$\Ogo$ur $\MyColi$ project is based on production mechanisms of proteins, toxin-antitoxin systems, and effect of an additional peptide.
Purpose and definitions
Migthy Coli aims at improving the yield and the quality of protein production in bioreactors.
Indeed, production of recombinant proteins by microorganisms such as bacteria ($\small Escherichia$ $\small coli$) or yeasts ($\small Saccharomyces$ $\small cerevisiae$, $\small Pichia$ $\small pastoris$) is a key process in pharmacy (vaccines, insulin) and biotechnology (enzymes, antibodies). The tank in which the protein-producing microorganisms are grown is called a bioreactor. One can define it as a controlled environment where a chemical reaction (in our case, protein synthesis) is catalyzed by micro-organisms.
Heterogeneity in bioreactors
Micro-organisms used to produce recombinant proteins in bioreactors are often seen as a homogeneous population. However, stressed subpopulations may appear, resulting in reduced quantity and quality of the production. Indeed, stressed cells consume nutrients and space but have a reduced productivity [1]. Several factors may induce heterogeneity in a population : desynchronisation in cell cycle phases, emergence of mutants or local variations in physico-chemical conditions within the reactor [2]. Getting rid of these stressed subpopulations might be an effective way to increase both quality and quantity of production in bioreactors.
The Mighty Coli solution
We figured that the underlying problem of population heterogeneity is that the micro-organism do not have any advantage in the production of a $\small Protein$ $\small of$ $\small Interest$ (PI); it's a unnecessary energy charge for the cell. They do not gain in fitness if they produce, and do not lose in fitness if they stop producing. If anything ... it would rather be the opposite!
We thus decided to give microorganisms some incentive to overproduce the PI. That would be done by killing the non-productive bacteria, or that would enter a stressed physiological state.
We used two genetic compounds to apply this principle and design Migthy Coli : the TA system and the 2A peptide.
Toxin-Antitoxin Systems
$\small Toxin$-$\small Antitoxin$ (TA) systems are
two linked genes encoding respectively for a stable toxic protein and an unstable inhibitor of this toxin.
Thus, to ensure the survival of bacteria expressing one of these toxins, the corresponding antitoxin must be continuously expressed in order to compensate its unstability.
TA systems naturally occur in mobile genetic elements such as plasmids, and are used by plasmids to maintain themselves in a microbial population. When a bacterium possessing such a plasmid divides, the generated daughter cells might not inherit a copy of the plasmid due to a stochastic partition. In this case, the antitoxin, unstable, is quickly degraded, allowing the toxin to perform its function and kill the daugther cell in a process known as $\small Post$-$\small Segregational$ $\small Killing$ (PSK) [Fig. 1]. This system allows a plasmid to be selected and maintained in a bacterial population even if it does not confer any advantage for the host. Therefore, TA systems can be seen as selfish entities, virtually making bacteria addicted to them [3].
Figure 1 $:\hspace{0.16cm}$ PSK and plasmid addiction. Cells that inherit a plasmid encoding a TA system can grow normally. As there is no system to part plasmids equivalently in daughter cells, some cells might not receive a plasmid during division. Such cells would still have toxins and antitoxins in their cytosol but these will not be renewed due to the loss of TA genes. Antitoxins are often unstable and quickly degraded by a protease under these conditions, leaving the toxins free and able to kill the cell, effectively eliminating cells losing plasmids that encode TA systems.
TA systems can be divided into three groups, depending on the nature and mode of action of its components [3]. We will mainly use type II TAs in which both components are proteins and the antitoxin binds to the toxin, preventing it from performing its function [Fig. 2]. Toxin functions and structures in type II TA systems are diversified, allowing us to chose how cells will die when stressed. Two systems will be used to illustrate our project : $\small CcdBA$ and $\small Kid/Kis$.
Figure 2 : Type II TA systems. The toxin is a protein that inhibits a vital function of the cell (translation, replication, peptidoglycan synthesis, etc.) and the antitoxin is another protein that binds to this toxin, preventing it from causing harm to the cell. This antitoxin is often unstable and subject to a quick degradation. Should the transcription of the TA operon stops, the antitoxin would swiftly be degraded, allowing the toxin to kill or damage the cell. Type II TA operons are negatively regulated.
CcdBA and the DNA gyrase
CcdBA is the most studied type II TA system where CcdB is the toxin and CcdA the antitoxin. CcdB is an inhibitor of the DNA gyrase, an enzyme that supercoils circular DNA, such as bacterial chromosomes and plasmids, making it more compact. DNA gyrase complexes must bind to DNA to perform negative supercoiling during replication. CcdB binds the DNA gyrase subunit that binds to DNA and inhibits its activity when it is bound to DNA, resulting in DNA double strand breaks due to the progession of the DNA polymerase [Fig. 3a & 3b]. It causes the activation of emergency signals and possibly death of the cell [4].
Figure 3a $:\hspace{0.16cm}$ Simplified model for DNA supercoiling by gyrase & CcdB poisoning [4]. $\hspace{0.2cm}$ When the G-segment of DNA is cleaved and attached to the GyrA (cleveable complex), the T-segment of DNA enters the GyrB clamp (c).$\hspace{0.2cm}$ Upon ATP binding, the GyrB closes and the GyrA is pushed to its open conformation (d).$\hspace{0.2cm}$ In absence of CcdB, the exit gate of GyrA opens and closes to release the T-segment (f) and the configuration returns to (b=g) when ATP is hydrolysed. At this point, another round of supercoiling can start (c-d-f-g) or the G-segment can be religated as in the beginning (b-a).$\hspace{0.2cm}$ But in presence of CcdB, just before the passage of the T-segment, CcdB binds and the cleavable complex is trapped (e).
Figure 3b $:\hspace{0.16cm}$ DNA gyrase mechanism & CcdB poisoning. $\hspace{0.2cm}a)$ The DNA gyrase is a tetramer made of two GyrA and two GyrB subunits. $\hspace{0.2cm}b)$ An undefined DNAsegment (G-segment) can bind between two GyrB subunits. $\hspace{0.2cm}c)$ Another segment (T-segment) binds, situated between both GyrA subunits of the complex. $\hspace{0.2cm}d)$ The gyrase catalyses a double strand break in the G-segment. $\hspace{0.2cm}e)$ The T-segment is translocated from GyrA to GyrB subunits, above the G-segment. $\hspace{0.2cm}f)$ Both ends of the G-segment are joined and supercoiled DNA is released from the complex. $\hspace{0.2cm}g)$ CcdB binds to GyrA subunits. $\hspace{0.2cm}h)$ CcdB prevents the gyrase from joining G-segment ends, resulting in DNA double strand breaks.
We want to build a biological system selecting only highly productive cells. By coupling the production of the Protein of Interest with an antitoxin (A-Tox) in a strain expressing its corresponding toxin, we hope that stressed cells experiencing a drop in PI productivity will be killed by the ensuing drop in A-Tox production. There are many ways to couple the production of two proteins, f.e. polycistronic mRNAs in procaryotes or Internal Ribosome Entry Sites. We chose to use a 2A peptide to pair the PI and the A-Tox.
The 2A Peptide
The 2A peptide sequence (18 amino-acids) allows the post-transcriptional cleavage of 1 ARN sequence into 2 amino-acid sequences: one upstream and one downstream of 2A peptide. This cleavage is done by ribosome skipping between the last amino-acid of the 2A peptide and the first amino-acid of the downstream protein, if this first amino-acid is a proline. It results in the termination of the translation of the upstream mRNA sequence. The ribosome can then continue to translate the downstream sequence into a second, separated protein. Since the downstream protein does not necessarily begins by a prolin, we added the DNA sequence for the prolin at the end of the gene for the 2A peptide. This ensures that the 2A peptide will always be followed by a proline undependantely of the nature of the downstream protein. It is thus this construction of 2A peptide + proline that is referred to as "2A peptide" in the other sections of our project. Hence, the C-terminal extremity of the upstream protein is fused with the 2A peptide, and N-terminal extremity of the downstream protein is fused with the proline we added to the 2A peptide.
A great advantage of the use of the 2A peptide over other methods is that it allows a powerful quality control: the antitoxin will be produced only and only if the upstream protein is correctly translated (or punctually muted, which is very rare). Any premature stop codon or “frame-shift” will be detected.
There are several 2A-like sequences, but a 2A peptide working well within E.coli could not be found in the literature, exceptely some studies about the 2A peptide F2A [5]. However, the 2A peptide P2A was found to works properly in S.cerevisiae. We thus decided to separate our wetlab in two separate projects: on the first hand, we would try to find a 2A peptide that works in procaryotes (Escherichia coli); on the other hand, we will build the Mighty Coli system in eukaryotes (Saccharomyces cerevisiae) using the P2A. We will thus use two different TA systems: ccdB-ccdA for E.coli, and Kid-Kis for S.cerevisiae (respectively Toxin-Antitoxin).
Stability of Mighty Coli
The regulation of natural TA system can be complex, and is not always well understood. Since we want our system to be as simple, as safe and as productive as possible, we decided to use well characterized promoters for our system. We thus decided to synthetize first the toxin and the antitoxin from different plasmids, each under the control of a different promoter and each bearing a different antibiotic resistance gene. The TA system is thus used to boost protein production and the plasmid stability is assured by antibiotic resistance.
Figure 4 :
Distinction between Toxin and Antitoxin Vectors: the plasmid on the left containing the toxin gene (when not added in the bacterial chromosome) and the second plasmid (regulated by the T7 constitutive promoter) containing the protein of interest (RFP/GFP marker) and the antitoxin gene.
Aim
The aim of our project is thus double. On the one hand, we would try to build Mighty Coli into two different chassis (E.coli and S.cerevisiae), and characterize the quantity and quality of their protein production. On the other hand, we will test several 2A peptide sequences to find one that would work efficiently in E.coli.
Bibliography
- [1] H.M. Davey & D.B. Kell, (1996). Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses. Microbiological reviews, 60(4), 641-696.
- [2] S. Müller, H. Harms & T. Bley, (2010). Origin and analysis of microbial population heterogeneity in bioprocesses. Current opinion in biotechnology, 21(1), 100-113.
- [3] F. Hayes & L. Van Melderen, (2011). Toxins-antitoxins: diversity, evolution and function. Critical Reviews in Biochemistry and Molecular Biology, 46(5), 386-408.
- [4] M.H. Dao-Thi, L. Van Melderen, E. De Genst, H. Afif, L. Buts, L. Wyns & R. Loris, (2005). Molecular basis of gyrase poisoning by the addiction toxin CcdB. Journal of molecular biology, 348(5), 1091-1102.
- [5] G.A. Luke, (2012). Translating 2A research into practice, Innovations in Biotechnology, E.C. Agbo ed., ISBN: 978-953-51-0096-6, InTech Croatia, 161-186.
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- Université Libre de Bruxelles -
