Team:Jilin China/Part Collection


Part Collection

  • Abstract

    This year, Jilin_China made a RNA-based thermosensor toolkit for users, which includes four types of RNA-based thermosensors: heat-inducible, heat-repressible, cold-inducible and cold-repressible RNA-based thermosensors. But due to the numbers of cold-inducible RNA-based thermosensors is less than 10, which can't meet the number requirement(more than 10) of collection, we added three types of collections to the parts registry as follows:

    heat-inducible RNA-based thermosensor collection, heat-repressible RNA-based thermosensor collection and cold-repressible RNA-based thermosensor collection.

    In order to make it easier for users to select an appropriate RNA-based thermosensor, we also developed a search engine for our toolkit, you can click here to enter the search engine page.

    The introduction of each type of part collection is as follows:

  • Heat-inducible RNA-based thermosensor collection

    In this collection, we provide a total of 48 different Heat-inducible RNA-based thermosensors, which can regulate the expression of genes with the changed temperature. The RNA-based thermosensors we designed has been characterized and mathematically fitted to prove that they have different melting temperature, expression intensity and sensitivity. Users can choose the appropriate RNA-based thermosensors according to their own needs.

    Heat-inducible RNA-based thermosensor collection contains these parts:

    Part NamePart Number
    Heat-inducible RNA-based thermosensor-1BBa_K2541001
    Heat-inducible RNA-based thermosensor-2BBa_K2541002
    Heat-inducible RNA-based thermosensor-3BBa_K2541003
    Heat-inducible RNA-based thermosensor-4BBa_K2541004
    Heat-inducible RNA-based thermosensor-5BBa_K2541005
    Heat-inducible RNA-based thermosensor-6BBa_K2541006
    Heat-inducible RNA-based thermosensor-7BBa_K2541007
    Heat-inducible RNA-based thermosensor-8BBa_K2541008
    Heat-inducible RNA-based thermosensor-9BBa_K2541009
    Heat-inducible RNA-based thermosensor-10BBa_K2541010
    Heat-inducible RNA-based thermosensor-11BBa_K2541011
    Heat-inducible RNA-based thermosensor-12BBa_K2541012
    Heat-inducible RNA-based thermosensor-13BBa_K2541013
    Heat-inducible RNA-based thermosensor-14BBa_K2541014
    Heat-inducible RNA-based thermosensor-15BBa_K2541015
    Heat-inducible RNA-based thermosensor-16BBa_K2541016
    Heat-inducible RNA-based thermosensor-17BBa_K2541017
    Heat-inducible RNA-based thermosensor-18BBa_K2541018
    Heat-inducible RNA-based thermosensor-19BBa_K2541019
    Heat-inducible RNA-based thermosensor-20BBa_K2541020
    Heat-inducible RNA-based thermosensor-21BBa_K2541021
    Heat-inducible RNA-based thermosensor-25BBa_K2541025
    Heat-inducible RNA-based thermosensor-26BBa_K2541026
    Heat-inducible RNA-based thermosensor-27BBa_K2541027
    Heat-inducible RNA-based thermosensor-28BBa_K2541028
    Heat-inducible RNA-based thermosensor-29BBa_K2541029
    Heat-inducible RNA-based thermosensor-30BBa_K2541030
    Heat-inducible RNA-based thermosensor-31BBa_K2541031
    Heat-inducible RNA-based thermosensor-32BBa_K2541032
    Heat-inducible RNA-based thermosensor-33BBa_K2541033
    Heat-inducible RNA-based thermosensor-34BBa_K2541034
    Heat-inducible RNA-based thermosensor-35BBa_K2541035
    Heat-inducible RNA-based thermosensor-36BBa_K2541036
    Heat-inducible RNA-based thermosensor-37BBa_K2541037
    Heat-inducible RNA-based thermosensor-38BBa_K2541038
    Heat-inducible RNA-based thermosensor-39BBa_K2541039
    Heat-inducible RNA-based thermosensor-40BBa_K2541040
    Heat-inducible RNA-based thermosensor-41BBa_K2541041
    Heat-inducible RNA-based thermosensor-42BBa_K2541042
    Heat-inducible RNA-based thermosensor-43BBa_K2541043
    Heat-inducible RNA-based thermosensor-44BBa_K2541044
    Heat-inducible RNA-based thermosensor-45BBa_K2541045
    Heat-inducible RNA-based thermosensor-46BBa_K2541046
    Heat-inducible RNA-based thermosensor-47BBa_K2541047
    Heat-inducible RNA-based thermosensor-48BBa_K2541048
    Heat-inducible RNA-based thermosensor-49BBa_K2541049
    Heat-inducible RNA-based thermosensor-50BBa_K2541050
    Heat-inducible RNA-based thermosensor-51BBa_K2541051

    Heat-inducible RNA-based thermosensor collection can cover melting temperature from 33 to 55 degrees with different intensity and sensitivity.

    For more detailed principles of Heat-inducible RNA-based thermosensors, you can read our design page.

    >Click here to read the design of the Heat-inducible RNA-based thermosensors!<
  • Heat-repressible RNA-based thermosensor collection

    In order to make our RNA-based thermosensor toolkit more suitable for users' needs, we updated the toolkit to version 2.0. We added the RNase E-based heat-repressible RNA-based thermosensors, including 23 different thermosensors. The stem-loop structure of the thermosensor contains the RNase E cleavage site. At the elevated temperature, the cleavage site is exposed, and the mRNA will be degraded, which turns the translation off.

    Heat-repressible RNA-based thermosensor collection contain these parts:

    Part NamePart Number
    Heat-repressible RNA-based thermosensor-1BBa_K2541101
    Heat-repressible RNA-based thermosensor-2BBa_K2541102
    Heat-repressible RNA-based thermosensor-3BBa_K2541103
    Heat-repressible RNA-based thermosensor-4BBa_K2541104
    Heat-repressible RNA-based thermosensor-5BBa_K2541105
    Heat-repressible RNA-based thermosensor-6BBa_K2541106
    Heat-repressible RNA-based thermosensor-8BBa_K2541108
    Heat-repressible RNA-based thermosensor-9BBa_K2541109
    Heat-repressible RNA-based thermosensor-10BBa_K2541110
    Heat-repressible RNA-based thermosensor-11BBa_K2541111
    Heat-repressible RNA-based thermosensor-12BBa_K2541112
    Heat-repressible RNA-based thermosensor-13BBa_K2541113
    Heat-repressible RNA-based thermosensor-14BBa_K2541114
    Heat-repressible RNA-based thermosensor-15BBa_K2541115
    Heat-repressible RNA-based thermosensor-16BBa_K2541116
    Heat-repressible RNA-based thermosensor-17BBa_K2541117
    Heat-repressible RNA-based thermosensor-18BBa_K2541118
    Heat-repressible RNA-based thermosensor-19BBa_K2541119
    Heat-repressible RNA-based thermosensor-20BBa_K2541120
    Heat-repressible RNA-based thermosensor-21BBa_K2541121
    Heat-repressible RNA-based thermosensor-22BBa_K2541122
    Heat-repressible RNA-based thermosensor-23BBa_K2541123

    For more detailed principles of Heat-repressible RNA-based thermosensors, you can read our design page.

    >Click here to read the design of the Heat-repressible RNA-based thermosensors!<
  • Cold-inducible RNA-based thermosensor collection

    To expand the melting temprerature range of the thermosenor, we have made a second upgrade to the toolkit. In toolkit 3.0, we added cold-repressible and cold-inducible RNA thermosenor, and made 8 cold-inducible RNA-based thermosensors into the part collection.

    Cold-inducible RNA-based thermosensor collection contains these parts:

    Part NamePart Number
    Cold-inducible RNA-based thermosensor-1BBa_K2541301
    Cold-inducible RNA-based thermosensor-2BBa_K2541302
    Cold-inducible RNA-based thermosensor-3BBa_K2541303
    Cold-inducible RNA-based thermosensor-4BBa_K2541304
    Cold-inducible RNA-based thermosensor-5BBa_K2541305
    Cold-inducible RNA-based thermosensor-6BBa_K2541306
    Cold-inducible RNA-based thermosensor-7BBa_K2541307
    Cold-inducible RNA-based thermosensor-8BBa_K2541308

    For more detailed principles of Cold-inducible RNA-based thermosensors, you can read our design page.

    >Click here to read the design of the Cold-inducible RNA-based thermosensors!<
  • Cold-repressible RNA-based thermosensor collection

    To expand the melting temprerature range of the thermosenor, we have made a second upgrade to the toolkit. In toolkit 3.0, we added cold-repressible and cold-inducible RNA thermosenor, and made 10 cold-repressible RNA-based thermosensors into a part collection.

    Cold-repressible RNA-based thermosensor is based on the RNase III. The stem-loop of the thermosensor mRNA contains the recognition and cleavage site of RNase III. When the temperature is lower than the melting temperature, the RNase III will degrade the mRNA.

    Cold-repressible RNA-based thermosensor collection contain these parts:

    Part NamePart Number
    Cold-repressible RNA-based thermosensor-1BBa_K2541201
    Cold-repressible RNA-based thermosensor-2BBa_K2541202
    Cold-repressible RNA-based thermosensor-3BBa_K2541203
    Cold-repressible RNA-based thermosensor-4BBa_K2541204
    Cold-repressible RNA-based thermosensor-5BBa_K2541205
    Cold-repressible RNA-based thermosensor-6BBa_K2541206
    Cold-repressible RNA-based thermosensor-7BBa_K2541207
    Cold-repressible RNA-based thermosensor-8BBa_K2541208
    Cold-repressible RNA-based thermosensor-9BBa_K2541209
    Cold-repressible RNA-based thermosensor-10BBa_K2541210

    For more detailed principles of Cold-repressible RNA-based thermosensors, you can read our design page.

    >Click here to read the design of the Cold-repressible RNA-based thermosensors!<
  • References

    • [1] Sen S, Apurva D, Satija R, et al. Design of a Toolbox of RNA Thermometers[J]. Acs Synthetic Biology, 2017, 6(8).
    • [2] Hoynes-O’Connor, A., Hinman, K., Kirchner, L., and Moon, T.S. (2015) De novo design of heat-repressible RNA thermosensors in E.coli. Nucleic Acids Res. 43, 6166−6179.
    • [3] Pertzev A V, Nicholson A W. Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III[J]. Nucleic Acids Research, 2006, 34(13):3708-3721.
    • [4] Giuliodori A M, Pietro F D, Marzi S, et al. The cspA, mRNA Is a Thermosensor that Modulates Translation of the Cold-Shock Protein CspA[J]. Molecular Cell, 2010, 37(1):21-33.
    • [5] Engler C, Kandzia R, Marillonnet S. A one pot, one step, precision cloning method with high throughput capability[J]. Plos One, 2008, 3(11):e3647.