Purpose and definitions
Production of recombinant proteins by microorganisms such as bacteria (Escherichia coli) or yeasts (Saccharomyces cerevisiae, Pichia 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 insight
We thought that the underlying problem of population heterogeneity is that micro-organisms do not have any advantage to produce a protein of interest (PI). Such production would be a unnecessary constraint for the cell,
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 toxin-antitoxin systems (TA) and the 2A peptides.
Toxin-Antitoxin Systems
TA systems are operons made of
two linked genes encoding respectively for a stable toxic protein and an unstable inhibitor of this toxin : an antitoxin. TA systems naturally occur in mobile genetic elements such as plasmids and are used to maintain these 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 post-segregational 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 : 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 : CcdBA and 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 at the transcriptionnal level by their respective TA complexes.
CcdBA and the DNA gyrase
CcdBA is the most studied type II TA system, an operon coming from the E.coli fertility factor (F plasmid). CcdB is the toxin and CcdA the antitoxin. CcdB is an inhibitor of the DNA gyrase, an enzyme that negatively supercoils circular DNA, such as bacterial chromosomes and plasmids. In the majority of the organism, the DNA is negatively supercoiled, but during transcription or replication, DNA gets positively supercoiled due to ADN/ARN polymerase activity. The role of gyrase is to reduce the linking number of the DNA by relaxing positive supercoiled DNA. CcdB associates with 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 polymerases during replication or transcription [Fig. 3]. It causes the activation of emergency signals and possibly death of the cell [4].
Figure 3 : DNA gyrase mechanism & CcdB poisoning. a : The DNA gyrase is a tetramer made of two GyrA and two GyrB subunits. b : An undefined DNAsegment (G-segment) can bind between two GyrB subunits. c : Another segment (T-segment) enters the GyrB clamps. d : Upon ATP biding, a conformationnal change occurs. It induces a double strand break in the G-segment and closes the GyrB clamps e : CcdB binds to GyrA subunits. h : CcdB prevents the gyrase from joining G-segment ends, resulting in DNA double strand breaks. f : The T-segment is released on the other side of the G-segment by an transitionnal state of GyrA subunits. g : ATP is hydrolysed to ligate the G-segment and to return the complex to its original conformation. The complex can start a new catalytic cycle of supercoiling.
The Kid/Kis system
The Kid/Kis system (also known as PemK/PemI) is a TA system that stabilizes the R100 plasmid, a plasmid that confers resistance to various compounds such as mercury or antibiotics. Kid is a toxin with endoribonuclease activity [5]. When the Kis antitoxin is not expressed, the Kid toxin inhibits cell growth and metabolism by cleaving mRNAs. Unlike CcdBA, the Kid/Kis system is functional in eukaryotes, making it suitable for developping Mighty Coli in S. cerevisiae.
Why TA systems ?
We want to build a biological system selecting only highly productive cells. By coupling the production of the PI with an antitoxin in a strain expressing the corresponding toxin, we hope that stressed cells experiencing a drop in PI productivity will be killed by the ensuing drop in antitoxin production. There are many ways to couple the production of two proteins, f.e. polycistronic mRNAs in procaryotes or internal ribosome entry sites (IRES). We chose to use a 2A peptide to pair the PI and the antitoxin.
2A Peptides
2A sequences are short peptides (corresponding to 18 amino-acids) encoded in some viral genomes [6]. It allows the production of two different proteins from a single open reading frame : one upstream and one downstream of 2A peptide. This cleavage is done by a ribosome skipping between a glycyl residue of the 2A peptide and the next prolyl of the peptidic sequence. The ribosome can then continue to translate the downstream sequence [Fig 4a] into a second, separated protein. The C-terminal extremity of the upstream protein is fused with the 2A while the N-terminal extremity of the downstream protein is fused with a proline.
The mechanism of this skipping is not yet understood, but it seems that the nascent peptidic chain binds the ribosome [Fig 4b] and inhbits its peptidyl transferase activity during the incorporation of the glycyl residue [7].
Figure 4: Cleavage of the 2A peptide. a) Peptidic sequence of a 2A peptide. The skipping occurs between the penultimate (G) and the last (P) residue of the 2A, resulting in two peptidic chains. b) Proposed mechanism for 2A ribosome skipping. The nascent chain incorporates a glycyl residue and binds the ribosome. This interaction results in an inhibition of ribosomal peptidyl transferase activity and an interruption of the peptidic chain [7].
2A sequences have been well characterized in eukaryotes but not in bacteria (except for the f2A peptde) [8]. Since these two domains of life have different ribosomal structures, 2A functionnality is still to be analysed in bacteria.
2A have an advantage over other methods to pair two proteins : it allows a powerful quality control. Indeed, the second peptide cannot be produced if the first one has been subjected to a frameshifting mutation.
Aim
Mighty Coli will combine the production of a PI with an antitoxin through the use of a 2A peptide ; the antitoxin will be translated first and the toxin will be constitutively expressed by the cell [Figure 5a]. Should PI expression fall due to a stress, antitoxin expression would diminish too, thus killing unproductive stressed cells [Figure 5b]. A frameshift in the PI reading frame will often result in a translation stop and a truncated PI. In Mighty Coli, such frameshifts will abolish antitoxin translation, leading to cell death [Figure 5c]. The PI::2A::Antitoxin plasmid will be stabilized in the population without using antibiotics resistance genes. Should this plasmid be lost, antitoxin expression would fade from the cell and the toxin would kill plasmid-free cells. Toxin genes can be stabilized by being directly integrated into genomic DNA [Figure 5d].
Figure 5 : Mighty Coli features. a : In normal conditions, PI traduction is paired with antitoxin production. Produced antitoxin is able to inhibit toxins and to ensure cell survival. b : Following a stress, PI and antitoxin expression might diminish, ensuring the death of unproductive cells. c : A frameshift in the PI will make translation of the antitoxin impossible, killing cells carrying mutated PI genes. d : Cells losing plasmids carrying the PI will also lose the antitoxin, leading to cell death.
We will have several tasks to do :
- Build plasmids for bacterial systems : One with CcdB and one with GFP::2A::CcdA.
- Build plasmids for yeast systems : One with Kid and one with GFP::2A::Kis.
- Test the cleavage rate of 2A peptides in E.coli.
- Test the activity of toxins with a N-terminal proline.
- Characterize the system to see whether it is functionnal and advantageous over standard production models.
Bibliography
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- [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] J. Zhang, Y. Zhang, L. Zhu, M. Suzuki, & M. Inouye (2004). Interference of mRNA function by sequence-specific endoribonuclease PemK, J. Biol. Chem., 279(20), 20678-20684.
- [6] M.D. Ryan, M.L.L. Donnelly, A. Lewis, A.P. Mehrotra, J. Wilkie & D. Gani, (1999). A model for Nonstoechiometric, Co-translational Protein Scission in Eukaryotic Ribosomes, Bioorganic Chemistry, 27, ISSN 0045-206, 55-798.
- [7] V.A. Doronina, P. de Felipe, C. Wu, P. Sharma, M.S. Sachs, M.D. Ryan & J.D. Brown, (2008). Dissection of a co-translational nascent chain separation event. Biochemical Society Transactions, 36(4), 712-716.
- [8] 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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