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

BMC Genomics

Research Article

Miaomiao Zhou¹  Roland J Siezen²  Sacha AFT van Hijum²  Marnix H Medema³  Marc Strous⁴  Jolein Gloerich⁵  Hans JCT Wessels⁵ 

[1] Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500, Nijmegen, HB, the Netherlands;Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500, Nijmegen, HB, the Netherlands;NIZO food research, PO Box 20, 6710, Ede, BA, the Netherlands;TI Food and Nutrition, Kluyver Centre for Genomics of Industrial Fermentation, Wageningen, the Netherlands;Department of Microbiology, Radboud University Nijmegen, Toernooiveld 1, 6525, Nijmegen, ED, the Netherlands;Department of Microbial Physiology and Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751, Haren, NN, the Netherlands;Department of Microbiology, Radboud University Nijmegen, Toernooiveld 1, 6525, Nijmegen, ED, the Netherlands;MPI for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany;CeBiTec, University of Bielefeld, Universitätsstraße 27, D-33615, Bielefeld, Germany;Nijmegen Proteomics Facility, Laboratory of Pediatrics & Neurology, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands;

关键词: Signal Peptide;    Random Forest;    Cell Envelope;    Anammox Bacterium;    Random Forest Model;   

DOI  :  10.1186/1471-2164-11-299

 received in 2010-01-29, accepted in 2010-05-12,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundAnaerobic 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.ResultsTwo 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.ConclusionsA 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.

【 授权许可】

Unknown   
© Medema et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.