Characterization of the genes encoding beta-ketoadipate: succinyl-coenzyme A transferase in Pseudomonas putida

Parales, Rebecca E.; Harwood, Caroline S.

doi:10.1128/jb.174.14.4657-4666.1992

Cited by 67 publications

(80 citation statements)

References 56 publications

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“…4B) were constructed to localize the pcaI and pcaJ genes. The P. putida and Acinetobacter calcoaceticus pcaIJ gene sequences have been determined and are about 1.4 kb in size (23,31). Sequencing of the EcoRI end of the insertion in pARO61 and translation of the nucleotide sequence revealed an open reading frame with homology to PcaI of P. putida (31) (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Supraoperonic clustering of pca genes for catabolism of the phenolic compound protocatechuate in Agrobacterium tumefaciens

Parke

1995

J Bacteriol

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The protocatechuate branch of the ␤-ketoadipate pathway comprises the last six enzymatic steps in the catabolism of diverse phenolic compounds to citric acid cycle intermediates. In this paper, the regulation and tight supraoperonic clustering of the protocatechuate (pca) genes from Agrobacterium tumefaciens A348 are elucidated. A previous study found that the pcaD gene is controlled by an adjacent regulatory gene, pcaQ, which encodes an activator. The activator responded to ␤-carboxy-cis,cis-muconate and was shown to control the synthesis of at least three genes (pcaD and pcaHG). In this work, eight genes required for the catabolism of protocatechuate were localized within a 13.5-kb SalI region of DNA. Isolation and characterization of transposon Tn5 mutant strains facilitated the localization of pca genes. Five structural genes were found to respond to the tricarboxylic acid and to be contiguous in an operon transcribed in the order pcaDCHGB. These genes encode enzymes ␤-ketoadipate enol-lactone hydrolase, ␥-carboxymuconolactone decarboxylase, protocatechuate 3,4-dioxygenase (pcaHG), and ␤-carboxy-cis,cis-muconate lactonizing enzyme, respectively. Approximately 4 kb from the pcaD gene are the pcaIJ genes, which encode ␤-ketoadipate succinyl-coenzyme A transferase for the next-to-last step of the pathway. The pcaIJ genes are transcribed divergently from the pcaDCHGB operon and are expressed in response to ␤-ketoadipate. The pattern of induction of pca genes by ␤-carboxy-cis,cis-muconate and ␤-ketoadipate in A. tumefaciens is similar to that observed in Rhizobium leguminosarum bv. trifolii and is distinct from induction patterns for the genes from other microbial groups.Diverse aromatic compounds, arising in soil and water from origins in living plants, plant litter, or industrial processes, are degraded to common diphenolic intermediates, catechol and protocatechuate. Specific dioxygenases cleave these two phenolics, initiating the two branches of the ␤-ketoadipate pathway which funnel aromatic compounds into the tricarboxylic acid cycle (48). The ability of members of the bacterial family Rhizobiaceae to catabolize numerous aromatic compounds via the catechol or protocatechuate branch of the ␤-ketoadipate pathway has been documented (6,7,26,37,38). Remarkably, the protocatechuate branch of the pathway (Fig. 1) appears to be universally distributed among members of this highly diverse bacterial group (21, 37). Previous research has demonstrated the inducibility of enzymes of the ␤-ketoadipate pathway in fast-growing representatives of the family Rhizobiaceae and the constitutivity of most enzymes in slowly growing Bradyrhizobium species (38).As a multistep ensemble, peripheral to the heart of bacterial metabolism, the ␤-ketoadipate pathway provides a model system for studying the mechanisms of regulation and evolution of catabolic pathways. Its acquisition and maintenance in the face of different selection pressures might be expected to be mediated by diversification of gene organization and regulation. The reg...

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Section: Resultsmentioning

confidence: 99%

“…(B) Similar presentation of the pcaI and pcaJ sequences (determined from the noncoding strands of the EcoRI site of pARO61 and the NcoI site of pARO60, respectively). Published sequences were the sources of data for Acinetobacter calcoaceticus (15,23) and P. putida (14,31).…”

Section: Resultsmentioning

confidence: 99%

Supraoperonic clustering of pca genes for catabolism of the phenolic compound protocatechuate in Agrobacterium tumefaciens

Parke

1995

J Bacteriol

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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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“…In many cases, a single ancestral enzyme was the evolutionary source of a range of enzymes catalyzing similar reactions with different substrates. Thus, different evolutionary families are represented by each of the following genes (and encoded enzymes) associated with quinate catabolism in A. calcoaceticus: quiA (quinate/shikimate dehydrogenase) (12), pcaHG (protocatechuate 3,4-dioxygenase) (17,24,55), pcaD (␤-ketoadipate enol-lactone hydrolase) (25,40), pcaIJ (␤-ketoadipate-succinyl coenzyme A transferase) (31,44), and pcaF (␤-ketoadipyl coenzyme A thiolase) (26,31,45). Genes encoding the fumarase II family of dehydratases include pcaB, the structural gene for ␤-carboxymuconate cycloisomerase in bacteria (56).…”

Section: Discussionmentioning

confidence: 99%

Unusual ancestry of dehydratases associated with quinate catabolism in Acinetobacter calcoaceticus

Elsemore

Ornston

1995

J Bacteriol

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Catabolism of quinate to protocatechuate requires the consecutive action of quinate dehydrogenase (QuiA), dehydroquinate dehydratase (QuiB), and dehydroshikimate dehydratase (QuiC). Genes for catabolism of protocatechuate are encoded by the pca operon in the Acinetobacter calcoaceticus chromosome. Observations reported here demonstrate that A. calcoaceticus qui genes are clustered in the order quiBCXA directly downstream from the pca operon. Sequence comparisons indicate that quiX encodes a porin, but the specific function of this protein has not been clearly established. Properties of mutants created by insertion of ⍀ elements show that quiBC is expressed as part of a single transcript, but there is also an independent transcriptional initiation site directly upstream of quiA. The deduced amino acid sequence of QuiC does not resemble any other known sequence. A. calcoaceticus QuiB is most directly related to a family of enzymes with identical catalytic activity and biosynthetic AroD function in coliform bacteria. Evolution of A. calcoaceticus quiB appears to have been accompanied by fusion of a leader sequence for transport of the encoded protein into the inner membrane, and the location of reactions catalyzed by the mature enzyme may account for the failure of A. calcoaceticus aroD to achieve effective complementation of null mutations in quiB. Analysis of a genetic site where a DNA segment encoding a leader sequence was transposed adds to evidence suggesting horizontal transfer of nucleotide sequences within genes during evolution.Dehydroquinate dehydratase (QuiB) and dehydroshikimate dehydratase (QuiC) catalyze consecutive reactions allowing growth of microorganisms with quinate by its conversion to protocatechuate ( Fig. 1) and subsequent metabolism by the ␤-ketoadipate pathway (41, 52). The enzymatic activity of QuiB is identical to that of AroD, an enzyme that catalyzes biosynthetic formation of dehydroshikimate (Fig. 1). Enzymes with similar catalytic activities often can be traced to a common ancestor (32), and the similarity of dehydratases associated with dehydroshikimate metabolism raised the possibility that a single ancestral protein was the evolutionary precursor of two or more of these enzymes.In contrast to this prediction, biosynthetic dehydroquinate dehydratases differ substantially from catabolic enzymes with this activity (18,30). With the exception of the dehydroquinate dehydratases of gram-positive bacteria (13, 15), enzymes with the biosynthetic function indicated as AroD in Fig. 1 are classified as type I and are thermolabile, a property that distinguishes them from the isofunctional type II enzymes which are heat stable and mediate the activity indicated as QuiB in Fig. 1 Some gram-negative bacteria elaborate a single dehydroquinate dehydratase associated solely with the biosynthetic function indicated as AroD in Fig. 1. Genes for this enzyme from Enterococcus faecalis (3), Salmonella typhi (51), and Escherichia coli (10) have been sequenced and shown to encode type I enzymes. These fi...

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Characterization of the genes encoding beta-ketoadipate: succinyl-coenzyme A transferase in Pseudomonas putida

Cited by 67 publications

References 56 publications

Supraoperonic clustering of pca genes for catabolism of the phenolic compound protocatechuate in Agrobacterium tumefaciens

Supraoperonic clustering of pca genes for catabolism of the phenolic compound protocatechuate in Agrobacterium tumefaciens

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

Unusual ancestry of dehydratases associated with quinate catabolism in Acinetobacter calcoaceticus

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