A Comparison of Protein and mRNA Expression during Development of the Soil Dwelling Prokaryote (S. coelicolor)

Abstract

In this paper, correlation analysis of protein and mRNA levels in the soil dwelling bacteria Streptomyces coelicolor (S. coelicolor M145) is presented during development of the population as it grew in liquid medium using three biological and two technical replicates, measured during exponential growth, and its entry into the stationary phase. The proteome synthesis time series are compared with the gene expression time series measured previously under identical experimental conditions. Results reveal that about one third of protein/mRNA synthesis profiles are well correlated while another third are correlated negatively. Functional analysis of the highly correlated groups is presented. Based on numerical simulation, the negative correlation between protein and mRNA is shown to be caused by the difference between the rate of translation and protein degradation.

σE of Streptomyces coelicolor can function both as a direct activator or repressor of transcription

“…After germination, cultures were washed by 5 ml of ion-free water and inoculated into Na-glutamate medium (Na-glutamate, 61 g/l; glucose monohydrate, 44 g/l; MgSO 4 , 2.0 mM; Na 2 HPO 4 , 2.3 mM; KH 2 PO 4 , 2.3 mM) supplemented with 8 ml/l of trace element solution (ZnSO 4 ×7H 2 O, 0.1 g/l; FeSO 4 × 7H 2 O, 0.1 g/l; MnCl 2 ×4H 2 O, 0.1 g/l, CaCl 2 ×6H 2 O, 0.1 g/l; NaCl, 0.1 g/l) and 5.6 ml/l of TMS1 (FeSO 4 ×7H 2 O, 5 g/l; CuSO 4 ×5H 2 O, 390 mg/l; ZnSO 4 ×7H 2 O, 440 mg/l; MnSO 4 ×H 2 O, 150 mg/l; Na 2 MoO 4 ×2H 2 O, 10 mg/l; CoCl 2 × 6 H 2 O, 20 mg/l; HCl, 50 ml/l) 63 . Bacteria were shaken for 23 h (corresponding to exponential phase 64 at 30 °C, 250 rpm, and pH 7 was maintained during the growth. After 23 h, the culture was harvested and processed specifically for Western blot, ChIP-seq, or RT-qPCR (described separately in the following paragraphs).…”

“…The wt (LK3801) and Δσ E (LK3804) strains were used for qPCR analyses of 13 selected genes under normal conditions (w/o stress) or EtOH treatment. Bacteria were shaken for 23 h (corresponding to exponential phase 64 at 30 °C, 250 rpm, and pH 7 was maintained during the growth. After 23 h of growth in Na-glutamate medium, the strains were stressed or not with 4% EtOH for 1 h. RNA was isolated from 2 ml of bacterial culture (at OD 600 = 0.8) using RNeasy Mini Kit (QIAGEN, Cat.…”

Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded inStreptomycesgenomes

“…The majority of genes encoding RNA polymerase, housekeeping sigma factors, and ribosome proteins showed a sharp decrease in mRNA levels in the stationary phase, but not for protein level. 199 This divergent mRNA-protein relationship was correlated with the codon usage, RBS strength, and degradation rate, reflecting the presence of complex translational regulatory elements. 200 To this end, proteomics is essential to directly measure the actual cellular protein profiles for understanding SM production, which is interconnected with numerous regulatory systems.…”