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

Abstract

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.

l‐Rhamnose catabolism in archaea

“…). It is interesting to note, that RAD of S. solfataricus is distinct from d ‐arabinonate/ l ‐fuconate dehydratase in this organism (Brouns et al , ; Wolf et al , ) and thus does not constitute a promiscuous enzyme as RDH (see above).…”

“…The recombinant enzyme catalyzed the NADP + ‐dependent oxidation of l ‐rhamnose with specific activity of 21 U mg –1 and a K m value of 0.2 mM for l ‐rhamnose. It is interesting to note that SSO1300 has previously been reported to encode for bifunctional l ‐fucose/ d ‐arabinose dehydrogenase being involved in l ‐fucose and d ‐arabinose degradation pathways (Brouns et al , ; Wolf et al , ). In accordance with the presence of the diketo‐hydrolase genes in S. solfataricus , the organism was found to grow on l ‐rhamnose with a doubling time of 18.5 h up to an optical density at 600 nm of 1.8 (Supplementary Fig.…”

“…Recently, degradation of the deoxy sugar l ‐fucose has been studied in some detail in the crenarchaeon Sulfolobus solfataricus . This organism degrades l ‐fucose via an oxidative pathway that is promiscuous for l ‐fucose and d ‐arabinose (Brouns et al , ; Wolf et al , ).…”

Oxidative Stickland reactions in an obligate aerobic organism – amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus

“…Intracellular metabolites and supernatants for analysis of amino acid depletion were extracted, analysed and resulting data were processed and statistically analysed as described earlier .…”

“…For the simulation of growth on d ‐glucose or caseinhydrolysate as sole carbon sources, the uptake of carbonaceous compounds was restricted to zero mmol·g CDW ·h −1 with the exception of CO 2 , d ‐glucose or amino acids that were experimentally observed to be taken up. The uptake rate of d ‐glucose was restricted to the previously observed value of 1.13 mmol·g CDW ·h −1 . The uptake rates of individual amino acids were restricted to the maximum of the experimentally observed uptake rates.…”