Article Figures & Data
Figures
- FIG. 1.
Positions of all proteins mentioned in this paper on a 2-D gel of a sample of E. coli AM134 (MC4100 clpX1::kan) stained with SYPRO red. The growth-phase-regulated proteins controlled by ClpP-containing proteases and identified by MALDI (MS) (peptide mass fingerprinting) are listed in Table 1.
- FIG. 2.
Growth phase regulation of proteins in wild-type and clpP E. coli. Corresponding regions of gels obtained from logarithmically growing (A and C) and starved (for 21 h) (B and D) samples of the wild type (A and B) and the clpP mutant (C and D). In panel A, the positions of relevant spots are indicated with the identification numbers used in Fig. 1, Table 1, and the text.
- FIG. 3.
Levels of proteins displaying increased amounts in one or more of the protease mutants compared to the wild type. Relative protein levels were determined from SYPRO-stained 2-D gels as described in Materials and Methods. Data are shown from the AhpC protein (spot 116) (A), the RbsB protein (spot 94) (B), and the LeuA protein (spot 55) (C). Wild-type protein levels are shown as filled black bars, data from clpP mutant cultures are presented as hatched bars, data from clpA cultures are presented as double-hatched bars, and data from clpX cultures are presented as open (white) bars. SP, stationary phase; 70′SP, 70 min after reaching the stationary phase; O/N, overnight.
- FIG. 4.
Levels of proteins displaying reduced amounts in one or more of the protease mutants compared to the wild type. Relative protein levels were determined from SYPRO-stained 2-D gels as described in Materials and Methods. Data are shown for the Dps protein (spot 101) (A), the ArgT protein (spot 107) (B), and the WrbA protein (spot 152) (C). Wild-type protein levels are shown as filled black bars, data from clpP mutant cultures are presented as hatched bars, data from clpA cultures are presented as double hatched bars, and data from clpX cultures are presented as open (white) bars. SP, stationary phase; 70′SP, 70 min after reaching the stationary phase; O/N, overnight.
Tables
- TABLE 1.
Protease-dependent regulation of growth-phase-regulated proteins
Spot no. Proteina Description Ratio relative to log levels after time in stationary phaseb: Level during log phase significantlyc: 70 min 21 h WT clpP clpA clpX WT clpP clpA clpX Elevated Reduced 14 GroEL 60-kDa chaperonin 1.4 1.1 1.1 1.3 1.4 1.2 1.3 1.0 clpP, clpA, clpX 94 RbsB Periplasmic d-ribose binding protein 1.4 0.9 1.3 1.1 2.2 4.5 2.8 3.6 101 Dps DNA protection during starvation 5.3 2.5 7.6 2.3 43.6 5.8 16.1 16.5 107 ArgT Periplasmic LAO-binding proteind 1.9 1.6 1.6 1.0 4.9 2.2 2.5 2.1 147 AldA Aldehyde dehydrogenase A 1.2 1.2 0.8 1.3 1.4 2.0 1.2 1.9 152 WrbA Trp repressor binding protein 1.3 4.5 0.9 0.9 2.8 3.6 1.5 1.6 clpP 15 Tig Trigger factor 1.0 1.2 0.7 1.1 0.7 0.9 0.8 0.8 22 GlnA Glutamine synthetase 1.5 0.9 0.9 0.8 0.4 0.7 0.7 0.5 clpA 34 TalB Transaldolase B 1.0 1.0 1.0 1.0 0.8 1.0 1.0 0.8 37 TrxB Thioredoxin reductase 0.9 1.3 0.9 1.0 0.7 0.9 0.8 1.0 55 LeuA Isopropylmalate synthase 1.0 1.1 0.9 1.6 0.6 0.7 0.9 0.9 108 LeuD Isopropylmalate isomerase small subunit 0.6 0.9 0.9 0.4 0.2 0.3 0.3 0.4 clpA 116 AhpC Alkyl hydroperoxide reductase C22 protein 0.8 1.0 1.1 0.9 0.2 1.0 0.3 0.6 130 RpsF 30S ribosomal protein S6 RS-6Ce 0.8 1.3 1.1 1.0 0.6 0.7 0.4 0.6 131 RpsF 30S ribosomal protein S6 RS-6Be 0.5 0.9 1.0 0.7 0.3 0.3 0.2 0.4 148 IlvC Ketol acid reductoisomerase 1.2 1.1 1.3 1.4 0.6 0.8 1.0 1.1 clpA 168 MetK S-adenosylmethionine synthetase 1.0 0.9 0.9 1.0 0.8 0.9 0.9 1.1 173 GdhA NADP-specific glutamate dehydrogenase 1.3 0.8 0.9 1.0 0.3 0.7 0.3 0.5 ↵ a The spots identified by MALDI (MS) are shown with their protein names according to SWISSPROT. The first 6 proteins are induced during the stationary phase compared to the log phase, and the remaining 12 are repressed in the stationary phase.
↵ b Mean spot intensities in the stationary phase were divided by the corresponding mean levels in the log phase (6 parallels each) to give mean ratios, and significant (P < 0.05) changes relative to levels in the log phase are highlighted in bold.
↵ c Genotypes of strains in which protein levels observed in the log phase were significantly (P < 0.05) different from wild-type levels.
↵ d LAO, lysine-arginine-ornithine.
↵ e The proteins in spots 130 and 131 are two different posttranslationally modified species of the same translation product (54).
