Project name: A genome-wide transcription analysis of the ∆ohkA and ∆orrA mutants in comparion with the wild type strain M145

Description: We conducted a genome-wide transcription profiling experiment using Agilent GeneChip S. coelicolor DNA microarrays (custom-specific design) to determine whether OhkA and OrrA function in the same pathway. From the complete transcriptome data, we observed that, totally, 981 and 1242 genes had significantly altered transcription levels (with at least two-fold increases or decreases) in the mutants of ΔohkA and ΔorrA, respectively, compared with the wild-type strain M145. Importantly, among the genes differentially expressed in the ΔohkA and ΔorrA mutants, 877 genes were similarly affected in these two mutants, in which 427 were downregulated and 450 were upregulated; moreover, none showed an opposite transcription alteration.The large number of genes with similar transcription alterations identified in the ΔohkA and ΔorrA mutants is in good agreement with the speculation that OhkA and OrrA function in the same signaling pathway.Overall design: Total RNA samples were isolated from cultures of M145, the ΔohkA and ΔorrA mutants, which were grown on MS agar plates covered with plastic cellophanes for 48 h. As one custom-designed DNA array (8×15 K) only contains eight microarrays, here we tested eight RNA samples from three independent replicates for both mutants (ΔohkA and ΔorrA) and two independent replicates for the wild-type strain M145. Significantly regulated genes (ΔohkA/M145 or ΔorrA/M145) were selected according to the fold-change (linear==2) in combination with a T-test p-value <0.05.

Data type: Transcriptome or Gene expression

Sample scope: Multiisolate

Relevance: Environmental

Last updated: 2020-12-01