Identification and characterization of 2-keto-3-deoxy-l-rhamnonate dehydrogenase belonging to the MDR superfamily from the thermoacidophilic bacterium Sulfobacillus thermosulfidooxidans: implications to l-rhamnose metabolism in archaea

Abstract

We identified the non-phosphorylated L-rhamnose metabolic pathway (Rha_NMP) genes that are homologous to those in the thermoacidophilic archaeon Thermoplasma acidophilum in the genome of the thermoacidophilic bacterium Sulfobacillus thermosulfidooxidans. However, unlike previously known 2-keto-3-deoxy-L-rhamnonate (L-KDR) dehydrogenase (KDRDH) which belongs to the short chain dehydrogenase/reductase superfamily, the putative KDRDHs in S. thermosulfidooxidans (Sulth_3557) and T. acidophilum (Ta0749) belong to the medium chain dehydrogenase/reductase (MDR) superfamily. We demonstrated that Sulth_3559 and Sulth_3557 proteins from S. thermosulfidooxidans function as L-rhamnose dehydrogenase and KDRDH, respectively. Sulth_3557 protein is an NAD(+)-specific KDRDH with optimal temperature and pH of 50 °C and 9.5, respectively. The K m and V max values for L-KDR were 2.0 mM and 12.8 U/mg, respectively. Sulth_3557 also showed weak 2,3-butanediol dehydrogenase activity. Phylogenetic analysis suggests that Sulth_3557 and its homologs form a new subfamily in the MDR superfamily. The results shown in this study imply that thermoacidophilic archaea metabolize L-rhamnose to pyruvate and L-lactate by using the MDR-family KDRDH similarly to that of the thermoacidophilic bacterium S. thermosulfidooxidans.

In vivo functional analysis of L-rhamnose metabolic pathway in Aspergillus niger: a tool to identify the potential inducer of RhaR

“…LRA5 (KDRDH) was identified as an NAD+ specific enzyme belonging to the short-chain dehydrogenase/reductase (SDR) superfamily [ 11 ] and has been shown to convert L-KDR to 2, 4-diketo-3-deoxy-L-rhamnonate. Interestingly, another KDRDH belonging to the medium chain dehydrogenase reductase (MDR) superfamily has been biochemically characterized in Sulfobacillus thermosulfidooxidans and was found to catalyze the same metabolic reaction [ 10 ]. We analysed and compared the PFAM domains in the protein sequences of LRA5 of both species.…”

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

“…Via formation of 2-keto-3-deoxy-L-fuconate (KDF) this sugar acid is further oxidized to 2,4-diketo-3-deoxy-Lfuconate, which is finally cleaved to pyruvate and lactate. Recent studies revealed the existence of a closely related route for degradation of L-rhamnose in the thermoacidophilic bacterium Sulfobacillus thermosulfidooxidans (Bae et al, 2015).…”

l‐Rhamnose catabolism in archaea

“…In contrast, the predicted l ‐rhamnono‐lactonases from S. thermosulfidooxidans and T. acidophilum belong to the metallo‐hydrolase‐like MBL fold superfamily (Supplementary Fig. ) (Bae et al , ). It should be noted that the only characterized sugar lactonase in archaea is the H. volcanii pentonolactonase, which is a member of the SMP‐30/gluconolactonase/LRE‐like protein family (Sutter et al , ).…”

“…Beside in haloarchaea, we also identified lut genes in the diketo‐hydrolase gene cluster of Sphingomonas sp. and S. thermosulfidooxidans (Watanabe and Makino, ; Bae et al , ) suggesting that Lud‐containing proteins have a similar function in l ‐rhamnose degradation in these bacteria.…”

“…A second type of an oxidative non-phosphorylated pathway of l-rhamnose degradation -designated 'diketo-hydrolase pathway' -was identified in the bacteria Sphingomonas sp. and Sulfobacillus thermosulfidooxidans (Watanabe and Makino, 2009;Bae et al, 2015) (Fig. 1).…”