Cloning and Characterization of Helicobacter pyloriSuccinyl CoA:Acetoacetate CoA-transferase, a Novel Prokaryotic Member of the CoA-transferase Family

Corthésy–Theulaz, Irène; Bergonzelli, Gabriela; Henry, Hugues; Bachmann, Daniel; Schorderet, D.F.; Blum, A. L.; Ornston, L N

doi:10.1074/jbc.272.41.25659

Cited by 50 publications

(42 citation statements)

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“…The TCA cycle in the metabolic reconstruction is complete, but not in a traditional sense as in E. coli. There are reactions included such as ␣-ketoglutarate oxidase (AKO) (55), succinyl coenzyme A (CoA):acetoacetate CoA transferase (SCOT) (13), and malate:quinone oxidoreductase (MQO) (31), which allow complete connectivity between the metabolites of the TCA cycle, although these reactions are not typically considered to be part of a TCA cycle. Notably, the fumarate reductase included in the reconstruction is reversible, as evidenced from experimental literature, indicating the oxidation of succinate (11,31) and as supported by a number of modeling calculations in agreement with physiological findings.…”

Section: H Pylori Metabolic Reconstructionmentioning

confidence: 99%

Genome-Scale Metabolic Model of Helicobacter pylori 26695

et al. 2002

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A genome-scale metabolic model of Helicobacter pylori 26695 was constructed from genome sequence annotation, biochemical, and physiological data. This represents an in silico model largely derived from genomic information for an organism for which there is substantially less biochemical information available relative to previously modeled organisms such as Escherichia coli. The reconstructed metabolic network contains 388 enzymatic and transport reactions and accounts for 291 open reading frames. Within the paradigm of constraint-based modeling, extreme-pathway analysis and flux balance analysis were used to explore the metabolic capabilities of the in silico model. General network properties were analyzed and compared to similar results previously generated for Haemophilus influenzae. A minimal medium required by the model to generate required biomass constituents was calculated, indicating the requirement of eight amino acids, six of which correspond to essential human amino acids. In addition a list of potential substrates capable of fulfilling the bulk carbon requirements of H. pylori were identified. A deletion study was performed wherein reactions and associated genes in central metabolism were deleted and their effects were simulated under a variety of substrate availability conditions, yielding a number of reactions that are deemed essential. Deletion results were compared to recently published in vitro essentiality determinations for 17 genes. The in silico model accurately predicted 10 of 17 deletion cases, with partial support for additional cases. Collectively, the results presented herein suggest an effective strategy of combining in silico modeling with experimental technologies to enhance biological discovery for less characterized organisms and their genomes.Genomics has reshaped many approaches to studying the biology of an organism. It has made possible studies in comparative genomics (1, 2, 17, 34), genome-wide transcriptional profiling (16), and a host of integrated analyses aimed at understanding the systems biology of organisms (14,25,68).For model organisms such as Escherichia coli and Saccharomyces cerevisiae genome sequencing has generated a wealth of insight into the physiology of these microbes. However, the availability of extensive biological information and literature regarding these organisms has undoubtedly made it easier to reconcile data against the genome and interpret many characteristic properties of the genome and its genetic contents.To date most of the common model organisms have had their genomes sequenced and current sequencing efforts are naturally moving on to less-well characterized organisms. This begs the question: what can be learned about less characterized organisms from their genomic sequence in the relative absence of extensive previous laboratory research? Additionally, how can the genome be utilized to assist in guiding future research and discovery into the particular organism of interest?Herein we explore one aspect of these questions as it relates to metab...

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Section: H Pylori Metabolic Reconstructionmentioning

confidence: 99%

Genome-Scale Metabolic Model of Helicobacter pylori 26695

et al. 2002

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“…The succinyl-CoA : acetoacetate CoA-transferase (SCOT)-encoding gene (sco) of H. pylori was discovered by Corthe! sy- Theulaz et al (1997). In contrast to the monomeric eukaryotic homologues, the H. pylori enzyme consists of two subunits, A and B.…”

Section: Methodsmentioning

confidence: 99%

Population genetics of Helicobacter pylori in the southern part of Switzerland analysed by sequencing of four housekeeping genes (atpD, glnA, scoB and recA), and by vacA, cagA, iceA and IS605 genotyping The GenBank accession numbers for the sequences reported in this paper are AY004351–AY004662

Solcà¹,

Bernasconi²,

Valsangiacomo³

et al. 2001

Microbiology

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The population biology of 78 Helicobacter pylori strains (71 from Swiss Italian, 4 from East Asian and 3 from South African patients) was investigated by sequence analysis of four housekeeping genes : atpD, scoB, glnA and recA. The vacA genotype, the presence of cagA and IS605, the iceA allelic type, and the resistance to metronidazole, clarithromycin and amoxycillin were determined. A high percentage of DNA polymorphic sites (198 % for atpD, 213 % for scoB, 237 % for glnA and 203 % for recA) was found. The phylogenetic trees based on the nucleotide sequences of the four gene fragments showed different topologies and were incongruent. The virulence-associated markers were distributed over the dendrograms and no association was found with phylogenetic clusters or clinical manifestations (chronic gastritis, gastric or duodenal ulcer, MALT lymphoma). Moreover, the H ratios (calculated with the homoplasy test) ranged from 0742 to 0799, depending on the gene fragment examined. All these observations suggest that H. pylori exists as a recombinant population. The clustering of the strains according to their geographical origin (USA/Europe, East Asia, South Africa) that has recently been demonstrated elsewhere could only be confirmed for the East Asian vacA s1c strains. In contrast, the South African strains clustered together only in the atpD tree. Presumably, recombination at the different loci has masked the evolutionary relationship among the strains. Keywords : H. pylori, housekeeping genes, antibiotic resistance INTRODUCTIONHelicobacter pylori is a microaerophilic, Gram-negative, slow-growing, spiral-shaped and flagellate microorganism. Its ecological niche is the human gastric mucosa, where it can survive in an acid environment thanks to a powerful urease activity (Blaser, 1997). The bacterium, discovered in 1983 by Robin Warren and Barry Marshall, has been associated with various gastropathologies such as chronic atrophic gastritis, Abbreviation :MALT lymphoma, gastric mucosa-associated lymphoid tissue lymphoma.The GenBank accession numbers for the sequences reported in this paper are AY004351-AY004662 peptic ulcer, gastric cancer and mucosa-associated lymphoid tissue lymphoma (MALT lymphoma) Roggero et al., 1995). Once acquired, H. pylori usually persists for life, unless eradicated by antimicrobial therapy. Even though the prevalence of infection may be very high (70-90 % in developing countries, 25-50 % in developed countries), most humans infected with H. pylori are asymptomatic and only a few patients develop peptic ulcer or gastric cancer (Pounder, 1995). Host genetic predisposition and local environmental factors, together with bacterial genotypes, may play an important role in the development of disease.Since H. pylori is involved in gastric pathology, researchers have tried to identify specific virulence No 186A MALT S S s1b-m1 Yes A2 No 18A CG R R s1a-m1 Yes A2 Yes 192A DU S S s1a-m1 Yes A2 Yes 22A CG S S s1a-m1 Yes A1 No 24C CG S S s2-m2a Yes A2 No 25A DU ...

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“…YdiF is grouped with ϳ330 other proteins in the coenzyme A transferase superfamily IPR004165 (InterPro data base (30)) with rather diverse substrate specificities (31)(32)(33)(34)(35). Within the E. coli K12 genome, the individual N-terminal domain (residues 12-255) and C-terminal domain (residues 285-512) of YdiF are related in sequence to AtoD (24% identity) and AtoA (25% identity), representing the ␣-and ␤-subunits, respectively, of ACT (36).…”

Section: Ydif Is An Acyl-coa Transferasementioning

confidence: 99%

Crystallographic Trapping of the Glutamyl-CoA Thioester Intermediate of Family I CoA Transferases

Rangarajan

Ajamian

et al. 2005

Journal of Biological Chemistry

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Coenzyme A is a cofactor utilized by as many as 4% of all enzymes for a diverse variety of biological functions, including cell-cell-mediated recognition, nerve impulse conductance, transcription, and fatty acid biosynthesis and degradation (1, 2). Mainly, these reactions involve the binding and transfer of an acyl group from one substrate to another as part of an enzymatic reaction; it has been noted that coenzyme A is the most prominent acyl group carrier in all living systems (3). Enzymecatalyzed reactions employing CoA thioesters can be divided into two categories, (i) those where the thioester carbonyl C atom reacts as an electrophile and (ii) those where the thioester ␣-carbon is deprotonated and reacts as a nucleophile, in Claisen enzymes (1). CoA transferases, which catalyze the reversible transfer of CoA from a donor CoA thioester to a carboxylic acid acceptor generating the free donor and a new acyl-CoA (Scheme 1), belong to the first category of enzymes. Among the large number of CoA transferases, much attention has focused on mitochondrial succinyl-CoA:3-oxoacid CoA-transferase (SCOT), 4 as its autosomal recessive deficiency in humans results in improper ketone body utilization causing episodic severe ketosis, hypoglycemia, and ultimately coma (4, 5).Three classes of CoA transferases have been defined based mainly on mechanistic and sequence criteria (6). Family I enzymes employ as acceptors 3-oxoacids, short-chain fatty acids, or glutaconate. These enzymes operate with a ping-pong kinetic mechanism and form a covalent thioester intermediate (7). The most thoroughly studied member of the Family I CoA transferases is SCOT. Family II consists of the multifunctional enzymes citrate or citramalate lyase, and unlike Family I enzymes, they do not form a covalent thioester intermediate. Family III enzymes have been discovered more recently, and are distinct both mechanistically (6, 8) and structurally (9) A wealth of biochemical and mechanistic data are available for SCOT, largely based on the pioneering studies of Jencks and collaborators (7,(11)(12)(13). These studies established a landmark for the concept of substrate binding energy utilization by an enzyme to effect catalysis, showing that SCOT utilizes its covalent (␥-glutamyl-CoA thioester) and noncovalent interactions with the CoA moiety of the acyl-CoA substrate differentially to reduce the Gibbs activation energy required for catalysis (13). The utilization of this binding energy for catalysis differs for different chemical moieties within the CoA cofactor, as well for the different steps along the reaction coordinate. Although crystal structures are available for three Family I CoA transferases, including glutaconate CoA transferase (GCT) from Acidaminococcus fermentens (14), acetate-CoA transferase (ACT, ␣-subunit) from Escherichia coli (15), and SCOT from pig heart (16, 17), no structure has yet been determined with bound substrate or product. The absence of an enzyme-substrate co-crystal structure for any Family I CoA transferase has prevented...

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Cloning and Characterization of Helicobacter pyloriSuccinyl CoA:Acetoacetate CoA-transferase, a Novel Prokaryotic Member of the CoA-transferase Family

Abstract: Sequencing of a fragment of

Cited by 50 publications

References 42 publications

Genome-Scale Metabolic Model of Helicobacter pylori 26695

Genome-Scale Metabolic Model of Helicobacter pylori 26695

Population genetics of Helicobacter pylori in the southern part of Switzerland analysed by sequencing of four housekeeping genes (atpD, glnA, scoB and recA), and by vacA, cagA, iceA and IS605 genotyping The GenBank accession numbers for the sequences reported in this paper are AY004351–AY004662

Crystallographic Trapping of the Glutamyl-CoA Thioester Intermediate of Family I CoA Transferases

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