A computational model of gene expression was applied to a novel test set of microarray time series measurements to reveal regulatory interactions between transcriptional regulators represented by 45 sigma factors and the genes expressed during germination of a prokaryote Streptomyces coelicolor. Using microarrays, the first 5.5 h of the process was recorded in 13 time points, which provided a database of gene expression time series on genome-wide scale. The computational modeling of the kinetic relations between the sigma factors, individual genes and genes clustered according to the similarity of their expression kinetics identified kinetically plausible sigma factor-controlled networks. Using genome sequence annotations, functional groups of genes that were predominantly controlled by specific sigma factors were identified. Using external binding data complementing the modeling approach, specific genes involved in the control of the studied process were identified and their function suggested.
- MeSH
- genetická transkripce MeSH
- genové regulační sítě * MeSH
- kinetika MeSH
- modely genetické * MeSH
- počítačová simulace MeSH
- regulace genové exprese u bakterií * MeSH
- sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
- sigma faktor metabolismus MeSH
- spory bakteriální genetika růst a vývoj metabolismus MeSH
- stanovení celkové genové exprese * MeSH
- Streptomyces coelicolor genetika metabolismus fyziologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Streptomycetes have been studied mostly as producers of secondary metabolites, while the transition from dormant spores to an exponentially growing culture has largely been ignored. Here, we focus on a comparative analysis of fluorescently and radioactively labeled proteome and microarray acquired transcriptome expressed during the germination of Streptomyces coelicolor. The time-dynamics is considered, starting from dormant spores through 5.5 hours of growth with 13 time points. Time series of the gene expressions were analyzed using correlation, principal components analysis and an analysis of coding genes utilization. Principal component analysis was used to identify principal kinetic trends in gene expression and the corresponding genes driving S. coelicolor germination. In contrast with the correlation analysis, global trends in the gene/protein expression reflected by the first principal components showed that the prominent patterns in both the protein and the mRNA domains are surprisingly well correlated. Analysis of the number of expressed genes identified functional groups activated during different time intervals of the germination.
- MeSH
- analýza hlavních komponent MeSH
- energetický metabolismus genetika MeSH
- fenotyp MeSH
- fyziologický stres genetika MeSH
- genové regulační sítě MeSH
- metabolické sítě a dráhy MeSH
- proteom * MeSH
- regulace genové exprese u bakterií * MeSH
- spory bakteriální genetika metabolismus MeSH
- Streptomyces coelicolor genetika metabolismus ultrastruktura MeSH
- transkriptom * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
An example of bacterium, which undergoes a complex development, is the genus of Streptomyces whose importance lies in their wide capacity to produce secondary metabolites, including antibiotics. In this work, a proteomic approach was applied to the systems study of germination as a transition from dormancy to the metabolically active stage. The protein expression levels were examined throughout the germination time course, the kinetics of the accumulated and newly synthesized proteins were clustered, and proteins detected in each group were identified. Altogether, 104 2DE gel images at 13 time points, from dormant state until 5.5 h of growth, were analyzed. The mass spectrometry identified proteins were separated into functional groups and their potential roles during germination were further assessed. The results showed that the full competence of spores to effectively undergo active metabolism is derived from the sporulation step, which facilitates the rapid initiation of global protein expression during the first 10 min of cultivation. Within the first hour, the majority of proteins were synthesized. From this stage, the full capability of regulatory mechanisms to respond to environmental cues is presumed. The obtained results might also provide a data source for further investigations of the process of germination.
- MeSH
- 2D gelová elektroforéza MeSH
- antibakteriální látky biosyntéza MeSH
- hmotnostní spektrometrie MeSH
- proteom analýza MeSH
- proteosyntéza * MeSH
- regulace genové exprese u bakterií MeSH
- spory bakteriální * růst a vývoj metabolismus MeSH
- Streptomyces coelicolor * genetika růst a vývoj metabolismus MeSH
- vývojová regulace genové exprese MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
