Towards the Regulatory Network of Methanotrophs Based on Available Gene Expression Profiles
摘要
Novel bioinformatics approaches for large-scale gene expression data analysis provide an opportunity to reconstruct transcriptional regulatory networks that control cellular response to different environmental stimulus for non-model microbial systems. In this study, we used published transcriptomic datasets for two closely related methanotrophs, Methylotuvimicrobium alcaliphilum 20ZR and Methylotuvimicrobium buryatense 5GB1C, in different growth conditions and a combination of bioinformatics methods in order to reveal co-expressed and functionally related genes regulated by one or two potential or experimentally verified transcription factors. The clustering and subsequent functional-structural analysis of the transcriptomic datasets revealed 49 potential transcription factors (TFs) common to both methanotrophic cultures. In addition to known global regulators, that control expression of methane utilization genes, such as mxaB and rpoN, two novel factors were predicted to control cellular metabolism by activation pathways for iron uptake (MEALZ_RS12170, FeoC, a [Fe–S]-dependent transcriptional regulator) and lanthanide (Ln)-dependent growth (MEALZ_RS09670, OmpR-family, a two-component system, response regulator). FeoC regulates a cluster that was down-expressed in methane and oxygen-limited growth conditions, which correlated with reduced cellular respiration. The study suggests that OmpR plays a role in regulating genes associated with lanthanide (Ln)-dependent metabolism, including an (Ln)-dependent methanol dehydrogenase xoxF and associated formaldehyde activating enzyme, fae2. Overall, the research revises the regulatory networks in two biotechnology-relevant methanotrophic chassis and highlights several novel factors that control their gene expression.