Biological Noise Abatement: Coordinating the Responses of Autonomous Bacteria in a Synthetic Biofilm to a Fluctuating Environment Using a Stochastic Bistable Switch

Abstract

Noise is inherent to single cell behavior. Its origins can be traced to the stochasticity associated with a few copies of genes and low concentrations of protein and ligands. We have studied the mechanisms by which the response of noisy elements can be entrained for biological signal processing. To elicit predictable biological function, we have engineered a gene environment that incorporates a gene regulatory network with the stringently controlled microenvironment found in a synthetic biofilm. The regulatory network leverages the positive feedback found in quorum-sensing regulatory components of the lux operon, which is used to coordinate cellular responses to environmental fluctuations. Accumulation of the Lux receptor in cells, resulting from autoregulation, confers a rapid response and enhanced sensitivity to the quorum-sensing molecule that is retained after cell division as epigenetic memory. The memory of the system channels stochastic noise into a coordinated response among quorum-sensing signal receivers in a synthetic biofilm in which the noise diminishes with repeated exposure to noisy transmitters on the input of a signaling cascade integrated into the same biofilm. Thus, gene expression in the receivers, which are autonomous and do not communicate with each other, is synchronized to fluctuations in the environment.

Wiring Together Synthetic Bacterial Consortia to Create a Biological Integrated Circuit

“…For example, due to crosstalk, the lux-genes in V. fischeri do not seem to discriminate between 3OC 6 HSL and C 8 HSL so that lux regulation can become noisy, 40 which could be used to suppress or even enhance the sensitivity of a gene switch. 14,39 What is new in this report is that information (associated with the pulses of inductants, IPTG and arabinose) was transmitted in isolated channels by diffusion of QS signal molecules to receivers with embedded memory, and coordinated through the precise placement of the transmitting and receiving elements and inductant clock pulses to create predictable responses. Diffusive, dispersive signal transmission like this also 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 occurs in dendritic processes in neurons, which form the basis for information processing in the nervous system.…”

“…It has been shown that LuxR, in combination with this promoter, positively auto-regulates the QS response by modulating its own expression. 14,30,42 While luxP(R) had only a low-level basal expression, it was strongly up-regulated in the presence of the luxR-3OC 6 HSL dimer and produced a variant of green fluorescent protein, GFP-LVA, in this case. GFP-LVA was unstable; it degraded by proteolytic digestion with a half-life of about 10-20 min.…”

“…14,30,42 In particular, it has been shown using laser cytometry that induction of these 203-receivers was hysteretic and bistable, 14,30 in correspondence with the up-regulation of luxR with inductant as demonstrated using RT-PCR. 30 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 on the remote-array resulted in fluorescence.…”

“…The rate equations and parameters for these models (Eqs. S(i-xxiv) and S(xxv-li) for the lux-and las-comlinks respectively) were based on equations described elsewhere, 14 …”

“…Two orthogonally mounted AODs give independent control of the x-and y-position of a trap, allowing the formation of 2D arrays of optical traps. The details of the setup are given elsewhere 14. Within the parameters defining the optimum optical trap and the hydrogel scaffold, it is still possible to extend the size, shape and constituency of a cell array without…”