title: Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Department of Chemical Engineering, Box 355014, University of Washington, Seattle, WA 98195, USA. qxia@chem.wisc.edu
authors.forename: Qiangwei
authors.initials: Q
authors.lastname: Xia
authors.forename: Tiansong
authors.initials: T
authors.lastname: Wang
authors.forename: Erik L
authors.initials: EL
authors.lastname: Hendrickson
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Lie
authors.forename: Murray
authors.initials: M
authors.lastname: Hackett
authors.forename: John A
authors.initials: JA
authors.lastname: Leigh
mesh_terms: D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism*; D019848:Gene Expression Regulation, Archaeal; D006859:Hydrogen / Q000378:metabolism; D017017:Methanococcus / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism*; D009584:Nitrogen / Q000378:metabolism; D009586:Nitrogen Fixation / Q000235:genetics; D010710:Phosphates / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D018085:Regulon
chemical_list: D019843:Archaeal Proteins; D010710:Phosphates; D006859:Hydrogen; D009584:Nitrogen