Use of RNA-seq to identify causes of slow expression kinetics of microbes to new nutrient substrate

Genes are differentially expressed in order to reduce the metabolic burden associated with gene expression. But, this regulatory framework also pose a challenge to cells particularly in the competitive uptake of specific nutrients relative to other bacterial species. Specifically, cells with slow kinetics in upregulating expression of particular genes upon the sensing of a new carbon source or nutrient would be at a competitive disadvantage relative to species able to rapidly express genes needed for the metabolism of a new substrate. Slow kinetics of upregulating gene expression could be due to a variety of factors that include high occupancy of RNA polymerase and ribosome, and the need to express a needed transcription factor which controls expression of a particular target gene. Such slow expression kinetics could theoretically be detected at the population level through determining the diauxic lag phase when the microbe switches from one nutrient to another. From the biotechnological standpoint, possible approach for enabling faster response to new available nutrients include overexpression of RNA polymerase and the various subunits of the ribosome. But, these methods built upon biochemical work dissecting the underlying reasons for a cell’s poor transcriptional and translational response to a new nutrient, an area which could tap on RNA-seq transcriptome analysis of a cell upon exposure to a new nutrient substrate. Using RNA-seq data, one could thus infer the cellular machinery that is limiting expression of target genes and therefore offer clues to the overexpression strategy that could likely help ameliorate the poor response to new substrate. Collectively, slow expression kinetics upon sensing a new nutrient substrate holds implications to the competitive success of a microbe in various environmental and nutritional conditions. This problem is of relevance to the use of microbes in environmental bioremediation where an engineered microbe tasked to detoxify a pollutant need to remain competitive under varied nutritional and environmental conditions. Hence, use of modern next-generation sequencing and molecular biology tools could help inform the causes of slow expression kinetics as well as implementing solutions for its amelioration.