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

Abstract

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.

Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function

“…Finally, an analysis of the 'Ca. Kuenenia stuttgartiensis' genome predicted a physico chemically distinct subproteome for the anammoxosome 88 . Although there are other examples of internal organelles that generate a PMF in bacteria, such as the thylakoids of cyanobacteria 89 (in which the direction and magnitude of the PMF are similar to those of the anammoxosome PMF but the energy source is different), the anammoxosome can in some ways be seen as a bacterial analogue of the eukaryotic mitochondrion, as both organelles generate non-photosynthetic PMFs.…”

Anaerobic Ammonium-Oxidizing Bacteria: Unique Microorganisms with Exceptional Properties

“…However, how anammox bacteria are capable of specifically transporting proteins from the riboplasm to either the paryphoplasm or anammoxosome remains unclear. No specific signal peptides could be detected for different compartments, and it has been hypothesized that protein sorting might be achieved through both the secretory (Sec) pathway (both the paryphoplasm and anammoxosome) and the twin-arginine translocation (Tat) system (anammoxosome) with additional chaperones to achieve specificity and facilitate separate translocation routes (62).…”

Nested Bacterial Boxes: Nuclear and Other Intracellular Compartments in Planctomycetes

“…Regarding protein secretion, in anammox planctomycetes, a bioinformatic study of the anammox planctomycete ' Candidatus Kuenenia stuttgartiensis' [Medema et al, 2010] has indicated that the Tat translocation system is exclusively located in the anammoxosome membrane, while the Sec system is found on both cytoplasmic and anammoxosome membranes, suggesting at least some specialization of secretion systems for internal compartment membrane. Significantly consistent with predicted metabolic functions of the anammoxosome membrane, but markedly different from most bacteria, the cytoplasmic membrane is predicted to be mainly a transport membrane rather than one harboring cytochromes and electron transfer.…”