanogen for the presence of this and other intermediates in the pentose phosphate pathway and have determined and compared the labeling patterns of sugar phosphates derived metabolically from [6,6-2H2]- and [U-13C]-labeled glucose-6-phosphate incubated with cell extracts. The results of this work have established the absence of pentose phosphate pathway intermediates erythrose-4-phosphate, xylose-5-phosphate, and sedoheptulose-7-phosphate in these cells and the presence of D-arabino-3-hexulose-6-phosphate, an intermediate in the ribulose monophosphate pathway. The labeling of the D-ara-bino-3-hexulose-6-phosphate, as well as the other sugar-Ps, indicates that this hexose-6-phosphate was the precursor to ribulose-5-phosphate that in turn was converted into ribose-5-phosphate by ribose-5-phosphate isomerase. Additional work has demonstrated that ribulose-5-phosphate is derived by the loss of formaldehyde from D-arabino-3-hexulose-6-phosphate, catalyzed by the protein product of the MJ1447 gene.

L-cysteine desulfidase: an [4Fe-4S] enzyme isolated from Methanocaldococcus jannaschii that catalyzes the breakdown of L-cysteine into pyruvate, ammonia, and sulfide

A [4Fe-4S] enzyme that decomposes L-cysteine to hydrogen sulfide, ammonia, and pyruvate has been isolated and characterized from Methanocaldococcus jannaschii. The sequence of the isolated enzyme demonstrated that the protein was the product of the M. jannaschii MJ1025 gene. The protein product of this gene was recombinantly produced in Escherichia coli and purified to homogeneity. Both the isolated and recombinant enzymes are devoid of pyridoxal phosphate (PLP) and are rapidly inactivated upon exposure to air. The air-inactivated enzyme is activated by reaction with Fe2+ and dithiothreitol in the absence of air. The air-inactivated enzyme contains 3 mol of iron per subunit (43 kDa, SDS gel electrophoresis), and the native enzyme has a measured molecular mass of 135 kDa (gel filtration), indicating it is a trimer. The enzyme is very specific for L-cysteine, with no activity being detected with D-cysteine, L-homocysteine, 3-mercaptopropionic acid (cysteine without the amino group), cysteamine (cysteine without the carboxylic acid), or mercaptolactate (the hydroxyl analogue of cysteine). The activity of the enzyme was stimulated by 40% when the enzyme was assayed in the presence of methyl viologen (4 mM) and inhibited by 70% when the enzyme was assayed in the presence of EDTA (7.1 mM). Preincubation of the enzyme with iodoacetamide (17 mM) completely abolishes activity. The enzymatic activity has a half-life of 8 or 12 min when the enzyme is treated at room temperature with 0.42 mM N-ethylmaleimide (NEM) or 0.42 mM iodoacetamide, respectively. MALDI analysis of the NEM-inactivated enzyme showed Cys25 as the site of alkylation. Site-directed mutagenesis of each of four of the cysteines conserved in the orthologues of the enzyme reduced the catalytic efficiency and thermal stability of the enzyme. The enzyme was found to catalyze exchange of the C-2 hydrogen of the L-cysteine with solvent. These results are consistent with three of the conserved cysteines being involved in the formation of the [4Fe-4S] center and the thiolate of Cys25 serving as a base to abstract the alpha-hydrogen in the first step of the elimination. Although the enzyme has no sequence homology to any known enzymes, including the non-PLP-dependent serine/threonine dehydratases or aconitases, the mechanisms of action of all of these enzymes are similar, in that each catalyzes an alpha,beta-elimination reaction adjacent to a carboxylate group. It is proposed that the enzyme may be responsible for the production of sulfide required for the biosynthesis of iron-sulfur centers in this archaea. A mechanism of action of the enzyme is proposed.

Identification and characterization of a L-tyrosine decarboxylase in Methanocaldococcus jannaschii

Methanofuran is the first coenzyme in the methanogenic pathway used by the archaeon Methanocaldococcus jannaschii, as well as other methanogens, to reduce CO2 to methane. The details of the pathway for the biosynthesis of methanofuran and the responsible genes have yet to be established. A clear structural element in all known methanofurans is tyramine, likely produced by the decarboxylation of L-tyrosine. We show here that the mfnA gene at M. jannaschii locus MJ0050 encodes a thermostable pyridoxal phosphate-dependent L-tyrosine decarboxylase that specifically produces tyramine. Homologs of this gene are widely distributed among euryarchaea but are not specifically related to known bacterial or plant tyrosine decarboxylases.

A Methanocaldococcus jannaschii archaeal signature gene encodes for a 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase. A new enzyme in purine biosynthesis

We have identified and characterized a new member of the ATP-grasp enzyme family that catalyzes the ATP- and formate-dependent formylation of 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (FAICAR) in the absence of folates. The enzyme, which we designate as PurP, is the product of the Methanocaldococcus jannaschii purP gene (MJ0136), which is a signature gene for Archaea. As is characteristic of reactions catalyzed by this family of enzymes, the other products of the reaction, ADP and P(i), were produced stoichiometrically with the amount of ATP, formate, and AICAR used. Formyl phosphate was found to substitute for ATP and formate in the reaction, yet the methylene analog, phosphonoacetaldehyde, was not an inhibitor or substrate for the reaction. The enzyme, along with PurO, which catalyzes the cyclization of FAICAR to inosine 5'-monophosphate, catalyzes the same overall transformation in purine biosynthesis as is accomplished by PurH in bacteria and eukaryotes. No homology exists between PurH and either PurO or PurP. 1H NMR and gas chromatography-mass spectrometry analysis of an M. jannaschii cell extract showed the presence of free formate that can be used by the enzyme for purine biosynthesis. This formate arises by the reduction of CO2 with hydrogen; this was demonstrated by incorporating 13C into the formate when M. jannaschii cell extracts were incubated with H13CO3- and hydrogen gas. The presence of this signature gene in all of the Archaea indicates the presence of a purine biosynthetic pathway proceeding in the absence of folate coenzymes.

Assessment of manure phosphorus export through turfgrass sod production in Erath County, Texas

A best management practice (BMP) for exporting manure phosphorus (P) in turfgrass sod from the North Bosque River (NBR) watershed in central Texas was assessed using a geographic information system (GIS). The NBR watershed has a mandate to reduce the total annual P load to the NBR by 50% as a result of total maximum daily load regulation. Since dairy waste applications to fields are identified as the major nonpoint source of P to the river, innovative BMPs, such as export of manure P in turfgrass, will be needed to achieve the 50% reduction. However, methods are needed to evaluate the feasibility of these innovative management practices prior to their implementation. A geospatial database of suitable turfgrass production sites was developed for Erath County using GIS. Erath County largely encompasses the upper portion of the NBR watershed. Information from field experiments, production practices, and ground-truthing was used to search, analyze, and verify a geospatial database developed from national and regional sources. The integration and analyses of large databases supports the search by turf producers for sites suitable for turfgrass sod production in Erath County. In addition, GIS enables researchers and regulators to estimate manure P exports and reduced P loading due to implementation of the manure export BMP on a county scale. Under optimal conditions 198,000 kg manure P yr(-1) could be used and 114,840 kg manure P yr(-1) exported from the NBR watershed through implementation of a system using dairy manure to produce turfgrass sod. This is the equivalent of the manure P applied from 10,032 dairy cows yr(-1) and exported from 5808 dairy cows yr(-1). Application of GIS to large-scale planning and decision-making transcends traditional field-scale applications in precision agriculture.

Effect of age on the incidence of venous thromboembolism after major surgery

BACKGROUND

Most guidelines for administration of thromboprophylaxis after major surgery use age as a major predictor of postoperative venous thromboembolism (VTE). We sought to quantify the effect of age on the risk of symptomatic VTE after a spectrum of surgical procedures.

METHODS

Using the California Patient Discharge Data Set and specific ICD-9-CM surgical procedure codes, we retrospectively determined the incidence of VTE diagnosed within 91 days after 40 different urgent or elective surgeries performed in the hospital between 1992 and 1996. Logistic regression was used to quantify the effect of age on the incidence of postoperative VTE and to adjust for other risk factors.

RESULTS

1,464,452 cases underwent one of 40 different procedures (mean cases per procedure = 35,718, range 4500-145 500). There was a significant interaction between age and the type of surgery performed (P<0.0001). Qualitative analysis of the effect of age on the incidence of VTE stratified by the presence or absence of malignancy revealed three general patterns: a steady increase in the incidence of VTE with age, exemplified by appendectomy or cholecystectomy; an increase in VTE up to approximately age 65 with no increase thereafter, exemplified by total hip arthroplasty; and no effect of age on the incidence of VTE, exemplified by vascular surgery.

CONCLUSIONS

The relationship between age and the risk of VTE after surgery is complex and depends on the nature of the surgery and the underlying pathologic process. Advancing age was a significant predictor for VTE following surgeries performed for conditions not inherently associated with significant comorbidity. Conversely, advancing age was not associated with a higher incidence of VTE after surgeries performed for conditions strongly associated with serious underlying comorbidity, such as a malignancy or severe peripheral vascular disease.

l-Aspartate Semialdehyde and a 6-Deoxy-5-ketohexose 1-Phosphate Are the Precursors to the Aromatic Amino Acids in Methanocaldococcus jannaschii

No orthologs are present in the genomes of the archaea encoding genes for the first two steps in the biosynthesis of the aromatic amino acids leading to 3-dehydroquinate (DHQ). The absence of these genes prompted me to examine the nature of the reactions involved in the archaeal pathway leading to DHQ in Methanocaldococcus jannaschii. Here I report that 6-deoxy-5-ketofructose 1-phosphate and l-aspartate semialdehyde are precursors to DHQ. The sugar, which is derived from glucose 6-P, supplies a "hydroxyacetone" fragment, which, via a transaldolase reaction, undergoes an aldol condensation with the l-aspartate semialdehyde to form 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid. Despite the fact that both hydroxyacetone and hydroxyacetone-P were measured in the cell extracts and confirmed to arise from glucose 6-P, neither compound was found to serve as a precursor to DHQ. This amino sugar then undergoes a NAD dependent oxidative deamination to produce 3,7-dideoxy-d-threo-hept-2,6-diulosonic acid which cyclizes to 3-dehydroquinate. The protein product of the M. jannaschii MJ0400 gene catalyzes the transaldolase reaction and the protein product of the MJ1249 gene catalyzes the oxidative deamination and the cyclization reactions. The DHQ is readily converted into dehydroshikimate and shikimate in M. jannaschii cell extracts, consistent with the remaining steps and genes in the pathway being the same as in the established shikimate pathway.

Runoff losses of phosphorus and nitrogen imported in sod or composted manure for turf establishment

Nutrient loading on impaired watersheds can be reduced through export of sod grown with manure and export of composted manure for turf production on other watersheds. Effects of the sod and manure exports on receiving watersheds were evaluated through monitoring of total dissolved phosphorus (TDP) and N concentrations and losses in runoff from establishing turf. Three replications of seven treatments were established on an 8.5% slope of a Booneville soil (loamy-skeletal, mixed, superactive Pachic Argicryolls). Three treatments comprised imported 'Tifway' bermudagrass [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy) sod grown with composted dairy manure (382 or 191 kg P ha(-1)) or fertilizer (50 kg P ha(-1)). Three treatments were sprigged with Tifway and top-dressed with either composted manure (92 or 184 kg P ha(-1)) or fertilizer (100 kg P ha(-1)). The control was established bermudagrass [Cynodon dactylon (L.) Pers. var. Guymon]. During eight fall rain events, mean TDP concentration in runoff (7.8 mg L(-1)) from sprigged Tifway top-dressed with manure (84 kg P ha(-1)) was 1.6 times greater than sod imported with 129 kg manure P ha(-1). During the first fall event, mass losses of TDP (232 mg m(-2)) and total Kjeldahl nitrogen (TKN) (317 mg m(-2)) from sprigged treatments top-dressed with manure or fertilizer were nearly three times greater than manure-grown sod. Percentages of manure P lost as TDP in runoff from imported sod were 33% of percentages lost from sprigged treatments top-dressed with manure. Sod grown with manure P rates of 190 kg P ha(-1) can be imported without increasing runoff losses of TDP compared with conventional fertilization of establishing turfgrass.

The biosynthesis of cysteine and homocysteine in Methanococcus jannaschii

The pathway for the biosynthesis of cysteine and homocysteine in Methanococcus jannaschii has been examined using a gas chromatography-mass spectrometry (GC-MS) stable isotope dilution method to identify and quantitate the intermediates in the pathways. The first step in the pathway, and the one responsible for incorporation of sulfur into both cysteine and methionine, is the reaction between O-phosphohomoserine and a presently unidentified sulfur source present in cell extracts, to produce L-homocysteine. This sulfur source was shown not to be sulfide. The resulting L-homocysteine then reacts with O-phosphoserine to form L-cystathionine, which is cleaved to L-cysteine. The pathway has elements of both the plant and mammalian pathways in that the sulfur is first incorporated into homocysteine using O-phosphohomoserine as the acceptor and the resulting homocysteine, via transsulfuration, supplies the sulfur for cysteine formation. The pathway leading to these two amino acids represents an example of metabolic thrift where the preexisting cellular metabolites O-phosphohomoserine and O-phosphoserine are used as the ultimate source of the carbon framework for the biosynthesis of these amino acids. These findings explain the absence of identifiable genes in the genome of this organism for the biosynthesis of cysteine and homocysteine.

The structural determination of phosphosulfolactate synthase from Methanococcus jannaschii at 1.7-A resolution: an enolase that is not an enolase

Members of the enolase mechanistically diverse superfamily catalyze a wide variety of chemical reactions that are related by a common mechanistic feature, the abstraction of a proton adjacent to a carboxylate group. Recent investigations into the function and mechanism of the phosphosulfolactate synthase encoded by the ComA gene in Methanococcus jannaschii have suggested that ComA, which catalyzes the stereospecific Michael addition of sulfite to phosphoenolpyruvate to form phosphosulfolactate, may be a member of the enolase superfamily. The ComA-catalyzed reaction, the first step in the coenzyme M biosynthetic pathway, likely proceeds via a Mg2+ ion-stabilized enolate intermediate in a manner similar to that observed for members of the enolase superfamily. ComA, however, has no significant sequence similarity to any known enolase. Here we report the x-ray crystal structure of ComA to 1.7-A resolution. The overall fold for ComA is an (alpha/beta)8 barrel that assembles with two other ComA molecules to form a trimer in which three active sites are created at the subunit interfaces. From the positions of two ordered sulfate ions in the active site, a model for the binding of phosphoenolpyruvate and sulfite is proposed. Despite its mechanistic similarity to the enolase superfamily, the overall structure and active site architecture of ComA are unlike any member of the enolase superfamily, which suggests that ComA is not a member of the enolase superfamily but instead acquired an enolase-type mechanism through convergent evolution.

Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase required for coenzyme F(420) biosynthesis

The hydride carrier coenzyme F(420) contains the unusual chromophore 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO). Microbes that generate F(420) produce this FO moiety using a pyrimidine intermediate from riboflavin biosynthesis and the 4-hydroxyphenylpyruvate precursor of tyrosine. The fbiC gene, cloned from Mycobacterium smegmatis, encodes the bifunctional FO synthase. Expression of this protein in Escherichia coli caused the host cells to produce FO during growth, and activated cell-free extracts catalyze FO biosynthesis in vitro. FO synthase in the methanogenic euryarchaeon Methanocaldococcus jannaschii comprises two proteins encoded by cofG (MJ0446) and cofH (MJ1431). Both subunits were required for FO biosynthesis in vivo and in vitro. Cyanobacterial genomes encode homologs of both genes, which are used to produce the coenzyme for FO-dependent DNA photolyases. A molecular phylogeny of the paralogous cofG and cofH genes is consistent with the genes being vertically inherited within the euryarchaeal, cyanobacterial, and actinomycetal lineages. Ancestors of the cyanobacteria and actinomycetes must have acquired the two genes, which subsequently fused in actinomycetes. Both CofG and CofH have putative radical S-adenosylmethionine binding motifs, and pre-incubation with S-adenosylmethionine, Fe(2+), sulfide, and dithionite stimulates FO production. Therefore a radical reaction mechanism is proposed for the biosynthesis of FO.

Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii

Potentially mutagenic uracil-containing nucleotide intermediates are generated by deamination of dCTP, either spontaneously or enzymatically as the first step in the conversion of dCTP to dTTP. dUTPases convert dUTP to dUMP, thus avoiding the misincorporation of dUTP into DNA and creating the substrate for the next enzyme in the dTTP synthetic pathway, thymidylate synthase. Although dCTP deaminase and dUTPase activities are usually found in separate but homologous enzymes, the hyperthermophile Methanococcus jannaschii has an enzyme, DCD-DUT, that harbors both dCTP deaminase and dUTP pyrophosphatase activities. DCD-DUT has highest activity on dCTP, followed by dUTP, and dTTP inhibits both the deaminase and pyrophosphatase activities. To help clarify structure-function relationships for DCD-DUT, we have determined the crystal structure of the wild-type DCD-DUT protein in its apo form to 1.42A and structures of DCD-DUT in complex with dCTP and dUTP to resolutions of 1.77A and 2.10A, respectively. To gain insights into substrate interactions, we complemented analyses of the experimentally defined weak density for nucleotides with automated docking experiments using dCTP, dUTP, and dTTP. DCD-DUT is a hexamer, unlike the homologous dUTPases, and its subunits contain several insertions and substitutions different from the dUTPase beta barrel core that likely contribute to dCTP specificity and deamination. These first structures of a dCTP deaminase reveal a probable role for an unstructured C-terminal region different from that of the dUTPases and possible mechanisms for both bifunctional enzyme activity and feedback inhibition by dTTP.

CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii

The protein product of the Methanococcus jannaschii MJ0768 gene has been expressed in Escherichia coli, purified to homogeneity, and shown to catalyze the GTP-dependent addition of two l-glutamates to the l-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F(420)-0) to form F(420)-0-glutamyl-glutamate (F(420)-2). Since the reaction is the fifth step in the biosynthesis of coenzyme F(420), the enzyme has been designated as CofE, the product of the cofE gene. Gel filtration chromatography indicates CofE is a dimer. The enzyme has no recognized sequence similarity to any previously characterized proteins. The enzyme has an absolute requirement for a divalent metal ion and a monovalent cation. Among the metal ions tested, a mixture of Mn(2+), Mg(2+), and K(+) is the most effective. CofE catalyzes amide bond formation with the cleavage of GTP to GDP and inorganic phosphate, likely involving the activation of the free carboxylate group of F(420)-0 to give an acyl phosphate intermediate. Evidence for the occurrence of this intermediate is presented. A reaction mechanism for the enzyme is proposed and compared with other members of the ADP-forming amide bond ligase family.

Glutathione synthetase homologs encode alpha-L-glutamate ligases for methanogenic coenzyme F420 and tetrahydrosarcinapterin biosyntheses

Proteins in the ATP-grasp superfamily of amide bond-forming ligases have evolved to function in a number of unrelated biosynthetic pathways. Previously identified homologs encoding glutathione synthetase, d-alanine:d-alanine ligase and the bacterial ribosomal protein S6:glutamate ligase have been vertically inherited within certain organismal lineages. Although members of this specificity-diverse superfamily share a common reaction mechanism, the nonoverlapping set of amino acid and peptide substrates recognized by each family provided few clues as to their evolutionary history. Two members of this family have been identified in the hyperthermophilic marine archaeon Methanococcus jannaschii and shown to catalyze the final reactions in two coenzyme biosynthetic pathways. The MJ0620 (mptN) locus encodes a tetrahydromethanopterin:alpha-l-glutamate ligase that forms tetrahydrosarcinapterin, a single carbon-carrying coenzyme. The MJ1001 (cofF) locus encodes a gamma-F420-2:alpha-l-glutamate ligase, which caps the gamma-glutamyl tail of the hydride carrier coenzyme F420. These two genes share a common ancestor with the ribosomal protein S6:glutamate ligase and a putative alpha-aminoadipate ligase, defining the first group of ATP-grasp enzymes with a shared amino acid substrate specificity. As in glutathione biosynthesis, two unrelated amino acid ligases catalyze sequential reactions in coenzyme F420 polyglutamate formation: a gamma-glutamyl ligase adds 1-3 l-glutamate residues and the ATP-grasp-type ligase described here caps the chain with a single alpha-linked l-glutamate residue. The analogous pathways for glutathione, F420, folate, and murein peptide biosyntheses illustrate convergent evolution of nonribosomal peptide biosynthesis through the recruitment of single-step amino acid ligases.

Methanococcus jannaschii coenzyme F420 analogs contain a terminal alpha-linked glutamate

Analyses of the F(420)s present in Methanococcus jannaschii have shown that these cells contain a series of gamma-glutamyl-linked F(420)s capped with a single, terminal alpha-linked L-glutamate. The predominant form of F(420) was designated as alpha-F(420)-3 and represented 86% of the F(420)s in these cells. Analyses of Methanosarcina thermophila, Methanosarcina barkeri, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Mycobacterium smegmatis showed that they contained only gamma-glutamyl-linked F(420)s.

The Methanococcus jannaschii dCTP deaminase is a bifunctional deaminase and diphosphatase

Most bacteria produce the dUMP precursor for thymine nucleotide biosynthesis using two enzymes: a dCTP deaminase catalyzes the formation of dUTP and a dUTP diphosphatase catalyzes pyrophosphate release. Although these two hydrolytic enzymes appear to catalyze very different reactions, they are encoded by homologous genes. The hyperthermophilic archaeon Methanococcus jannaschii has two members of this gene family. One gene, at locus MJ1102, encodes a dUTP diphosphatase, which can scavenge deoxyuridine nucleotides that inhibit archaeal DNA polymerases. The second gene, at locus MJ0430, encodes a novel dCTP deaminase that releases dUMP, ammonia, and pyrophosphate. Therefore this enzyme can singly catalyze both steps in dUMP biosynthesis, precluding the formation of free, mutagenic dUTP. Besides differing from the previously characterized Salmonella typhimurium dCTP deaminase in its reaction products, this archaeal enzyme has a higher affinity for dCTP and its steady-state turnover is faster than the bacterial enzyme. Kinetic studies suggest: 1) the archaeal enzyme specifically recognizes dCTP; 2) dCTP deamination and dUTP diphosphatase activities occur independently at the same active site, and 3) both activities depend on Mg(2+). The bifunctional activity of this M. jannaschii enzyme illustrates the evolution of a suprafamily of related enzymes that catalyze mechanistically distinct reactions.

Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms

The three-dimensional structure of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii was determined at 1.4 A resolution. The pyruvoyl group of arginine decarboxylase is generated by an autocatalytic internal serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide chains. The structure of the nonprocessing S53A mutant was also determined. The active site of the processed enzyme unexpectedly contained the reaction product agmatine. The crystal structure confirms that arginine decarboxylase is a homotrimer. The protomer fold is a four-layer alphabetabetaalpha sandwich with topology similar to pyruvoyl-dependent histidine decarboxylase. Highly conserved residues Asn47, Ser52, Ser53, Ile54, and Glu109 are proposed to play roles in the self-processing reaction. Agmatine binding residues include the C terminus of the beta chain (Ser52) from one protomer and the Asp35 side chain and the Gly44 and Val46 carbonyl oxygen atoms from an adjacent protomer. Glu109 is proposed to play a catalytic role in the decarboxylation reaction.

A member of a new class of GTP cyclohydrolases produces formylaminopyrimidine nucleotide monophosphates

The hyperthermophilic euryarchaeon Methanococcus jannaschii has no recognizable homologues of the canonical GTP cyclohydrolase enzymes that are required for riboflavin and pteridine biosyntheses. Instead, it uses a new type of thermostable GTP cyclohydrolase enzyme that produces 2-amino-5-formylamino-6-ribofuranosylamino-4(3H)-pyrimidinone ribonucleotide monophosphate and inorganic phosphate. Whereas canonical GTP cyclohydrolases produce this formylamino-pyrimidine nucleotide as a reaction intermediate, this compound is shown to be an end product of the purified recombinant M.jannaschii enzyme. Unlike other enzymes that hydrolyze the alpha-beta phosphate anhydride bond of GTP, this new enzyme completely hydrolyzes pyrophosphate to inorganic phosphate. As a result, the enzyme has a steady-state turnover of 21 min(-)(1), which is much faster than those of canonical GTP cyclohydrolase enzymes. The effects of substrate analogues and inhibitors suggest that the GTP cyclohydrolase and pyrophosphate phosphohydrolase activities occur at independent sites, although both activities depend on Mg(2+).

Export of manure phosphorus and nitrogen in turfgrass sod

Regulatory mandates have increased demand for best management practices (BMPs) that will reduce nutrient loading on watersheds impaired by excess manure P and N. Export of manure P and N in turfgrass sod harvests is one BMP under consideration. This study quantified amounts and percentages of P and N removed in a sod harvest for different rates of manure and inorganic P and N. Six treatments comprised an unfertilized control, two manure rates with and without supplemental inorganic N, and inorganic P and N only. The treatments were applied to 'Tifway' bermudagrass (Cynodon dactylon L. x C. transvaalensis Burtt-Davey), '609' buffalograss [Buchloe dactyloides (Nutt.) Engelm.], and 'Reveille' bluegrass (Poa arachnifera Torr. x P. pratensis L.) under field conditions. Comparisons among treatments revealed small variations of P and N content in clippings and the plant component of sod, but large variations in the soil component of sod for each turf species. In addition, 2 to 10 times more P and 1.3 to 5 times more N was removed in soil than in plant components of sod for the two manure rates with and without added inorganic N. Percentages of applied P and N in harvested sod were similar for the two manure rates with and without added N for each species, but differed among turf species for each P (46 to 77%) and N (36 to 47%). The large amounts and percentages of manure P and N removed by sod harvest support the feasibility of this BMP in efforts to reduce nutrient loads on watersheds.

Anticoagulation therapy

Despite refinements and standardization in the use of anticoagulants, many problems remain for clinicians. Dr. Crowther describes appropriate starting and maintenance doses of warfarin, factors accounting for inter- and intra-observer variability and importantly, the management of the over-anticoagulated patients and bleeding patients. Dr. White compares unfractionated heparin (UFH) and low molecular weight heparin (LMWH) and addresses whether there truly are differences in the efficacy and safety of different LMWH's for both arterial and venous indications. Dr. Ortel discusses the management of the problem patient who requires anticoagulants, the management of heparin-induced thrombocytopenia, the pregnant patient, the obese patient, patients who have renal insufficiency and/or liver disease, patients with malignant disease, and other challenging patient populations.

Response of turf and quality of water runoff to manure and fertilizer

Manure applications can benefit turfgrass production and unused nutrients in manure residues can be exported through sod harvests. Yet, nutrients near the soil surface could be transported in surface runoff. Our research objective was to evaluate responses of bermudagrass [Cynodon dactylon (L.) Pers. var. Guymon] turf and volumes and P and N concentrations of surface runoff after fertilizer or composted manure applications. Three replications of five treatments were established on a Boonville fine sandy loam (fine, smectitic, thermic Vertic Albaqualf) that was excavated to create an 8.5% slope. Manure rates of 50 and 100 kg P ha(-1) at the start of two monitoring periods were compared with P fertilizer rates of 25 and 50 kg ha(-1) and an unfertilized control. Compared with initial soil tests, nitrate concentrations decreased and P concentrations increased after two manure or fertilizer applications and eight rain events over the two monitoring periods. The fertilizer sources of P and N produced 19% more dry weight and 21% larger N concentrations in grass clippings than manure sources. Yet, runoff volumes were similar between manure and fertilizer sources of P. Dissolved P concentration (30 mg L(-1)) in runoff during a rain event 3 d after application of 50 kg P ha(-1) was five times greater for fertilizer than for manure P. Observations during both monitoring periods indicated that total P and N losses in runoff were no greater for composted manure than for fertilizer sources of P at relatively large P rates on a steep slope of turfgrass.

Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase in polyamine biosynthesis

The genome sequence of the hyperthermophilic methanogen Methanococcus jannaschii contains homologs of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organism nor any other euryarchaeon have orthologs of the pyridoxal 5'-phosphate-dependent ornithine or arginine decarboxylase genes, required to produce putrescine. Instead, as shown here, these organisms have a new class of arginine decarboxylase (PvlArgDC) formed by the self-cleavage of a proenzyme into a 5-kDa subunit and a 12-kDa subunit that contains a reactive pyruvoyl group. Although this extremely thermostable enzyme has no significant sequence similarity to previously characterized proteins, conserved active site residues are similar to those of the pyruvoyl-dependent histidine decarboxylase enzyme, and its subunits form a similar (alphabeta)(3) complex. Homologs of PvlArgDC are found in several bacterial genomes, including those of Chlamydia spp., which have no agmatine ureohydrolase enzyme to convert agmatine (decarboxylated arginine) into putrescine. In these intracellular pathogens, PvlArgDC may function analogously to pyruvoyl-dependent histidine decarboxylase; the cells are proposed to import arginine and export agmatine, increasing the pH and affecting the host cell's metabolism. Phylogenetic analysis of Pvl- ArgDC proteins suggests that this gene has been recruited from the euryarchaeal polyamine biosynthetic pathway to function as a degradative enzyme in bacteria.

A divergent archaeal member of the alkaline phosphatase binuclear metalloenzyme superfamily has phosphoglycerate mutase activity

The hyperthermophilic archaeon Methanococcus jannaschii uses several non-canonical enzymes to catalyze conserved reactions in glycolysis and gluconeogenesis. A highly diverged gene from that organism has been proposed to function as a phosphoglycerate mutase. Like the canonical cofactor-independent phosphoglycerate mutase and other members of the binuclear metalloenzyme superfamily, this M. jannaschii protein has conserved nucleophilic serine and metal-binding residues. Yet the substrate-binding residues are not conserved. We show that the genes at M. jannaschii loci MJ0010 and MJ1612 encode thermostable enzymes with phosphoglycerate mutase activity. Phylogenetic analyses suggest that this gene family arose before the divergence of the archaeal lineage.

Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes

The hyperthermophilic euryarchaeon Methanococcus jannaschii uses coenzyme M (2-mercaptoethanesulfonic acid) as the terminal methyl carrier in methanogenesis. We describe an enzyme from that organism, (2R)-phospho-3-sulfolactate synthase (ComA), that catalyzes the first step in coenzyme M biosynthesis. ComA catalyzed the stereospecific Michael addition of sulfite to phosphoenolpyruvate over a broad range of temperature and pH conditions. Substrate and product analogs moderately inhibited activity. This enzyme has no significant sequence similarity to previously characterized enzymes; however, its Mg(2+)-dependent enzyme reaction mechanism may be analogous to one proposed for enolase. A diverse group of microbes and plants have homologs of ComA that could have been recruited for sulfolactate or sulfolipid biosyntheses.

The pyrimidine nucleotide reductase step in riboflavin and F(420) biosynthesis in archaea proceeds by the eukaryotic route to riboflavin

The Methanococcus jannaschii gene MJ0671 was cloned and overexpressed in Escherichia coli, and its gene product was tested for its ability to catalyze the pyridine nucleotide-dependent reduction of either 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (compound 3) to 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate (compound 4) or 5-amino-6-ribosylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate (compound 7) to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate (compound 5). Only compound 3 was found to serve as a substrate for the enzyme. NADPH and NADH functioned equally well as the reductants. This specificity for the reduction of compound 3 was also confirmed by using cell extracts of M. jannaschii and Methanosarcina thermophila. Thus, this step in riboflavin biosynthesis in these archaea is the same as that found in yeasts. The absence of the other genes in the biosynthesis of riboflavin in Archaea is discussed.

The genome of M. acetivorans reveals extensive metabolic and physiological diversity

Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived from acetate. Here we report the complete genome sequence of an acetate-utilizing methanogen, Methanosarcina acetivorans C2A. Methanosarcineae are the most metabolically diverse methanogens, thrive in a broad range of environments, and are unique among the Archaea in forming complex multicellular structures. This diversity is reflected in the genome of M. acetivorans. At 5,751,492 base pairs it is by far the largest known archaeal genome. The 4524 open reading frames code for a strikingly wide and unanticipated variety of metabolic and cellular capabilities. The presence of novel methyltransferases indicates the likelihood of undiscovered natural energy sources for methanogenesis, whereas the presence of single-subunit carbon monoxide dehydrogenases raises the possibility of nonmethanogenic growth. Although motility has not been observed in any Methanosarcineae, a flagellin gene cluster and two complete chemotaxis gene clusters were identified. The availability of genetic methods, coupled with its physiological and metabolic diversity, makes M. acetivorans a powerful model organism for the study of archaeal biology. [Sequence, data, annotations and analyses are available at http://www-genome.wi.mit.edu/.]

Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics

Methanogenesis, the anaerobic production of methane from CO2 or simple carbon compounds, requires seven organic coenzymes. This review describes pathways for the biosynthesis of methanofuran, 5,6,7,8-tetrahydromethanopterin, coenzyme F420, coenzyme M (2-mercaptoethanesulfonic acid) and coenzyme B (7-mercaptoheptanoyl-L-threonine phosphate). Spectroscopic evidence for the pathways is reviewed and recent efforts are described to identify and characterize the biosynthetic enzymes from methanogenic archaea. The literature from 1971 to September 2001 is reviewed, and 169 references are cited.

Characterization of the 2-phospho-L-lactate transferase enzyme involved in coenzyme F(420) biosynthesis in Methanococcus jannaschii

The protein product of the Methanococcus jannaschii MJ1256 gene has been expressed in Escherichia coli, purified to homogeneity, and shown to be involved in coenzyme F(420) biosynthesis. The protein catalyzes the transfer of the 2-phospholactate moiety from lactyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (Fo) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F(420)-0) and GMP. On the basis of the reaction catalyzed, the enzyme is named LPPG:Fo 2-phospho-L-lactate transferase. Since the reaction is the fourth step in the biosynthesis of coenzyme F(420), the enzyme has been designated as CofD, the product of the cofD gene. The transferase requires Mg(2+) for activity, and the catalysis does not appear to proceed via a covalent intermediate. To a lesser extent CofD also catalyzes a number of additional reactions that include the formation of Fo-P, when the enzyme is incubated with Fo and GDP, GTP, pyrophosphate, or tripolyphosphate, and the hydrolysis of F(420)-0 to Fo. All of these side reactions can be rationalized as occurring by a common mechanism. CofD has no recognized sequence similarity to any previously characterized enzyme.

New class of IMP cyclohydrolases in Methanococcus jannaschii

The enzyme responsible for observed IMP cyclohydrolase activity in Methanococcus jannaschii was purified and sequenced: its genetic locus was found to correspond to gene MJ0626. The MJ0626 gene was cloned, and its protein product was expressed in Escherichia coli and shown to catalyze the cyclization of 5-formylamidoimidazole-4-carboxamide ribonucleotide to IMP. The enzyme has no sequence similarity to known enzymes, and its catalytic properties appear distinct from any characterized IMP cyclohydrolase. The purO gene for the enzyme is currently found only in the domain Archaea.

Bermudagrass Dead Spot: A New Disease of Bermudagrass Caused by Ophiosphaerella agrostis

Hybrid bermudagrass (Cynodon dactylon (L.) Pers. × C. transvaalensis Burtt-Davy) is widely used on golf course putting greens in the southern United States. In March and April 1998, circular patches of dead grass 2 to 10 cm in diameter were observed on a bermudagrass putting green in College Station, TX, that had been overseeded with rough bluegrass (Poa trivialis L.) the previous October. Rapid death and deterioration of the rough bluegrass within the spot revealed extensive foliar and crown necrosis and root decay of the remaining bermudagrass. Diseased bermudagrass leaves in the patch were reddish brown to tan. Dark ectotrophic hyphae were not found on the roots or stolons, but dark hyphae were observed within the affected root tissues. Numerous pseudothecia were embedded in necrotic leaf and stolon tissues. The characteristics of the pseudothecia and ascospores coincide with the description of Ophiosphaerella agrostis Dernoeden, Camara, O'Neil, van Berkum, and Palm (1,2). This fungus was consistently isolated from stolons and roots, and single-ascospore isolates were obtained from pseudothecia. Inoculum was prepared by transferring fungal mycelium from a single-spore isolate grown in potato dextrose agar (PDA) to a moistened, autoclaved mixture of rice hulls (Oryza sativa L.) and milled rice (2:1, vol/vol) for 28 days at 24°C. 'FloraDwarf' bermudagrass was grown from stolons in 15-cm-diameter pots containing a mixture of sand, peat moss, and perlite (8:3:1, vol/vol). The bermudagrass was maintained at a height of 1 to 1.5 cm for ≈ 1 month. Plants were inoculated by forming a hole that was 0.8 cm in diameter and 7 cm deep in the center of the pot, using a rod and filling the hole with inoculum. Control pots received the same treatment, except uninoculated rice hull-milled rice mixture was used. The treatments were replicated three times, and the experiment was performed twice. The pots were maintained in a greenhouse for 6 weeks. In all inoculated pots, patches of dead bermudagrass 6 to 10 cm in diameter developed. Roots, stolons, and leaves were necrotic, and pseudothecia were abundant in stolon and leaf sheath tissues. O. agrostis was consistently reisolated from infected root and stolon tissues. All isolates produced colonies identical in appearance to the culture used for inoculation. To our knowledge, this is the first report that O. agrostis is pathogenic to hybrid bermudagrass. References: (1) M. P. S. Camara et al. Mycologia 92:317, 2000. (2) P. H. Dernoeden et al. Plant Dis. 83:397, 1999.