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. 2014 Dec 23;15(1):1173.
doi: 10.1186/1471-2164-15-1173.

Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor

Jan Bobek, Eva Strakova, Alice Zikova, Jiri Vohradsky  1
Affiliations

Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor

Jan Bobek et al. BMC Genomics. .

Abstract

Background: Bacterial spore germination is a developmental process during which all required metabolic pathways are restored to transfer cells from their dormant state into vegetative growth. Streptomyces are soil dwelling filamentous bacteria with complex life cycle, studied mostly for they ability to synthesize secondary metabolites including antibiotics.

Results: Here, we present a systematic approach that analyzes gene expression data obtained from 13 time points taken over 5.5 h of Streptomyces germination. Genes whose expression was significantly enhanced/diminished during the time-course were identified, and classified to metabolic and regulatory pathways. The classification into metabolic pathways revealed timing of the activation of specific pathways during the course of germination. The analysis also identified remarkable changes in the expression of specific sigma factors over the course of germination. Based on our knowledge of the targets of these factors, we speculate on their possible roles during germination. Among the factors whose expression was enhanced during the initial part of germination, SigE is though to manage cell wall reconstruction, SigR controls protein re-aggregation, and others (SigH, SigB, SigI, SigJ) control osmotic and oxidative stress responses.

Conclusions: From the results, we conclude that most of the metabolic pathway mRNAs required for the initial phases of germination were synthesized during the sporulation process and stably conserved in the spore. After rehydration in growth medium, the stored mRNAs are being degraded and resynthesized during first hour. From the analysis of sigma factors we conclude that conditions favoring germination evoke stress-like cell responses.

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Figures

Figure 1
Figure 1
Relationship between expression intervals (t) and sample collection times.
Figure 2
Figure 2
Pathway maps with highlighted genes and pathways activated at individual time intervals.
Figure 3
Figure 3
Total number of genes with enhanced and diminished (dashed) expression between two consecutive time points.
Figure 4
Figure 4
Number of pathways with >3 genes whose expression was enhanced/diminished (dashed) between two consecutive time intervals.
Figure 5
Figure 5
Percentage of the number of genes with enhanced (A) or diminished (B) expression as assigned to individual functional groups. The percentage is related to the total number of genes in a given metabolic group.
Figure 6
Figure 6
Differential expression profiles of sigma factors induced during germination. Sigma factors are sorted according to the time point in which their expression was enhanced (top – down) and the fold-increase in expression level between consecutive time points (right – left, vertical axis). Only intervals with significant changes are displayed.
See this image and copyright information in PMC

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