A Novel α-Ketoglutaric Semialdehyde Dehydrogenase

Watanabe, Shizuo; Kodaki, Tsutomu; Makino, Keisuke

doi:10.1074/jbc.m602585200

Cited by 45 publications

(39 citation statements)

References 49 publications

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“…solfataricus genome. The recently crystallized gluconolactonase from Xanthomonas campestris as well as the xylonolactonases/arabinolactonases from Azospirillum brasilense and Caulobacter crescentus belong to the same superfamily of SMP-30 proteins (284)(285)(286). In Hfx.…”

Section: Bacteria Eukaryamentioning

confidence: 99%

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Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

279

294

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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Section: Bacteria Eukaryamentioning

confidence: 99%

“…brasilense and to the characterized KGSADH enzyme from Sul. solfataricus (SSO3117) (283)(284)(285). In Cau.…”

Section: ␣-Ketoglutarate Semialdehyde Dehydrogenasementioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

279

294

View full text Add to dashboard Cite

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“…Previous work has shown that L-arabinose is degraded by a pathway that conceptually resembles the Entner-Doudoroff pathway (14). By analogy, L-arabinose is first oxidized to L-2-keto-3-deoxyarabonate (L-KDA) (15)(16)(17), which is then converted into ␣-ketoglurate in the case of fast-growing rhizobia (18)(19)(20) or to glycolaldehyde and pyruvate in the case of slow-growing species like B. japonicum (14). While pyruvate most likely is oxidized in the TCA cycle, the fate of glycolaldehyde has not been resolved yet.…”

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confidence: 99%

A Link between Arabinose Utilization and Oxalotrophy in Bradyrhizobium japonicum

Koch

Delmotte

Ahrens

et al. 2014

Appl Environ Microbiol

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cRhizobia have a versatile catabolism that allows them to compete successfully with other microorganisms for nutrients in the soil and in the rhizosphere of their respective host plants. In this study, Bradyrhizobium japonicum USDA 110 was found to be able to utilize oxalate as the sole carbon source. A proteome analysis of cells grown in minimal medium containing arabinose suggested that oxalate oxidation extends the arabinose degradation branch via glycolaldehyde. A mutant of the key pathway genes oxc (for oxalyl-coenzyme A decarboxylase) and frc (for formyl-coenzyme A transferase) was constructed and shown to be (i) impaired in growth on arabinose and (ii) unable to grow on oxalate. Oxalate was detected in roots and, at elevated levels, in root nodules of four different B. japonicum host plants. Mixed-inoculation experiments with wild-type and oxc-frc mutant cells revealed that oxalotrophy might be a beneficial trait of B. japonicum at some stage during legume root nodule colonization.

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“…Although the genome sequence of A. brasilense NBRC 102289 is currently unavailable, the nucleotide sequences of several genes from this bacterium show very high similarities (ϳ98%) to those of Burkholderia lata (17,20,(29)(30)(31). Therefore, a homology search using the protein BLAST program was performed against the genome sequence of B. lata using the hypI and hypJ genes as the probe protein sequences.…”

Section: Resultsmentioning

confidence: 99%

“…We previously revealed that its type strain NBRC 102289 (ATCC 29145) possesses alternative pathways of L-arabinose (29)(30)(31) Plant (cell wall) Table 1. Homologous genes are indicated in the same color and correspond to those shown in panels A to C. Gray and TR genes are putative L-Hyp transporters and transcriptional regulators, respectively.…”

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confidence: 99%

Characterization of a Novel cis -3-Hydroxy- l -Proline Dehydratase and a trans -3-Hydroxy- l -Proline Dehydratase from Bacteria

et al. 2017

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Hydroxyprolines, such as trans-4-hydroxy-L-proline (T4LHyp), trans-3-hydroxy-L-proline (T3LHyp), and cis-3-hydroxy-L-proline (C3LHyp), are present in some proteins including collagen, plant cell wall, and several peptide antibiotics. In bacteria, genes involved in the degradation of hydroxyproline are often clustered on the genome (L-Hyp gene cluster). We recently reported that an aconitase X (AcnX)-like hypI gene from an L-Hyp gene cluster functions as a monomeric C3LHyp dehydratase (AcnX Type I ). However, the physiological role of C3LHyp dehydratase remained unclear. We here demonstrate that Azospirillum brasilense NBRC 102289, an aerobic nitrogen-fixing bacterium, robustly grows using not only T4LHyp and T3LHyp but also C3LHyp as the sole carbon source. The small and large subunits of the hypI gene (hypI S and hypI L , respectively) from A. brasilense NBRC 102289 are located separately from the L-Hyp gene cluster and encode a C3LHyp dehydratase with a novel heterodimeric structure (AcnX Type IIa ). A strain disrupted in the hypI S gene did not grow on C3LHyp, suggesting its involvement in C3LHyp metabolism. Furthermore, C3LHyp induced transcription of not only the hypI genes but also the hypK gene encoding Δ 1 -pyrroline-2-carboxylate reductase, which is involved in T3LHyp, D-proline, and D-lysine metabolism. On the other hand, the L-Hyp gene cluster of some other bacteria contained not only the AcnX Type IIa gene but also two putative proline racemase-like genes (hypA1 and hypA2). Despite having the same active sites (a pair of Cys/Cys) as hydroxyproline 2-epimerase, which is involved in the metabolism of T4LHyp, the dominant reaction by HypA2 was clearly the dehydration of T3LHyp, a novel type of T3LHyp dehydratase that differed from the known enzyme (Cys/Thr). L-hydroxyproline) degradation in aerobic bacteria, its genetic and molecular information has only recently been elucidated. L-Hydroxyproline metabolic genes are often clustered on bacterial genomes. These loci frequently contain a hypothetical gene(s), whose novel enzyme functions are related to the metabolism of trans-3-hydroxyL-proline and/or cis-3-hydroxyL-proline, a relatively rare L-hydroxyproline in nature. Several L-hydroxyproline metabolic enzymes show no sequential similarities, suggesting their emergence by convergent evolution. Furthermore, transcriptional regulation by trans-4-hydroxy-L-proline, trans-3-hydroxy-L-proline, and/or cis-3-hydroxy-L-proline significantly differs between bacteria. The results of the present study show that several L-hydroxyprolines are available for bacteria as carbon and energy sources and may contribute to the discovery of potential metabolic pathways of another hydroxyproline(s). IMPORTANCE More than 50 years after the discovery of trans-4-hydroxy-L-proline (generally calledKEYWORDS aconitase X, proline racemase superfamily, gene cluster, hydroxyproline, convergent evolution

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A Novel α-Ketoglutaric Semialdehyde Dehydrogenase

Cited by 45 publications

References 49 publications

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

A Link between Arabinose Utilization and Oxalotrophy in Bradyrhizobium japonicum

Characterization of a Novel cis -3-Hydroxy- l -Proline Dehydratase and a trans -3-Hydroxy- l -Proline Dehydratase from Bacteria

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