title: Proteomic analyses of nucleoid-associated proteins in Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus.
abstract: BACKGROUND
  The bacterial nucleoid contains several hundred kinds of nucleoid-associated proteins (NAPs), which play critical roles in genome functions such as transcription and replication. Several NAPs, such as Hu and H-NS in Escherichia coli, have so far been identified.
  
  
  RESULTS
  Log- and stationary-phase cells of E. coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus were lysed in spermidine solutions. Nucleoids were collected by sucrose gradient centrifugation, and their protein constituents analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Over 200 proteins were identified in each species. Envelope and soluble protein fractions were also identified. By using these data sets, we obtained lists of contaminant-subtracted proteins enriched in the nucleoid fractions (csNAP lists). The lists do not cover all of the NAPs, but included Hu regardless of the growth phases and species. In addition, the csNAP lists of each species suggested that the bacterial nucleoid is equipped with the species-specific set of global regulators, oxidation-reduction enzymes, and fatty acid synthases. This implies bacteria individually developed nucleoid associated proteins toward obtaining similar characteristics.
  
  
  CONCLUSIONS
  Ours is the first study to reveal hundreds of NAPs in the bacterial nucleoid, and the obtained data set enabled us to overview some important features of the nucleoid. Several implications obtained from the present proteomic study may make it a landmark for the future functional and evolutionary study of the bacterial nucleoid.
authors.affiliation: Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan. ohniwa@md.tsukuba.ac.jp
authors.forename: Ryosuke L
authors.initials: RL
authors.lastname: Ohniwa
authors.forename: Yuri
authors.initials: Y
authors.lastname: Ushijima
authors.forename: Shinji
authors.initials: S
authors.lastname: Saito
authors.forename: Kazuya
authors.initials: K
authors.lastname: Morikawa
mesh_terms: D001412:Bacillus subtilis / Q000378:metabolism*; D001426:Bacterial Proteins / Q000378:metabolism*; D015153:Blotting, Western; D004269:DNA, Bacterial / Q000302:isolation & purification / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004926:Escherichia coli / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D011550:Pseudomonas aeruginosa / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism; D013211:Staphylococcus aureus / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; C031908:H-NS protein, bacteria; D016601:RNA-Binding Proteins