Some Bacterial Species Activate Multitude of Gene Expression Programmes Evenly While Others use a Tiered Approach

Abstract

Not all genes in a genome are expressed at the same time, and this aspect of cell biology confers an evolutionary advantage to the species due primarily to the fitness advantage of conserving scarce cellular buildings blocks for use during times of need. Known as differential gene expression, this aspect of cell biology has been extensively studied using the unbiased sequence based approach of RNA-seq. Indeed, RNA-seq transcriptome of many bacterial species under different conditions have been obtained. For gaining an initial understanding of the physiology and phenotype of a bacterial species, the gene expression pattern resulting from growth under optimal conditions is obtained. But, what does the gene expression pattern look like? What can we learn from them? From a preliminary analysis of the broad architecture of transcriptome of bacterial species profiled under different nutritional and environmental conditions via the approach of RNA-seq, there are two broad classes of differential gene expression patterns. In the first class, which is typified by the gene expression pattern in the Gram-positive model bacterium, Bacillus subtilis, a representative gene from each major gene expression module in the species gain high expression level. This suggests that there is likely even activation of different branches of metabolism, cell signalling and systems in the species. Furthermore, such a gene expression pattern does not negatively affect particular module or system in the cell given that most system modules are reasonably well activated. In the second class, where the gene expression pattern of Vibrio cholerae is representative, gene expression takes on a tiered approach. Specifically, cursory profiling of the most highly expressed genes in the species are ribosomal protein genes. This suggests that the cell is poised for protein translation and growth. But, there aren't many representatives from other branches of metabolism or system in the list of most highly expressed genes. Hence, gene expression takes on a tiered approach in this bacterial species of pathogenic importance. Specifically, some cellular systems are more highly activated or expressed compared to others, which is an uneven form of gene expression with important implications for infection control and disease management. Importantly, such a tiered approach of gene expression may have evolutionary significance given that activation of under-used systems may result in secretion of metabolites or small proteins that may, in turn, activate the immune system. Hence, natural selection may have selected for such a gene expression programme in V. cholerae. Overall, depending on evolutionarily forces, different bacterial species are endowed with different gene expression architecture. Some species such as B. subtilis select a broad base approach of activating multiple systems and pathway to poise the cell to respond to many possible turns in events in its immediate environment. Others such as V. cholerae may choose a tiered approach to reduce expression of under-used systems in an effort to escape from immune detection in a pathogenic scenario.

Keywords: gene expression architecture, Bacillus subtilis, Vibrio cholerae, RNA-seq, cellular physiology, biochemistry, genomics, cell physiology, cell biology, systems biology