||Stable protein modifications were compiled from several sources:
a-L-glutamate ligation – NCBI Structure reports that RimK adds 4 additional Glu residues to the native E. coli Glu-Glu C-terminus of ribosomal protein S6 [PUB_0110].
Lipoate ligation – Stephens et al observed lipoate ligation sites in E. coli [PUB_0288]. The kinetic rate of lipoate ligation was measured by Morris et al [PUB_0290].
Phosphorylation – Su, Hutchison, and Giddings identified phosphorylated protein residues on a genome scale by mass-spec in M. genitalium and M. pneumoniae [PUB_0094]. For cases where multiple phosphorylations were consistent with the same mass-spec data, we assigned the phosphorylation to the most conserved residue as determined by ClustalW multiple sequence alignment. Kinetic rate of protein phosphorylation was measured by Fan, Fromm, and Bobik [PUB_0289].
Additionally we considered including modifications reported by the following sources:
Computational prediction of phosphorylations by NetPhosBac [PUB_0575]. We did not include NetPhosBac predictions because it predicted over 20000 sites, and therefore its predictions likely have low specificity.
Computational prediction of modifications by dbPTM [PUB_0268]. We did not include dbPTM predictions because it predicted over 2000 modifications, and therefore its predictions likely have low specificity. Additionally enzymes have not been identified in M. genitalium which generate many of the predicted modifications.
Gupta et al performed a whole proteome analysis of post-translational modifications in Shewanella oneidensis MR-1[PUB_0280]. We excluded this study because it was of unclear relevance to M. genitalium. For example the study did not identify any phosphorylations, which we expected is a major form of protein modification in M. genitalium.
Peril catalogued ribosomal proteins modifications including methylations and acetylations [PUB_0105]. We did not include these modifications because no enzymes have been identified in M. genitalium which generate these modifications.
Hesketh et al catalogued modifications in Streptomyces coelicolor [PUB_0276]. We did not include this data because Hesketh et al did not ascertain the specific chemical composition of each modification.
Krebes et al [PUB_0277], Demina et al [PUB_0282], and Macek et al [PUB_0283] identified phosphosites in Mycoplasma pneumoniae, Mycoplasma gallisepticum, and Bacillus subtilis on a genome scale. We excluded these modifications because they had no overlap with sites identified in the Su, Hutchison, and Giddings whole proteome screen [PUB_0094].
Phospho.ELM database of protein modifications [PUB_0278]. We did not include Phospo.ELM results because they are based on data from distantly related species.
Unstable or transient protein modifications such as disulfide bonds were reconstructed from computational prediction and the primary literature.
See Note_DisulfideBonds for a discussion of the reconstruction of disulfide bonds.
Additional sources: [PUB_0281, PUB_0672, PUB_0673, PUB_0674].
Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, Mazumder R, Nikolskaya AN, Rao BS, Panchenko AR, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. MMDB: Entrez's 3D-structure database. Nucleic Acids Res 31, 474-7 (2003). WholeCell: PUB_0110, PubMed: 12520055, URL: http://www.ncbi.nlm.nih.gov/Structure/
Demina IA, Serebryakova MV, Ladygina VG, Rogova MA, Zgoda VG, Korzhenevskyi DA, Govorun VM. Proteome of the bacterium Mycoplasma gallisepticum. Biochemistry (Mosc) 74, 165-74 (2009). WholeCell: PUB_0282, PubMed: 19267672
Diella F, Gould CM, Chica C, Via A, Gibson TJ. Phospho.ELM: a database of phosphorylation sites--update 2008. Nucleic Acids Res 36, D240-4 (2008). WholeCell: PUB_0278, PubMed: 17962309, URL: http://phospho.elm.eu.org/
Fan C, Fromm HJ, Bobik TA. Kinetic and functional analysis of L-threonine kinase, the PduX enzyme of Salmonella enterica. J Biol Chem 284, 20240-8 (2009). WholeCell: PUB_0289, PubMed: 19509296
Green DE, Morris TW, Green J, Cronan JE Jr, Guest JR. Purification and properties of the lipoate protein ligase of Escherichia coli. Biochem J 309 ( Pt 3), 853-62 (1995). WholeCell: PUB_0290, PubMed: 7639702
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