Cell-free protein synthesis platforms derived from clostridia extracts
Disclosed are compositions, methods, and kits for performing cell-free RNA transcription and/or cell-free protein synthesis (CFPS). The disclosed compositions, methods, and kits include or utilize components prepared from a species of Clostridia such as cellular extracts from Clostridium autoethanogenum.
1. A cell-free protein synthesis platform for in vitro transcription of mRNA and in vitro translation of polypeptides, the platform comprising as a component a cellular extract prepared from a cell culture of a species of Clostridia, wherein the species of Clostridia is engineered to express an upregulated gene product that is a positive effector for cell-free protein synthesis (CFPS), and wherein the positive effector for CFPS is the Clostridia homolog of E. coli ackA.
2. The platform of claim 1 , wherein the species of Clostridia is Clostridium autoethanogenum.
3. The platform of claim 1 , wherein the species of Clostridia is engineered to be deficient in a negative effector for cell-free protein synthesis (CFPS).
4. The platform of claim 3 , wherein the negative effector for CFPS is selected from the group consisting of the Clostridia homolog of E. coli endA, mazF, rna, rnb, rne, gar, lon, ompT, gdhA, gshA, sdaA, sdaB, speA, WaaL, tnaA, glpK, and any combination thereof.
5. The platform of claim 1 , wherein the species of Clostridia is engineered to express an additional positive effector for CFPS, wherein the additional positive effector for CFPS is selected from the group consisting of the Clostridia homolog of E. coli ndk, pykF, cdd, dsbC, dnaK, dnaJ, crpE, tig, groS, groL, infA, injB, fusA, efp, lepA, tujB, hslR, ffr, and any combination thereof.
6. The platform of claim 1 , wherein the species of Clostridia is engineered to be deficient in a release factor 1.
7. The platform of claim 1 , wherein the species of Clostridia has been engineered to express T7 RNA polymerase.
8. The platform of claim 1 , wherein the cell culture is in stationary phase defined as the cell culture having an OD 600 of greater than about 3.0.
9. The platform of claim 1 , wherein cellular extract is prepared from cells that are harvested from a continuous cell culture.
10. The platform of claim 1 , wherein the cellular extract comprises an S12 fraction and/or S30 fraction of the cell culture.
11. The platform of claim 1 further comprising: a reaction buffer; an RNA polymerase; and a transcription template, wherein the RNA polymerase is capable of transcribing the transcription template to form a translation template and the cellular extract can sustain protein synthesis through a combined transcription/translation reaction.
12. The platform of claim 1 further comprising one or more components selected from the group consisting of amino acids, salts, a macromolecular crowding agent, cofactors, an energy source comprising phosphoenol pyruvate (PEP) at a concentration of greater than about 30 mM but less than about 100 mM, a translation template, a transcription template, a DNA dependent RNA polymerase.
13. The platform of claim 1 further comprising magnesium (Mg + ) at a concentration greater than about 1 mM, but less than about 60 mM.
14. The platform of claim 1 further comprising potassium (K + ) at a concentration greater than about 10 mM, but less than about 500 mM.
15. The platform of claim 1 , wherein the platform or one or more components thereof are preserved by freeze-drying.
16. A method for in vitro transcription of mRNA and translation of mRNA to prepare a polypeptide, the method comprising transcribing the mRNA from a transcription template and translating an mRNA in the platform of claim 1 .
17. A kit comprising as components: (a) a cellular extract prepared from a cell culture of a species of Clostridia; and (b) a reaction mixture for transcribing and/or translating an mRNA in the cellular extract.
18. A recombinant Clostridium autoethanogenum engineered to be deficient in a negative effector for cell-free protein synthesis (CFPS).
19. A method for identifying and characterizing genetic parts of Clostridia and gene expression of Clostridia used for transcription and/or translation, the method comprising:
(a) creating a test library of genetic parts or variant gene sequences of Clostridia; and
(b) testing the genetic parts of the test library and/or an alternative codon expressed in the platform of claim 1 .