Abstract
Systems biology based approaches have been effectively utilized to mine high throughput data. In the current study, we have performed system-level analysis for Deinococcus radiodurans R1 by constructing a gene co-expression network based on several microarray datasets available in the public domain. This condition-independent network was constructed by Weighted Gene Co-expression Network Analysis (WGCNA) with 61 microarray samples from 9 different experimental conditions. We identified 13 co-expressed modules, of which, 11 showed functional enrichments of one or more pathway/s or biological process. Comparative analysis of differentially expressed genes and proteins from radiation and desiccation stress studies with our co-expressed modules revealed the association of cyan with radiation response. Interestingly, two modules viz darkgreen and tan was associated with radiation as well as desiccation stress responses. The functional analysis of these modules showed enrichment of pathways important for adaptation of radiation or desiccation stress. To decipher the regulatory roles of these stress responsive modules, we identified transcription factors (TFs) and then calculated a Biweight mid correlation between modules hub gene and the identified TFs. We obtained 7 TFs for radiation and desiccation responsive modules. The expressions of 3 TFs were validated in response to gamma radiation using qRT-PCR. Along with the TFs, selected close neighbor genes of two important TFs, viz., DR_0997 (CRP) and DR_2287 (AsnC family transcriptional regulator) in the darkgreen module were also validated. In our network, among 13 hub genes associated with 13 modules, the functionality of 5 hub genes which are annotated as hypothetical proteins (hypothetical hub genes) in D. radiodurans genome has been revealed. Overall the study provided a better insight of pathways and regulators associated with relevant DNA damaging stress response in D. radiodurans.
Highlights
The Deinococcaceae family bacterium D. radiodurans R1 is a gram-positive coccus that withstands several stress conditions such as gamma radiation, UV radiation, desiccation and various other clastogens like methyl methanesulfonate, N-methyl-N-nitro-N-nitrosoguanidine (MNNG), nitrous acid, and hydroxylamine [1, 2]
Based on the correlation of transcription factors (TFs) with the hub gene, our analysis indicated that genes involved in DNA repair and metabolism, amino acid, benzoate degradation, quorum sensing, oxidoreductase, ATPase, endonuclease activity, translation and transport etc. could be regulated by DR_0997 (Transcriptional regulator, FNR/CRP family), DR_A0071 or DR_2287 (AsnC family transcriptional regulator)
Microarray data sets available for D. radiodurans R1 under diverse stress conditions were downloaded from NCBI-GEO database [22, 23]
Summary
The Deinococcaceae family bacterium D. radiodurans R1 is a gram-positive coccus that withstands several stress conditions such as gamma radiation, UV radiation, desiccation and various other clastogens like methyl methanesulfonate, N-methyl-N-nitro-N-nitrosoguanidine (MNNG), nitrous acid, and hydroxylamine [1, 2]. WGCNA approach is one of the promising tools for studying the functionality of uncharacterized or hypothetical proteins [9, 10] This methodology has been extensively utilized in various organisms for predicting biological functions of gene/s in a cluster [9,10,11,12,13,14,15]. This approach has been applied in constructing a co-expression network using a diverse set of conditions or data sets [16, 17]
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