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J. Biol. Chem., Vol. 281, Issue 37, 27378-27388, September 15, 2006

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Identification of the Missing Links in Prokaryotic Pentose Oxidation Pathways

EVIDENCE FOR ENZYME RECRUITMENT^*

Stan J. J. Brouns¹, Jasper Walther, Ambrosius P. L. Snijders², Harmen J. G. van de Werken, Hanneke L. D. M. Willemen, Petra Worm, Marjon G. J. de Vos, Anders Andersson^¶, Magnus Lundgren^||, Hortense F. M. Mazon^**, Robert H. H. van den Heuvel^**, Peter Nilsson^¶, Laurent Salmon, Willem M. de Vos, Phillip C. Wright³, Rolf Bernander^||, and John van der Oost

From the Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, the Netherlands, the Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom, the ^¶Department of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden, the ^||Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden, the ^**Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, the Netherlands, and the Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS-UMR 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Université de Paris-Sud, Bâtiment 420, F-91405 Orsay, France

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.

Received for publication, June 9, 2006 , and in revised form, July 17, 2006.

^* This work was supported by a grant from the European Union in the framework of the SCREEN project contract QLK3-CT-2000-00649 and a dedicated functional genomics grant from the Swedish Research Council (to R. B.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Tables S1-S2, Figs. S1-S3, and additional references.

² Supported by the University of Sheffield and the United Kingdom's Engineering and Physical Sciences Research Council.

³ Supported by Engineering and Physical Sciences Research Council, Advanced Research Fellowship GR/A11311/01 and Grant GR/S84347/01.

¹ To whom correspondence should be addressed. Tel.: 31-317-483110; Fax: 31-317-483829; E-mail: stan.brouns{at}wur.nl.

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