l‐Rhamnose catabolism in archaea

Abstract

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.

Acetate Metabolism in Archaea: Characterization of an Acetate Transporter and of Enzymes Involved in Acetate Activation and Gluconeogenesis in Haloferax volcanii

“…Deletion mutants were generated by using the pop-in/pop-out strategy (Allers and Mevarech, 2005;Reinhardt et al, 2019). Flanking regions of the target genes were amplified and fused by PCR.…”

d -Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species

“…DNA fragments were each ligated into the plasmid pTA963, and H. volcanii H1209 (24) was transformed with the respective plasmids. The expression of target genes in H. volcanii H1209 was induced by the addition of 2 mM L-tryptophan, followed by further growth for 16 h at 42°C (25). Enzyme assays.…”

Biomass-degrading glycoside hydrolases of archaeal origin

“…One additional challenge of understanding and making use of archaeal GH machineries lies in the whole metabolism of archaea, which is considered to be a complex "mixture" of bacterial-and eukaryotic-like pathways resulting in modified pathways [102][103][104]. Studies focusing on transcriptomics of cultured archaea or reassembling of uncultured archaeal genomes will provide highly useful insights into new archaeal metabolisms, and novel catabolism reactions could be investigated for degradation of complex substrates [105]. [46,47], Pyrococcus horikoshii [52], Saccharolobus shibatae [65], Saccharolobus solfataricus [41], and three unknown archaea [42,81,83]; amylases of Pyrococcus furiosus [43,44,48,49], Sulfolobus acidocaldarius [67], Pyrococcus woesei [54], and Staphylothermus marinus [59]; sylanase of Saccharolobus solfataricus [69]; glucosidases of Pyrococcus furiosus [50,51], Pyrobaculum aerophilum [78] and two unknown archaea [22,40]; galactosidases of Saccharolobus solfataricus [70,71] and Caldivirga maquilingensis [76]; xylosidase of Saccharolobus solfataricus [73]; mannosidase of Saccharolobus solfataricus [74]…”

“…One additional challenge of understanding and making use of archaeal GH machineries lies in the whole metabolism of archaea, which is considered to be a complex “mixture” of bacterial- and eukaryotic-like pathways resulting in modified pathways [ 102 – 104 ]. Studies focusing on transcriptomics of cultured archaea or reassembling of uncultured archaeal genomes will provide highly useful insights into new archaeal metabolisms, and novel catabolism reactions could be investigated for degradation of complex substrates [ 105 ].…”