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Open Access Research

A comparative genomics study of genetic products potentially encoding ladderane lipid biosynthesis

Jayne E Rattray1, Marc Strous2*, Huub JM Op den Camp2, Stefan Schouten1, Mike SM Jetten2 and Jaap S Sinninghe Damsté1

Author Affiliations

1 NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands

2 Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands

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Biology Direct 2009, 4:8  doi:10.1186/1745-6150-4-8

Published: 16 February 2009

Abstract

Background

The fatty acids of anaerobic ammonium oxidizing (anammox) bacteria contain linearly concatenated cyclobutane moieties, so far unique to biology. These moieties are under high ring strain and are synthesised by a presently unknown biosynthetic pathway.

Results

Gene clusters encoding enzymes of fatty acid biosynthesis in the anammox bacterium Kuenenia stuttgartiensis and 137 other organisms were analysed and compared in silico to gain further insight into the pathway of (ladderane) fatty acid biosynthesis. In K. stuttgartiensis four large gene clusters encode fatty acid biosynthesis. Next to the regular enzyme complex needed for fatty acid biosynthesis (FASII), the presence of four putative S-adenosyl-methionine (SAM) radical enzymes, two enzymes similar to phytoene desaturases and many divergent paralogues of β-ketoacyl-ACP synthase (fabF) were unusual. Surprisingly, extensive synteny was observed with FASII gene clusters in the deltaproteobacterium Desulfotalea psychrophila. No ladderane lipids were detected in lipid extracts of this organism but we did find unusual polyunsaturated hydrocarbons (PUHC), not detected in K. stuttgartiensis.

Conclusion

We suggest that the unusual gene clusters of K. stuttgartiensis and D. psychrophila encode a novel pathway for anaerobic PUFA biosynthesis and that K. stuttgartiensis further processes PUFA into ladderane lipids, in similar fashion to the previously proposed route of ladderane lipid biosynthesis. However, the presence of divergent paralogues of fabF with radically different active site topologies may suggest an alternative pathway where ladderane moieties are synthesised externally and are recruited into the pathway of fatty acid biosynthesis.

Reviewers

This article was reviewed by Dr Michael Galperin (nominated by Prof E. Koonin), Dr Andrei Osterman and Dr Jeremy Selengut.