Characterization of NADP+-specific l-rhamnose dehydrogenase from the thermoacidophilic Archaeon Thermoplasma acidophilum

Kim, Suk Min; Paek, Kwang Hyun; Lee, Sun Bok

doi:10.1007/s00792-012-0444-1

Cited by 17 publications

(19 citation statements)

References 45 publications

(32 reference statements)

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“…While L-fucose utilisation is well understood in bacteria, very little is known about possible degradation routes in archaea. Previous studies claimed that the thermoacidophilic archaeon Thermoplasma acidophilum is able to grow on deoxysugars like, L-fucose or Lrhamnose, however, the underlying pathway of L-fucose degradation is still unknown (Kim et al, 2012). In the genome of S. solfataricus, only an a-L-fucosidase presumably regulated by translational frameshifting was identified so far (Cobucci-Ponzano et al, 2003, 2006.…”

Section: Introductionmentioning

confidence: 99%

A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L‐fucose versus D‐glucose

Wolf

Stark

Fafenrot

et al. 2016

Molecular Microbiology

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SummaryArchaea are characterised by a complex metabolism with many unique enzymes that differ from their bacterial and eukaryotic counterparts. The thermoacidophilic archaeon Sulfolobus solfataricus is known for its metabolic versatility and is able to utilize a great variety of different carbon sources. However, the underlying degradation pathways and their regulation are often unknown. In this work, the growth on different carbon sources was analysed, using an integrated systems biology approach. The comparison of growth on L-fucose and D-glucose allows first insights into the genome-wide changes in response to the two carbon sources and revealed a new pathway for L-fucose degradation in S. solfataricus. During growth on L-fucose major changes in the central carbon metabolic network, as well as an increased activity of the glyoxylate bypass and the 3-hydroxypropionate/4-hydroxybutyrate cycle were observed. Within the newly discovered pathway for L-fucose degradation the following key reactions were identified: (i) L-fucose oxidation to L-fuconate via a dehydrogenase, (ii) dehydration to 2-keto-3-deoxy-Lfuconate via dehydratase, (iii) 2-keto-3-deoxy-Lfuconate cleavage to pyruvate and L-lactaldehyde via aldolase and (iv) L-lactaldehyde conversion to Llactate via aldehyde dehydrogenase. This pathway as well as L-fucose transport shows interesting overlaps to the D-arabinose pathway, representing another example for pathway promiscuity in Sulfolobus species.

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Section: Introductionmentioning

confidence: 99%

A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L‐fucose versus D‐glucose

Wolf

Stark

Fafenrot

et al. 2016

Molecular Microbiology

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“…No activity was found with l ‐fucose, d ‐arabinose, d ‐xylose, d ‐ribose, d ‐glucose, d ‐fructose and d ‐galactose. A conserved domain analysis classifies the RDH of V. distributa and S. solfataricus (see below) as members of the MDR superfamily and thus is different to RDHs from H. volcanii , from T. acidophilum (Kim et al , ) and from the bacterium Sphingomonas sp. (Watanabe and Makino, ), which belong to SDR superfamily (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Proposed analogous gene functions are indicated in the same color: l-rhamnose mutarotase (RhM, olive), l-rhamnose dehydrogenase (RDH, orange), l-rhamnonolactonase (RNL, purple), l-rhamnonate dehydratase (RAD, green), 2-keto-3-deoxy-l-rhamnonate dehydrogenase (KDRDH, light blue), 2,4-diketo-3-deoxy-l-rhamnonate hydrolase (DKDRH, red), lutBC genes (yellow), transcriptional regulator RhcR (brown) and ABC transporter (blue). Genes encoding enzymes of the diketo-hydrolase pathway from T. acidophilum were reported by Kim et al, (2012). Genes without prediction ( were overexpressed in E. coli and recombinant enzymes were purified and characterized.…”

Section: The Diketo-hydrolase Pathway Is Widespread In Archaeamentioning

confidence: 99%

“…So far, degradation of l ‐rhamnose in the archaeal domain has not been studied in detail. The euryarchaeon Thermoplasma acidophilum has been reported to contain genes of the diketo‐hydrolase pathway and one enzyme, RDH, has been characterized (Kim et al , ). Recently, degradation of the deoxy sugar l ‐fucose has been studied in some detail in the crenarchaeon Sulfolobus solfataricus .…”

Section: Introductionmentioning

confidence: 99%

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l‐Rhamnose catabolism in archaea

Reinhardt

Johnsen

Schönheit

2019

Molecular Microbiology

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Summary The halophilic archaeon Haloferax volcanii utilizes l‐rhamnose as a sole carbon and energy source. It is shown that l‐rhamnose is taken up by an ABC transporter and is oxidatively degraded to pyruvate and l‐lactate via the diketo‐hydrolase pathway. The genes involved in l‐rhamnose uptake and degradation form a l‐rhamnose catabolism (rhc) gene cluster. The rhc cluster also contains a gene, rhcR, that encodes the transcriptional regulator RhcR which was characterized as an activator of all rhc genes. 2‐keto‐3‐deoxy‐l‐rhamnonate, a metabolic intermediate of l‐rhamnose degradation, was identified as inducer molecule of RhcR. The essential function of rhc genes for uptake and degradation of l‐rhamnose was proven by the respective knockout mutants. Enzymes of the diketo‐hydrolase pathway, including l‐rhamnose dehydrogenase, l‐rhamnonolactonase, l‐rhamnonate dehydratase, 2‐keto‐3‐deoxy‐l‐rhamnonate dehydrogenase and 2,4‐diketo‐3‐deoxy‐l‐rhamnonate hydrolase, were characterized. Further, genes of the diketo‐hydrolase pathway were also identified in the hyperthermophilic crenarchaeota Vulcanisaeta distributa and Sulfolobus solfataricus and selected enzymes were characterized, indicating the presence of the diketo‐hydrolase pathway in these archaea. Together, this is the first comprehensive description of l‐rhamnose catabolism in the domain of archaea.

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“…The difference in the relatively high optimal temperature of the enzyme to the comparably low thermostability indicated that the enzyme is more prone to inactivation in the absence of substrate. Other enzymes obtained from this organism have been shown to display optimal temperatures in the range of 55 °C to 70 °C [15,[28][29][30]. Following the identification of the crucial metal cofactors required for TaManD activity and determination of its optimal reaction temperature, we acquired enzyme kinetic data for the purified enzyme.…”

Section: Enzyme Characterisationmentioning

confidence: 99%

Characterisation of the First Archaeal Mannonate Dehydratase from Thermoplasma acidophilum and Its Potential Role in the Catabolism of D-Mannose

2019

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Mannonate dehydratases catalyse the dehydration reaction from mannonate to 2-keto-3-deoxygluconate as part of the hexuronic acid metabolism in bacteria. Bacterial mannonate dehydratases present in this gene cluster usually belong to the xylose isomerase-like superfamily, which have been the focus of structural, biochemical and physiological studies. Mannonate dehydratases from archaea have not been studied in detail. Here, we identified and characterised the first archaeal mannonate dehydratase (TaManD) from the thermoacidophilic archaeon Thermoplasma acidophilum. The recombinant TaManD enzyme was optimally active at 65 °C and showed high specificity towards D-mannonate and its lactone, D-mannono-1,4-lactone. The gene encoding for TaManD is located adjacent to a previously studied mannose-specific aldohexose dehydrogenase (AldT) in the genome of T. acidophilum. Using nuclear magnetic resonance (NMR) spectroscopy, we showed that the mannose-specific AldT produces the substrates for TaManD, demonstrating the possibility for an oxidative metabolism of mannose in T. acidophilum. Among previously studied mannonate dehydratases, TaManD showed closest homology to enzymes belonging to the xylose isomerase-like superfamily. Genetic analysis revealed that closely related mannonate dehydratases among archaea are not located in a hexuronate gene cluster like in bacteria, but next to putative aldohexose dehydrogenases, implying a different physiological role of mannonate dehydratases in those archaeal species.

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Characterization of NADP+-specific l-rhamnose dehydrogenase from the thermoacidophilic Archaeon Thermoplasma acidophilum

Cited by 17 publications

References 45 publications

A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L‐fucose versus D‐glucose

A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L‐fucose versus D‐glucose

l‐Rhamnose catabolism in archaea

Characterisation of the First Archaeal Mannonate Dehydratase from Thermoplasma acidophilum and Its Potential Role in the Catabolism of D-Mannose

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