Table 1.
Main targets for tmRNA-mediated tagging in Streptomyces coelicolor
| ScoDB annotation | Protein name | Protein function and comments | Hits* in sample | ∑‡ | Sequence coverage (%) | Last residue identified§ | Reference (for function) | ||
|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | |||||||
| Stress-related functions | |||||||||
| Development and antibiotic production | |||||||||
| SCO3925 | SsgR | Transcriptional activator of SsgA | 11 | 29 | 28 | 23 | 56.8 | 223/241 (231) | Traag et al (2004) |
| SCO3926 | SsgA | Activator of sporulation-specific cell division | 5 | 6 | 5 | 5 | 43.4 | 89/136 (127) | van Wezel et al (2000) |
| SCO7175 | SsgF | Regulator of sporulation | 2 | 2 | — | 3 | 21.8 | 156/156 (156) | Noens et al (2005) |
| SCO5231 | DasR | Pleiotropic repressor of antibiotic production and N-acetylglucosamine metabolism; nutrient-sensing protein | 5 | 10 | 4 | 11 | 43.7 | 235/254 (250) | Rigali et al (2006, 2008) |
| SCO3413 | TipA | Thiostrepton antibiotic-induced regulator | 6 | 4 | 7 | 10 | 44.7 | 250/253 (250) | Kahmann et al (2003) |
| Stress proteins | |||||||||
| SCO3671 | DnaK | Heat-shock protein 70 (chaperone) | 2 | 3 | 2 | 5 | 10.7 | 285/618 (614) | Bucca et al (2003); Wickner et al (1991) |
| SCO0200 | UspA | Starvation-related | — | 3 | — | 3 | 16.3 | 247/301 (273) | Nystrom & Neidhardt (1992) |
| SCO1321 | EF-Tu3 | Induced by stress conditions and relating to antibiotic resistance | — | 2 | 1 | 3 | 10.7 | 334/392 (381) | van Wezel et al (1994) |
| Other | |||||||||
| SCO1294 | Cystathionine γ-synthase | Cys/Met metabolism; selenate tolerance | — | 8 | 1 | 7 | 25.3 | 352/407 (405) | |
| SCO2582 | Peptidase | Peptidase M48, Ste24 family; highly conserved in actinomycetes | — | 5 | 4 | 5 | 9.7 | 335/402 (399) | |
| Non-specific binding (naturally His-rich proteins, which were also found in the control strain) | |||||||||
| SCO1858 | Hypothetical protein | Unknown function; His-rich carboxy-terminus | 7 | 29 | 10 | 21 | 66.6 | 272/305 (272) | |
| SCO6549 | Hypothetical protein | Unknown function; His-rich amino-terminus | 2 | 2 | 3 | 4 | 20.7 | 264/314 (296) | |
| Proteins were identified by capillary LC-MS/MS. Most proteins that are His-tagged by the tmRNA-mediated trans-translation mechanism in a strain expressing the tmRNA-His variant are important cell-cycle control or stress-related proteins. All targets are highly conserved in all streptomycetes. | |||||||||
| *Total number of tandem mass spectra matched to the protein as rank 1 hits by Sequest (sample 1) or Mascot (samples 2 and 3). | |||||||||
| ‡Total sum of unique peptides (that is, not sharing the same sequence) found in the three LC-MS/MS runs; only proteins identified with ⩾3 unique peptides in these three runs are reported. | |||||||||
| §Position of the last identified residue compared with the full length of the protein; the position before the last trypsin cleavage site in the protein is given in brackets. | |||||||||
| EF-Tu3, elongation factor Tu3; LC-MS/MS, liquid chromatography–tandem mass spectrometry; ScoDB, Streptomyces coelicolor database; Ssg, sporulation of Streptomyces griseus; TipA, thiostrepton antibiotic-induced protein; tmRNA, transfer–messenger RNA; Usp, universal stress protein | |||||||||