Translation-coupling systems
Disclosed are systems and methods for coupling translation of a target gene to a detectable response gene. A version of the invention includes a translation-coupling cassette. The translation-coupling cassette includes a target gene, a response gene, a response-gene translation control element, and a secondary structure-forming sequence that reversibly forms a secondary structure masking the response-gene translation control element. Masking of the response-gene translation control element inhibits translation of the response gene. Full translation of the target gene results in unfolding of the secondary structure and consequent translation of the response gene. Translation of the target gene is determined by detecting presence of the response-gene protein product. The invention further includes RNA transcripts of the translation-coupling cassettes, vectors comprising the translation-coupling cassettes, hosts comprising the translation-coupling cassettes, methods of using the translation-coupling cassettes, and gene products produced with the translation-coupling cassettes.
1. A translation-coupling cassette comprising:
a target gene or a target-gene cloning site;
a response gene or a response-gene cloning site;
a response-gene translation control element that, in a transcript of the translation-coupling cassette, controls translation of the response gene or a response gene inserted in the response-gene cloning site; and
a secondary structure-forming sequence that, in the transcript of the translation-coupling cassette, reversibly forms a secondary structure that masks the response-gene translation control element, wherein at least part of the secondary structure that masks the response-gene translation control element is translationally linked with the target-gene cloning site or the target gene, and wherein the secondary structure is configured to confer increased response-gene translation with full target-gene translation compared to any response-gene translation without full target-gene translation.
2. The translation-coupling cassette of claim 1 wherein the target-gene cloning site or the response-gene cloning site includes a multiple cloning site.
3. The translation-coupling cassette of claim 1 wherein the target-gene cloning site or the response-gene cloning site includes a ligation-independent cloning site.
4. The translation-coupling cassette of claim 1 further comprising a protein tag-encoding sequence, wherein the protein tag-encoding sequence is translationally linked with the target-gene cloning site or translationally linked in-frame with the target gene.
5. The translation-coupling cassette of claim 1 wherein the response gene is a screenable gene.
6. The translation-coupling cassette of claim 1 wherein the response gene is a selectable gene.
7. The translation-coupling cassette of claim 1 wherein the response-gene translation control element is a ribosome binding site.
8. The translation-coupling cassette of claim 7 wherein the ribosome binding site comprises a Shine-Dalgarno sequence or derivative thereof.
9. The translation-coupling cassette of claim 7 wherein the ribosome binding site comprises an AT-rich sequence.
10. The translation-coupling cassette of claim 1 further comprising a linker disposed between the response-gene translation control element and the response gene or the response-gene cloning site.
11. The translation-coupling cassette of claim 1 further including a stop codon upstream, within, or downstream of the secondary structure-forming sequence, the stop codon being translationally linked with the target-gene cloning site or translationally linked in-frame with the target gene.
12. The translation-coupling cassette of claim 1 wherein the secondary structure formed by the secondary structure-forming sequence in the transcript includes a stem loop.
13. The translation-coupling cassette of claim 1 wherein the secondary structure-forming sequence at least partially includes the response-gene translation control element.
14. The translation-coupling cassette of claim 13 wherein the secondary structure-forming sequence further includes a stop codon, the stop codon being translationally linked with the target-gene cloning site or translationally linked in-frame with the target gene.
15. The translation-coupling cassette of claim 14 wherein the secondary structure-forming sequence at least partially includes a protein tag-encoding sequence, wherein the protein tag-encoding sequence is translationally linked with the target-gene cloning site or translationally linked in-frame with the target gene.
16. The translation-coupling cassette of claim 1 wherein the secondary structure-forming sequence is selected from the group consisting of bases 18-46 of SEQ ID NO:1, bases 26-60 of SEQ ID NO:2, bases 26-60 of SEQ ID NO:3, bases 26-60 of SEQ ID NO:4, and bases 5-51 of SEQ ID NO:5.
17. The translation-coupling cassette of claim 1 wherein the translation-coupling cassette is included within a vector capable of being introduced in a host.
18. The translation-coupling cassette of claim 1 wherein the translation-coupling cassette is encompassed within a host.
19. The translation-coupling cassette claim 18 wherein the host is a prokaryote.
20. A method of assessing expression including:
introducing a translation-coupling cassette into a host, wherein the translation-coupling cassette comprises:
a target gene;
a response gene;
a response-gene translation control element that, in a transcript of the translation-coupling cassette, controls translation of the response gene; and
a secondary structure-forming sequence that, in the transcript of the translation-coupling cassette, reversibly forms a secondary structure that masks the response-gene translation control element, wherein at least part of the secondary structure that masks the response-gene translation control element is translationally linked with the target gene, and wherein the secondary structure is configured to confer increased response-gene translation with full target-gene translation compared to any response-gene translation without full target-gene translation; and
determining a level of response-gene expression.
21. The method of claim 20 further including
generating a mutated version of the target gene;
cloning the mutated version of the target gene into a second translation-coupling cassette;
introducing the second translation-coupling cassette into a second host of same type as the host;
determining a level of response-gene expression in the second host; and
comparing the level of response-gene expression in the host with the level of response-gene expression in the second host.
22. The method of claim 20 further including, prior to the determining step, culturing the host in a plurality of culture conditions, wherein the determining the level of response-gene expression includes determining a level of response-gene expression for each of the plurality of culture conditions, and further including comparing the levels of response-gene expression for each of the plurality of culture conditions.
23. The method of claim 20 wherein the introducing step further includes introducing and expressing a clone from a DNA library.
24. The translation-coupling cassette of claim 1 wherein the at least the part of the secondary structure-forming sequence is translationally linked with the target-gene cloning site or the target gene such that the response gene is translationally coupled to the target gene or a target gene formed with the response-gene cloning site.
25. A translation-coupling cassette comprising:
a target gene or a target-gene cloning site;
a response gene or a response-gene cloning site;
a response-gene translation control element that, in a transcript of the translation-coupling cassette, controls translation of the response gene or a response gene inserted in the response-gene cloning site; and
a secondary structure-forming sequence that, in the transcript of the translation-coupling cassette, reversibly forms a secondary structure that masks the response-gene translation control element, wherein the secondary structure comprises a base-paired portion comprising at least a portion of the response-gene translation control element, wherein the base-paired portion of the secondary structure is translationally linked with the target-gene cloning site or the target gene, and wherein the secondary structure is configured to confer increased response-gene translation with full target-gene translation compared to any response-gene translation without full target-gene translation.
26. A translation-coupling cassette comprising:
a target gene or a target-gene cloning site;
a response gene or a response-gene cloning site;
a response-gene translation control element that, in a transcript of the translation-coupling cassette, controls translation of the response gene or a response gene inserted in the response-gene cloning site; and
a secondary structure-forming sequence that, in the transcript of the translation-coupling cassette, reversibly forms a secondary structure that masks the response-gene translation control element, wherein translation of the target gene or a target gene inserted in the target-gene cloning site unmasks the response-gene translation control element, and wherein the secondary structure is configured to confer increased response-gene translation with full target-gene translation compared to any response-gene translation without full target-gene translation.