Added value of autoregulation and multi-step kinetics of transcription initiation.

Bacterial gene expression regulation occurs mostly during transcription, which has two main rate-limiting steps: the close complex formation, when the RNA polymerase binds to an active promoter, and the subsequent open complex formation, after which it follows elongation. Tuning these steps' kinetics by the action of e.g.

Logic of two antagonizing intra-species quorum sensing systems in bacteria.

Bacteria release signaling molecules into the surrounding environment and sense them when present in their proximity. Using this strategy, a cell estimates the number of neighbors in its surrounding. Upon sensing a critical number of individuals, bacteria coordinate a number of cellular processes.

Analysis of a strategy for cooperating cells to survive the presence of cheaters.

Cooperation benefits individual cells in a microbial population by helping accomplish tasks which are difficult or non-beneficial for individuals in the population to carry out by themselves. Hence, numerous examples exist of bacteria cooperating and working towards a common objective. The sharing of a common public good via quorum sensing is one of the ways of cooperation among individuals of many microbial populations.

Revisiting demand rules for gene regulation.

Starting with Savageau's pioneering work regarding demand rules for gene regulation from the 1970s, here, we choose the simplest transcription network and ask: how does the cell choose a particular regulatory topology from all available possibilities? According to the demand rules, a cell chooses an activator based regulation of a target if the target protein is required for most of the time. On the other hand, if the target protein is only required sporadically, its control tends to be via a repressor-based regulatory topology. We study the natural distribution of topologies at genome, systems, and micro-levels in E.

Control of MarRAB Operon in Escherichia coli via Autoactivation and Autorepression.

Choice of network topology for gene regulation has been a question of interest for a long time. How do simple and more complex topologies arise? In this work, we analyze the topology of the marRAB operon in Escherichia coli, which is associated with control of expression of genes associated with conferring resistance to low-level antibiotics to the bacterium. Among the 2102 promoters in E.

Role of feedback and network architecture in controlling virulence gene expression in Bordetella.

Bordetella is a Gram-negative bacterium responsible for causing whooping cough in a broad range of host organisms. For successful infection, Bordetella controls expression of four distinct classes of genes (referred to as class 1, 2, 3, and 4 genes) at distinct times in the infection cycle. This control is executed by a single two-component system, BvgAS.

Interplay between Fur and HNS in controlling virulence gene expression in Salmonella typhimurium.

Salmonella enterica is responsible for a large number of diseases in a wide-range of hosts. Two of the global regulators involved in controlling gene expression during the infection cycle of the bacterium are Fur and HNS. In this paper, we demonstrate computationally that Fur and HNS have disproportionately high density of binding sites in the Pathogenicity Islands on the Salmonella chromosome.