Is it possible to make bacteria respond to physical changes in a customizable way?

We analyze the question piecewise. First, how do bacteria adapt to physical change in their environment. These physical parameters typically comprise of temperature, pH, osmolarity. An additional environmental stress that bacteria face is that of nutrient starvation. These stresses pose a challenge to the organisms survival. The starting point for the idea was when we came to know of temperature rise being entangled with DnaK levels, termed as a heat shock.

How is the bacteria able to selectively switch on expression of a small subset of proteins based on a change in temperature? Based on recent literature reports, it's learnt that sigma 32, a subunit of the RNA Polymerase Holoenzyme twists into a functional conformation only after a rise in temperature. This sigma subunit confers promoter sequence based selectivity to RNA Polymerase.

To deal with different environmental niches, bacteria employ a family of such sigma factors to express different sets of proteins to adapt to these conditions. Usually, the number of these sigma factors vary from one bacterial species to another, with the more exotic ones having 50+ kinds of sigma subunits.

E.Coli has a family of 7 sigma subunits to partition it's genome into various programs. This division is as follows,

1. σ⁷⁰, rpoD: Houskeeping genes
2. σ⁵⁴, rpoN: Activated on nitrogen starvation
3. σ³⁸, rpoS: Master regulator for a generalized stress response
4. σ³², rpoH: Activated on increase in unfolded proteins
5. σ²⁸, rpoF: Initiates flagellar biosynthesis
6. σ²⁴, rpoE: Activated on rise of unfolded proteins in the cellular envelope
7. σ¹⁹, FecI: Activated on iron starvation

We used the database ecocyc.org to survey the genes being controlled by these different sigmas and how exactly are they induced. Identifying and isolating the promoters of these genes would be the next step. A library of promoters which would be expressed by these different sigmas would make for novel BioBricks.

These new promoters would cover the different environmental stresses that E.Coli responds to. Being designed within the specifications set out by the parts registry, it would be extensible with all the existing devices. A point to appreciate is that these promoters, unlike pLac, are expressed without any external chemical for induction and yet are not constitutive. This sets it apart in a league of environmental context specific promoters without the need for external inducer.

To resolve this, we looked into the kind of structural requirements for σ factor + RNA Polymerase to bind DNA. Activation is key for expression from genes under σ⁵⁴. For the others, the pattern of RNA Polymerase binding is similar to that of σ⁷⁰, which involves base specific interaction only in the -10 and -35 promoter region.