Analyzing stochastic transcription to elucidate the nucleoid's organization

Spatial organization of transcription in bacterial cells

Prokaryotic transcription has been extensively studied over the past half a century. However, there often exists a gap between the structural, mechanistic description of transcription obtained from in vitro biochemical studies, and the cellular, phenomenological observations from in vivo genetic studies. It is now accepted that a living bacterial cell is a complex entity; the heterogeneous cellular environment is drastically different from the homogenous, well-mixed situation in vitro. Where molecules are inside a cell may be important for their function; hence, the spatial organization of different molecular components may provide a new means of transcription regulation in vivo, possibly bridging this gap. In this review, we survey current evidence for the spatial organization of four major components of transcription [genes, transcription factors, RNA polymerase (RNAP) and RNAs] and critically analyze their biological significance.

Transcriptional regulation shapes the organization of genes on bacterial chromosomes

Transcription factors (TFs) are the key elements responsible for controlling the expression of genes in bacterial genomes and when visualized on a genomic scale form a dense network of transcriptional interactions among themselves and with other protein coding genes. Although the structure of transcriptional regulatory networks (TRNs) is well understood, it is not clear what constrains govern them. Here, we explore this question using the TRNs of model prokaryotes and provide a link between the transcriptional hierarchy of regulons and their genome organization. We show that, to drive the kinetics and concentration gradients, TFs belonging to big and small regulons, depending on the number of genes they regulate, organize themselves differently on the genome with respect to their targets. We then propose a conceptual model that can explain how the hierarchical structure of TRNs might be ultimately governed by the dynamic biophysical requirements for targeting DNA-binding sites by TFs. Our results suggest that the main parameters defining the position of a TF in the network hierarchy are the number and chromosomal distances of the genes they regulate and their protein concentration gradients. These observations give insights into how the hierarchical structure of transcriptional networks can be encoded on the chromosome to drive the kinetics and concentration gradients of TFs depending on the number of genes they regulate and could be a common theme valid for other prokaryotes, proposing the role of transcriptional regulation in shaping the organization of genes on a chromosome.