Discovery of the catalytic function of a putative 2‐oxoacid dehydrogenase multienzyme complex in the thermophilic archaeon <i>Thermoplasma acidophilum</i>

Heath, Caroline; Jeffries, Alex C.; Hough, David W.; Danson, Michael J.

doi:10.1016/j.febslet.2004.10.058

Cited by 20 publications

(22 citation statements)

References 24 publications

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“…The hypothesis that the heterotetrameric E1p proteins derived from E1b proteins, rather than the reverse direction, is in agreement with the assumption that early environments have been rich in amino acids and thus that amino acid-degrading enzymes such as BCOADHCs should be an earlier development in the evolution than the "aerobic" PDHCs. The notion that BCOADHCs have existed early in evolution is substantiated by the fact that BCOADHCs are present in archaea, which indicates that BCOADHC have developed before the divergence of bacteria and archaea (22). The finding that heterotetrameric PDHCs are abundant only in ␣-proteobacteria, low-GC-content grampositive bacteria, and cyanobacteria thus suggests that heterotetrameric PDHCs trace back to developments that probably occurred late during the diversification of bacteria.…”

Section: Discussionmentioning

confidence: 99%

E1 Enzyme of the Pyruvate Dehydrogenase Complex in Corynebacterium glutamicum : Molecular Analysis of the Gene and Phylogenetic Aspects

et al. 2005

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The E1p enzyme is an essential part of the pyruvate dehydrogenase complex (PDHC) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the E2p enzyme within the complex. We analyzed the Corynebacterium glutamicum aceE gene, encoding the E1p enzyme, and constructed and characterized an E1p-deficient mutant. Sequence analysis of the C. glutamicum aceE gene and adjacent regions revealed that aceE is not flanked by genes encoding other enzymes of the PDHC. Transcriptional analysis revealed that aceE from C. glutamicum is monocistronic and that its transcription is initiated 121 nucleotides upstream of the translational start site. Inactivation of the chromosomal aceE gene led to the inability to grow on glucose and to the absence of PDHC and E1p activities, indicating that only a single E1p enzyme is present in C. glutamicum and that the PDHC is essential for the growth of this organism on carbohydrate substrates. Surprisingly, the E1p enzyme of C. glutamicum showed up to 51% identity to homodimeric E1p proteins from gram-negative bacteria but no similarity to E1 ␣-or ␤-subunits of heterotetrameric E1p enzymes which are generally assumed to be typical for gram-positives. To investigate the distribution of E1p enzymes in bacteria, we compiled and analyzed the phylogeny of 46 homodimeric E1p proteins and of 58 ␣-subunits of heterotetrameric E1p proteins deposited in public databases. The results revealed that the distribution of homodimeric and heterotetrameric E1p subunits in bacteria is not in accordance with the rRNA-based phylogeny of bacteria and is more heterogeneous than previously assumed.The pyruvate dehydrogenase complex (PDHC) represents a member of a multienzyme complex family that also comprises the 2-oxoglutarate dehydrogenase complex (OGDHC) and the branched-chain 2-oxoacid dehydrogenase complex (BCOADHC). These enzymes catalyze the oxidative decarboxylation of pyruvate, 2-oxoglutarate, and the 2-oxo acids of the branched-chain amino acids L-leucine, L-valine, and L-isoleucine, respectively. In general, the multienzyme complexes are composed of multiple copies of three different enzymes, a thiamine pyrophosphate (TPP) containing 2-oxoacid decarboxylase (E1), a lipoic acid-containing dihydrolipoamide acyltransferase (E2), and the flavin-containing lipoamide dehydrogenase (LPD). The E1 enzyme catalyzes the irreversible, TPP-dependent oxidative decarboxylation of the 2-oxoacid, followed by the acylation of the lipoyl prosthetic group covalently attached to the E2 chain. The E2 component catalyzes the transfer of the acyl group from the lipoyl group to coenzyme A (CoA). The resulting dihydrolipoyl group is reoxidized by LPD, generating NADH and H ϩ from NAD ϩ (for a recent review, see reference 11). The E1 and E2 enzymes are specific for each of the three multienzyme complexes and therefore specified as E1p and E2p in the PDHC, E1o and E2o in the OGDHC, and E1b, and E2b in the BCOADHC. In contrast, the LPD component is common in the three multienzyme complexes in most organ...

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Section: Discussionmentioning

confidence: 99%

E1 Enzyme of the Pyruvate Dehydrogenase Complex in Corynebacterium glutamicum : Molecular Analysis of the Gene and Phylogenetic Aspects

et al. 2005

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“…(2) The enzymic activity is redundantly encoded by members of two very different protein families. It is possible that this happened in Thermoplasma, because the characterization of an E1 after heterologous production in E. coli revealed that it is specific for branched-chain 2-oxoacids (Heath et al, 2004). (3) The OADHCs could have adapted to new substrates and to new cellular functions.…”

Section: Discussionmentioning

confidence: 99%

“…Two alternative views of the evolution of archaeal OADHCs have been proposed: (1) some archaeal genomes acquired oadhc genes by lateral gene transfer from bacteria (Wanner & Soppa, 2002) and (2) the common ancestor of all archaea and bacteria possessed one (or several) oadhc genes, and they were retained in aerobic species, but got lost from anaerobic species (Heath et al, 2004). A first approach to clarify the evolution of archaeal OADHCs was to tabulate the oadhc genes present in the 28 completely sequenced archaeal genomes.…”

Section: Evolution Of Archaeal 2-oadhcsmentioning

confidence: 99%

Three 2-oxoacid dehydrogenase operons in Haloferax volcanii: expression, deletion mutants and evolution

Ooyen

Soppa

2007

Microbiology

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Two unrelated protein families catalyse the oxidative decarboxylation of 2-oxoacids, i.e. the 2-oxoacid dehydrogenase complexes (OADHCs) and the 2-oxoacid ferredoxin oxidoreductases (OAFORs). In halophilic archaea, OAFORs were found to be responsible for decarboxylation of pyruvate and 2-oxoglutarate. Nevertheless, two gene clusters encoding OADHCs were found previously in Haloferax volcanii, but their biological function remained obscure. Here a third oadhc gene cluster of H. volcanii is presented. To characterize the function, the genes encoding the E1 subunit were inactivated in all three gene clusters by in-frame deletions. Under aerobic conditions none of the three mutants showed any phenotypic difference from the wild-type in various media. However, growth yields of two mutants were considerably lower than that of wild-type under nitrate-respirative conditions in complex medium. Northern blot analyses revealed (1) that polycistronic transcripts are formed and all three gene clusters are bona fide operons and (2) that transcription of all three operons is induced under anaerobic conditions compared to aerobic conditions. Taken together, the three H. volcanii enzymes do not fulfil one of the 'usual' aerobic functions of typical OADHCs, but decarboxylate an as-yet-unidentified novel substrate under anaerobic conditions. A survey of all 28 fully sequenced archaeal genomes revealed that nearly all archaea contain several OAFORs (three to four on average), suggesting that this protein family was already present in their last common ancestor. In contrast, only nine archaea encode one or two OADHCs, indicating that this protein family entered archaea by lateral transfer of the cognate genes from bacteria. This view is underscored by a phylogenetic tree of 33 archaeal and bacterial OADHCs.

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“…5 in van Ooyen & Soppa, 2007). In this case it was shown that the recent archaeal genes still encode a bona fide BCDHC that uses all three 2-oxoacids as substrates (Heath et al, 2004(Heath et al, , 2007. In addition, it also decarboxylates pyruvate, albeit with reduced efficiency.…”

Section: Discussionmentioning

confidence: 99%

A 2-oxoacid dehydrogenase complex of Haloferax volcanii is essential for growth on isoleucine but not on other branched-chain amino acids

et al. 2010

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The halophilic archaeon Haloferax volcanii contains three operons encoding 2-oxoacid dehydrogenase complexes (OADHCs) OADHC1-OADHC3. However, the biological role of these OADHCs is not known as previous studies have demonstrated that they cannot use any of the known OADHC substrates. Even the construction of single mutants in all three oadhc operons, reported recently, could not identify a substrate. Therefore, all three possible double mutants and a triple mutant were generated, and single, double and triple mutants were compared to the wild-type. The four mutants devoid of a functional OADHC1 had a reduced growth yield during nitrate-respirative growth on tryptone. A metabolome analysis of the medium after growth of the triple mutant in comparison to the wild-type revealed that the mutant was unable to degrade isoleucine and leucine, in contrast to the wild-type. It was shown that oadhc1 mutants were unable to grow in synthetic medium on isoleucine, in contrast to the other mutants and the isogenic parent strain. However, all strains grew indistinguishably on valine and leucine. The transcript of the oadhc1 operon was highly induced during growth on isoleucine. However, attempts to detect enzymic activity were unsuccessful, while the branched-chain OADHC (BCDHC) of Pseudomonas putida could be measured easily. Therefore, the growth capability of the triple mutant and the wild-type on the two first degradation intermediates of isoleucine was tested and provided further evidence that OADHC is involved in isoleucine degradation. Taken together, the results indicate that OADHC1 is a specialized BCDHC that uses only one (or maximally two) of the three branched-chain 2-oxoacids, in contrast to BCDHCs from other species.

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Discovery of the catalytic function of a putative 2‐oxoacid dehydrogenase multienzyme complex in the thermophilic archaeon Thermoplasma acidophilum

Cited by 20 publications

References 24 publications

E1 Enzyme of the Pyruvate Dehydrogenase Complex in Corynebacterium glutamicum : Molecular Analysis of the Gene and Phylogenetic Aspects

E1 Enzyme of the Pyruvate Dehydrogenase Complex in Corynebacterium glutamicum : Molecular Analysis of the Gene and Phylogenetic Aspects

Three 2-oxoacid dehydrogenase operons in Haloferax volcanii: expression, deletion mutants and evolution

A 2-oxoacid dehydrogenase complex of Haloferax volcanii is essential for growth on isoleucine but not on other branched-chain amino acids

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