Memo-Cell project

Introduction

The Memo-cell project is a novel and original approach to allow for limitless counting of signals a cell receives.

Counting is an essential process in our daily life, and so humans have invented many ways to count, from very simple manual counters to more complex logic gates implemented within electrical circuits. While counting is an essential process in our daily life, implementing an automated counter into bacteria is essential for following steps in synthetic processes, in controlling sequential events and could have many applications, from medical to industrial.

Counting with single-cells is a concept that has already been tackled but which is still in its infancy. Some counters have already been designed and implemented, but could only count up to three. Extension to achieve counting more that 3 has limited feasibility, as these systems rely on the number of different transcription factors / recombination enzymes available and characterized. Moreover, it is important to notice that for these designs, once an element has been used for counting, it can not be reused. In contrast, the approach we took here is free from all these constraints, because we're essentially using the same regulatory circuits cyclically.



The framework for this approach is fairly simple. We implement memory in the bacteria using a sequential integration of the same DNA pieces into the bacteria chromosome, controlled in space and time. Memory will then be hardcoded in the genome by the number of DNA pieces integrated one after other in the genome.

Our design hijacks the phage integration mechanism to allow the bacteria to integrate in its chromosome a specific piece of DNA at a specific location called attachment site, every time it detects a specific input signal. Then we regenerate this attachment site through a second recombination events, by again hijacking the transposon systems. The successive detection of signals will results in the successive integration of DNA pieces one after the other into the chromosome. The total number of DNA pieces integrated on the chromosome will then correspond to the number of times the signal has been detected. For instance, we could integrate the previously developed light sensing module and plug it to our memo-cell module. Hence, the memo-cell module would be triggered when there is light, and our bacteria will count the number of days.

To achieve this goal, we had to hijack and to extensively engineer three mechanisms:

• 1. The recombination system of Phages Lambda and HK022;
• 2. The recombination system of Transposon Tn916;
• 3. The microcin C51 from a specific E.coli strain.