title: Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment.
abstract: The pentose metabolism of Archaea is largely unknown. Here, we have employed an integrated genomics approach including DNA microarray and proteomics analyses to elucidate the catabolic pathway for D-arabinose in Sulfolobus solfataricus. During growth on this sugar, a small set of genes appeared to be differentially expressed compared with growth on D-glucose. These genes were heterologously overexpressed in Escherichia coli, and the recombinant proteins were purified and biochemically studied. This showed that D-arabinose is oxidized to 2-oxoglutarate by the consecutive action of a number of previously uncharacterized enzymes, including a D-arabinose dehydrogenase, a D-arabinonate dehydratase, a novel 2-keto-3-deoxy-D-arabinonate dehydratase, and a 2,5-dioxopentanoate dehydrogenase. Promoter analysis of these genes revealed a palindromic sequence upstream of the TATA box, which is likely to be involved in their concerted transcriptional control. Integration of the obtained biochemical data with genomic context analysis strongly suggests the occurrence of pentose oxidation pathways in both Archaea and Bacteria, and predicts the involvement of additional enzyme components. Moreover, it revealed striking genetic similarities between the catabolic pathways for pentoses, hexaric acids, and hydroxyproline degradation, which support the theory of metabolic pathway genesis by enzyme recruitment.
authors.affiliation: Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, the Netherlands. stan.brouns@wur.nl
authors.forename: Stan J J
authors.initials: SJ
authors.lastname: Brouns
authors.forename: Jasper
authors.initials: J
authors.lastname: Walther
authors.forename: Ambrosius P L
authors.initials: AP
authors.lastname: Snijders
authors.forename: Harmen J G
authors.initials: HJ
authors.lastname: van de Werken
authors.forename: Hanneke L D M
authors.initials: HL
authors.lastname: Willemen
authors.forename: Petra
authors.initials: P
authors.lastname: Worm
authors.forename: Marjon G J
authors.initials: MG
authors.lastname: de Vos
authors.forename: Anders
authors.initials: A
authors.lastname: Andersson
authors.forename: Magnus
authors.initials: M
authors.lastname: Lundgren
authors.forename: Hortense F M
authors.initials: HF
authors.lastname: Mazon
authors.forename: Robert H H
authors.initials: RH
authors.lastname: van den Heuvel
authors.forename: Peter
authors.initials: P
authors.lastname: Nilsson
authors.forename: Laurent
authors.initials: L
authors.lastname: Salmon
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
authors.forename: Phillip C
authors.initials: PC
authors.lastname: Wright
authors.forename: Rolf
authors.initials: R
authors.lastname: Bernander
authors.forename: John
authors.initials: J
authors.lastname: van der Oost
mesh_terms: D001089:Arabinose / Q000737:chemistry; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli / Q000378:metabolism; D005947:Glucose / Q000378:metabolism; D007656:Ketoglutaric Acids / Q000737:chemistry; D008954:Models, Biological; D008956:Models, Chemical; D008969:Molecular Sequence Data; D010429:Pentoses / Q000737:chemistry; D040901:Proteomics / Q000379:methods; D019289:Pyruvic Acid / Q000737:chemistry; D011994:Recombinant Proteins / Q000737:chemistry; D048229:Sulfolobus solfataricus / Q000201:enzymology* / Q000378:metabolism
chemical_list: D007656:Ketoglutaric Acids; D010429:Pentoses; D011994:Recombinant Proteins; D019289:Pyruvic Acid; D001089:Arabinose; D005947:Glucose