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A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis

Marnix H Medema18, Miaomiao Zhou2*, Sacha AFT van Hijum235, Jolein Gloerich4, Hans JCT Wessels4, Roland J Siezen235 and Marc Strous167

Author Affiliations

1 Department of Microbiology, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, the Netherlands

2 Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands

3 NIZO food research, PO Box 20, 6710 BA Ede, the Netherlands

4 Nijmegen Proteomics Facility, Laboratory of Pediatrics & Neurology, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands

5 TI Food and Nutrition, Kluyver Centre for Genomics of Industrial Fermentation, Wageningen, the Netherlands

6 MPI for Marine Microbiology, Celsiusstr. 1 D-28359, Bremen, Germany

7 CeBiTec, University of Bielefeld, Universitätsstraße 27, D-33615, Bielefeld, Germany

8 Current Address: Department of Microbial Physiology and Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, the Netherlands

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BMC Genomics 2010, 11:299  doi:10.1186/1471-2164-11-299

Published: 12 May 2010



Anaerobic ammonium-oxidizing (anammox) bacteria perform a key step in global nitrogen cycling. These bacteria make use of an organelle to oxidize ammonia anaerobically to nitrogen (N2) and so contribute ~50% of the nitrogen in the atmosphere. It is currently unknown which proteins constitute the organellar proteome and how anammox bacteria are able to specifically target organellar and cell-envelope proteins to their correct final destinations. Experimental approaches are complicated by the absence of pure cultures and genetic accessibility. However, the genome of the anammox bacterium Candidatus "Kuenenia stuttgartiensis" has recently been sequenced. Here, we make use of these genome data to predict the organellar sub-proteome and address the molecular basis of protein sorting in anammox bacteria.


Two training sets representing organellar (30 proteins) and cell envelope (59 proteins) proteins were constructed based on previous experimental evidence and comparative genomics. Random forest (RF) classifiers trained on these two sets could differentiate between organellar and cell envelope proteins with ~89% accuracy using 400 features consisting of frequencies of two adjacent amino acid combinations. A physicochemically distinct organellar sub-proteome containing 562 proteins was predicted with the best RF classifier. This set included almost all catabolic and respiratory factors encoded in the genome. Apparently, the cytoplasmic membrane performs no catabolic functions. We predict that the Tat-translocation system is located exclusively in the organellar membrane, whereas the Sec-translocation system is located on both the organellar and cytoplasmic membranes. Canonical signal peptides were predicted and validated experimentally, but a specific (N- or C-terminal) signal that could be used for protein targeting to the organelle remained elusive.


A physicochemically distinct organellar sub-proteome was predicted from the genome of the anammox bacterium K. stuttgartiensis. This result provides strong in silico support for the existing experimental evidence for the existence of an organelle in this bacterium, and is an important step forward in unravelling a geochemically relevant case of cytoplasmic differentiation in bacteria. The predicted dual location of the Sec-translocation system and the apparent absence of a specific N- or C-terminal signal in the organellar proteins suggests that additional chaperones may be necessary that act on an as-yet unknown property of the targeted proteins.