Abstract
BackgroundThe 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.ResultsGene 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.ConclusionWe 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.ReviewersThis article was reviewed by Dr Michael Galperin (nominated by Prof E. Koonin), Dr Andrei Osterman and Dr Jeremy Selengut.
Highlights
The fatty acids of anaerobic ammonium oxidizing bacteria contain linearly concatenated cyclobutane moieties, so far unique to biology
We studied in detail the active site residues essential for the functioning of β-ketoacyl-acyl carrier protein (ACP) synthases, since deviation in active site residues could point to the use of alternative substrates by different paralogues
The lower section of the tree displays the putative fabB (Kuste2805) and fabF paralogues (Kuste3348, Kuste3606) all of which are classified by National Centre for Biotechnology Information (NCBI) CDD [38] as having similarities to beta-ketoacyl protein synthase, but do not have the same essential active sites found in the E. coli fabB/F crystal structure
Summary
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. Anammox catabolism uses 1 mole of ammonia and 1.32 moles of nitrite to produce dinitrogen gas in the absence of oxygen [8]. Exploitation of this energy source under anaerobic conditions is thought to have resulted in the evolution of unique cellular architecture [9,10]. Ladderane lipids consist of units containing either 3 or 5 linearly fused cyclobutane moieties that can be synthesised into a variety of lipid structures; fatty acids (Figure 1), alcohols, mono-ethers, di-ethers and mixed ether-ester phospholipids [12,13]
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