Abstract
BackgroundMethanogenic Archaea play key metabolic roles in anaerobic ecosystems, where they use H2 and other substrates to produce methane. Methanococcus maripaludis is a model for studies of the global response to nutrient limitations.ResultsWe used high-coverage quantitative proteomics to determine the response of M. maripaludis to growth-limiting levels of H2, nitrogen, and phosphate. Six to ten percent of the proteome changed significantly with each nutrient limitation. H2 limitation increased the abundance of a wide variety of proteins involved in methanogenesis. However, one protein involved in methanogenesis decreased: a low-affinity [Fe] hydrogenase, which may dominate over a higher-affinity mechanism when H2 is abundant. Nitrogen limitation increased known nitrogen assimilation proteins. In addition, the increased abundance of molybdate transport proteins suggested they function for nitrogen fixation. An apparent regulon governed by the euryarchaeal nitrogen regulator NrpR is discussed. Phosphate limitation increased the abundance of three different sets of proteins, suggesting that all three function in phosphate transport.ConclusionThe global proteomic response of M. maripaludis to each nutrient limitation suggests a wider response than previously appreciated. The results give new insight into the function of several proteins, as well as providing information that should contribute to the formulation of a regulatory network model.
Highlights
Methanogenic Archaea play key metabolic roles in anaerobic ecosystems, where they use H2 and other substrates to produce methane
The average number of redundant heavy/light and light/heavy peptide pairs recovered for each detected ORF in each comparison of two nutrient limitation states, for purposes of abundance ratio generation, was 198. (Here the term "redundant" refers to measurements that include repeated sampling of the same peptide pair where each observed pair is an estimator of the relative change in protein abundance as in our previous work [8,10].) such statistical power is a mixed blessing in that one must distinguish between real regulatory trends and minor random changes in the system
H2 limitation affected the proteins of methanogenesis more widely than we had previously appreciated
Summary
Methanogenic Archaea play key metabolic roles in anaerobic ecosystems, where they use H2 and other substrates to produce methane. Methanococcus maripaludis is a model for studies of the global response to nutrient limitations. Methanogenic Archaea (methanogens) occupy a distinct position in phylogeny, ecology, and physiology. Occupying much of the phylum Euryarchaeota, and widespread in anaerobic environments, these organisms produce methane as the product of energy-generating metabolism [1]. Hydrogenotrophic methanogens specialize in the use of H2 as electron donor to reduce CO2 to methane. The pathways of methanogenesis are well characterized and the proteins that catalyze steps in the pathways are known. We are engaged in a long-term effort to understand regulatory networks in hydrogenotrophic methanogens. Our (page number not for citation purposes)
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