Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment.
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.
Brouns
Stan J J
SJ
Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, the Netherlands. stan.brouns@wur.nl
Walther
Jasper
J
Snijders
Ambrosius P L
AP
van de Werken
Harmen J G
HJ
Willemen
Hanneke L D M
HL
Worm
Petra
P
de Vos
Marjon G J
MG
Andersson
Anders
A
Lundgren
Magnus
M
Mazon
Hortense F M
HF
van den Heuvel
Robert H H
RH
Nilsson
Peter
P
Salmon
Laurent
L
de Vos
Willem M
WM
Wright
Phillip C
PC
Bernander
Rolf
R
van der Oost
John
J
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
D007656:Ketoglutaric Acids; D010429:Pentoses; D011994:Recombinant Proteins; D019289:Pyruvic Acid; D001089:Arabinose; D005947:Glucose