Difference between revisions of "Part:BBa K3610038"
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[[File:T--UZurich--NLuc BAK1.png|600px|thumb|none|Figure 1: Average Luminescence Levels over time]] | [[File:T--UZurich--NLuc BAK1.png|600px|thumb|none|Figure 1: Average Luminescence Levels over time]] | ||
− | ====Interpretation of | + | ====Interpretation of Luminescence Assay==== |
As expected the control sample (UT) did not show any luminescence in the presence of the NanoLuc substrate.<br> | As expected the control sample (UT) did not show any luminescence in the presence of the NanoLuc substrate.<br> | ||
eBAK1 coexpressed with eEFR showed a strong increase in luminescence. However, the highest levels were recorded in samples without the bacterial epitope elf18. This was unexpected as the epitope elf18 is the known elicitor to induce ligand-dependent interaction between the EFR receptor and its coreceptor BAK1 in <i>A. thaliana</i>. We later repeated the assay with the EFR ectodomain to get more data. Presence of the bacterial epitope elf18 did not lead to an increase in fluorescence levels again. | eBAK1 coexpressed with eEFR showed a strong increase in luminescence. However, the highest levels were recorded in samples without the bacterial epitope elf18. This was unexpected as the epitope elf18 is the known elicitor to induce ligand-dependent interaction between the EFR receptor and its coreceptor BAK1 in <i>A. thaliana</i>. We later repeated the assay with the EFR ectodomain to get more data. Presence of the bacterial epitope elf18 did not lead to an increase in fluorescence levels again. |
Revision as of 21:29, 22 October 2020
BAK1 ectodomain / LargeBit for S. cerevisiae
This part contains the sequence for the ectodomain of the plant surface receptor BAK1 from A. thaliana fused to the LargeBit of the split NanoLuc system. Additionally, instead of the signal peptide native to the plant receptor, there is the secretion signal of the alpha factor from yeast at the N-terminal domain of the receptor, replacing the original signal sequence.
Usage and Biology
BAK1
The BRI1-associated receptor kinase (BAK1) is a leucin-rich repeat receptor kinase (LRR-RK) which interacts with multiple other LRR-RKs with different functions in hormone signalling and defense response. BAK1 localizes at the plasma membrane and the endosome. The BAK1 protein forms a structure with an extracellular domain with leucin-rich repeats, a single pass transmembrane domain and an intracellular domain with a kinase function.
Among others, BAK1 interacts with the LRR-RKs EF-Tu receptor (EFR), Flagellin sensing 2 (FLS2) and cold-shock protein receptor (CORE), all of which are pathogen recognition receptors (PRR) in brassicaceae plants. Upon binding of a microbe-associated molecular pattern at the LRR domain of the PRR, BAK1 forms a heterodimer with the PRR which triggers a phosphorylation cascade, leading to upregulation of defense mechanisms.
Usage with split-NanoLuc
In this case, the C-terminal domain of BAK1, entailing the intracellular kinase domain, was removed from the sequence. Instead, the LargeBit part of the split-NanoLuc protein domain was fused to the C-terminal domain via a 15 amino acid linker.
Interaction between the BAK1, which is a coreceptor to many other PRRs, is driven by the extracellular ligand-binding domain, further necessary is the transmembrane domain, including the juxtamembrane domain. Therefore, dimerization can be achieved without the intracellular kinase domain. Coexpressed with, for example, Part:BBa_K3610043, which is the PRR EFR that contains the N-terminal domain of the split-mCherry protein instead of the intracellular kinase domain, elf18-induced interaction between BAK1 and EFR is driving the reassembly of the LargeBit and the SmallBit of the NanoLuc luciferase, reconstituting its function to react with furimazine in the presence of oxygen, yielding furimamide and a fluorescent output. During our project, we expressed this part in S. cerevisiae in an attempt to visualize the ligand-dependent interaction between BAK1 and the respective plant PRR. This enables us to use this part, in coordination with different PRRs, to test for the presence of the epitopes which are recognized by the plant receptors.
Characterization
In our iGEM project, we designed a system to sense the presence of bacterial epitopes in water using this part.
We assembled this part with Golden Gate Cloning in a plasmid with a spectinomycin acetyltransferase, a selection marker, and amplified the plasmids in E. coli. The plasmids also contained the TRP1 gene. This encodes phosphoribosylanthranilate isomerase, an enzyme necessary for tryptophan synthesis. This made the same plasmids also suitable for expression in S. cerevisiae. We created plasmids containing this part with different promoters and we also transformed yeast cells with the different types of our plasmid. We had multiple versions of the ADH1 promoter from S. cerevisiae, one version was the full length promoter and the other one a truncated version.
This part was coexpressed in our yeast cells together with different parts, the parts Part:BBa_K3610043 and Part:BBa_K3610051, which encode for the EFR and the CORE receptor ectodomain respectively, with the ectodomains fused to the SmallBit part of the NanoBit system. These plasmids were obtained in the same manner, with the only difference that the selction marker for S. cerevisiae cells was not TRP1 but a gene for Kanamycin resistance.
After coexpressing the BAK1 ectodomain with either EFR of CORE in our yeast cells, a dimerization assay under a fluorometer was performed with a plate reader of the type Synergy H1.
Dimerization Assay
A dimerization assay was performed with samples of S. cerevisiae cells which were transfected with the following receptors (receptor ectodomains fused to the respective NanoBit part are referred to as: eBAK1, eEFR and eCORE):
- Untransformed (UT)
- eBAK1 + eEFR (EFR)
- eBAK1 + eCORE (CORE)
Optical densities (OD600) of all samples were adjusted to 0.34.
For each type of sample, three types of measurements were made:
- 1 µL of deionized water added (no elicitor)
- 1 µL of epitope elf18 added
- 1 µL of epitope csp22 added
Each measurement was done four times with sample size 50µL. To each well 50 µL NanoGlo solution was added (50:1 buffer to furimazine)
The following table contains the results of the plate reader.
Time | T° Lum | UT | UT | UT | UT | UT + csp22 | UT + csp22 | UT + csp22 | UT + csp22 | UT + elf18 | UT + elf18 | UT + elf18 | UT + elf18 | CORE | CORE | CORE | CORE | CORE + csp22 | CORE + csp22 | CORE + csp22 | CORE + csp22 | CORE + elf18 | CORE + elf18 | CORE + elf18 | CORE + elf18 | EFR | EFR | EFR | EFR | EFR + csp22 | EFR + csp22 | EFR + csp22 | EFR + csp22 | EFR + elf18 | EFR + elf18 | EFR + elf18 | EFR + elf18 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
00:01:21 | 22.9 | 10 | 9 | 8 | 8 | 11 | 8 | 8 | 9 | 9 | 8 | 8 | 10 | 339 | 338 | 294 | 261 | 287 | 218 | 237 | 272 | 192 | 205 | 225 | 176 | 1279 | 1438 | 1524 | 1217 | 1160 | 1012 | 1071 | 1023 | 898 | 821 | 735 | 680 |
00:06:21 | 22.9 | 10 | 9 | 9 | 10 | 9 | 9 | 8 | 8 | 8 | 9 | 9 | 9 | 386 | 348 | 303 | 259 | 282 | 245 | 240 | 270 | 207 | 214 | 196 | 173 | 1258 | 1468 | 1409 | 1193 | 1079 | 955 | 958 | 973 | 931 | 840 | 739 | 718 |
00:11:21 | 23 | 8 | 9 | 10 | 8 | 8 | 9 | 8 | 10 | 8 | 8 | 8 | 8 | 392 | 379 | 302 | 296 | 309 | 239 | 264 | 271 | 209 | 204 | 199 | 168 | 1247 | 1369 | 1359 | 1160 | 992 | 869 | 932 | 933 | 956 | 914 | 814 | 760 |
00:16:21 | 23 | 11 | 8 | 9 | 9 | 8 | 10 | 8 | 9 | 9 | 9 | 9 | 9 | 409 | 357 | 325 | 301 | 307 | 241 | 265 | 254 | 214 | 199 | 197 | 171 | 1140 | 1314 | 1345 | 1120 | 979 | 860 | 1011 | 1010 | 969 | 901 | 853 | 801 |
00:21:21 | 23.1 | 9 | 9 | 9 | 10 | 10 | 10 | 8 | 8 | 9 | 8 | 10 | 9 | 401 | 375 | 305 | 300 | 295 | 253 | 244 | 279 | 216 | 194 | 207 | 166 | 1060 | 1234 | 1247 | 1072 | 993 | 871 | 1015 | 1037 | 955 | 889 | 806 | 812 |
00:26:21 | 23.1 | 9 | 11 | 9 | 10 | 9 | 9 | 9 | 9 | 9 | 9 | 8 | 8 | 398 | 395 | 318 | 273 | 295 | 238 | 254 | 256 | 212 | 203 | 183 | 169 | 997 | 1202 | 1199 | 1007 | 985 | 877 | 986 | 1003 | 911 | 876 | 827 | 821 |
00:31:21 | 23.1 | 8 | 9 | 9 | 8 | 9 | 9 | 9 | 9 | 8 | 9 | 8 | 9 | 404 | 369 | 310 | 294 | 303 | 238 | 267 | 230 | 204 | 192 | 165 | 157 | 964 | 1098 | 1077 | 943 | 988 | 843 | 970 | 978 | 865 | 859 | 808 | 824 |
00:36:21 | 23.2 | 10 | 10 | 9 | 8 | 8 | 8 | 9 | 8 | 8 | 9 | 9 | 8 | 405 | 387 | 290 | 282 | 290 | 239 | 232 | 231 | 194 | 196 | 175 | 160 | 906 | 1071 | 1061 | 909 | 946 | 834 | 952 | 984 | 861 | 816 | 795 | 809 |
00:41:21 | 23.2 | 9 | 8 | 9 | 9 | 9 | 9 | 9 | 8 | 8 | 11 | 8 | 8 | 407 | 380 | 270 | 292 | 304 | 239 | 256 | 228 | 203 | 188 | 161 | 146 | 883 | 1037 | 1023 | 895 | 882 | 824 | 923 | 968 | 803 | 843 | 789 | 795 |
00:46:21 | 23.2 | 11 | 8 | 9 | 8 | 8 | 9 | 8 | 12 | 8 | 11 | 8 | 8 | 413 | 364 | 266 | 272 | 269 | 220 | 240 | 222 | 192 | 169 | 170 | 149 | 865 | 992 | 978 | 868 | 889 | 790 | 882 | 894 | 784 | 779 | 780 | 797 |
00:51:21 | 23.3 | 9 | 9 | 8 | 13 | 9 | 8 | 9 | 10 | 8 | 8 | 12 | 9 | 383 | 355 | 266 | 247 | 274 | 227 | 222 | 213 | 189 | 151 | 162 | 140 | 821 | 933 | 964 | 864 | 849 | 749 | 871 | 875 | 819 | 782 | 759 | 741 |
00:56:21 | 23.3 | 9 | 9 | 8 | 10 | 9 | 8 | 9 | 9 | 9 | 8 | 10 | 9 | 388 | 369 | 269 | 272 | 266 | 204 | 222 | 195 | 182 | 166 | 137 | 138 | 823 | 918 | 952 | 835 | 800 | 726 | 835 | 846 | 787 | 765 | 716 | 746 |
01:01:21 | 23.3 | 9 | 10 | 9 | 9 | 9 | 8 | 9 | 9 | 9 | 8 | 9 | 8 | 379 | 349 | 235 | 228 | 273 | 221 | 208 | 184 | 164 | 158 | 145 | 133 | 755 | 884 | 879 | 821 | 788 | 687 | 850 | 902 | 779 | 731 | 727 | 746 |
01:06:21 | 23.3 | 8 | 10 | 9 | 10 | 9 | 9 | 9 | 11 | 9 | 8 | 9 | 10 | 376 | 340 | 223 | 238 | 263 | 208 | 194 | 195 | 176 | 152 | 140 | 121 | 745 | 851 | 855 | 760 | 804 | 697 | 809 | 834 | 754 | 722 | 710 | 715 |
01:11:21 | 23.3 | 9 | 8 | 9 | 8 | 8 | 10 | 8 | 9 | 10 | 9 | 8 | 9 | 346 | 339 | 238 | 216 | 242 | 211 | 190 | 175 | 162 | 138 | 131 | 119 | 739 | 838 | 843 | 765 | 739 | 708 | 783 | 791 | 739 | 713 | 720 | 732 |
01:16:21 | 23.3 | 9 | 9 | 8 | 9 | 9 | 9 | 9 | 9 | 11 | 10 | 9 | 9 | 345 | 345 | 189 | 218 | 247 | 199 | 189 | 165 | 149 | 127 | 135 | 133 | 722 | 820 | 799 | 754 | 730 | 650 | 770 | 792 | 680 | 708 | 680 | 703 |
01:21:21 | 23.3 | 8 | 8 | 10 | 10 | 9 | 10 | 10 | 8 | 9 | 9 | 8 | 10 | 345 | 319 | 203 | 214 | 250 | 195 | 188 | 169 | 148 | 148 | 127 | 127 | 720 | 794 | 794 | 746 | 716 | 646 | 707 | 788 | 716 | 679 | 663 | 678 |
01:26:21 | 23.3 | 9 | 9 | 9 | 9 | 9 | 10 | 10 | 9 | 9 | 10 | 10 | 10 | 347 | 326 | 199 | 212 | 244 | 189 | 189 | 159 | 159 | 128 | 136 | 121 | 693 | 799 | 779 | 720 | 697 | 619 | 753 | 762 | 698 | 650 | 645 | 695 |
01:31:21 | 23.3 | 9 | 9 | 9 | 9 | 9 | 8 | 9 | 9 | 9 | 11 | 9 | 9 | 326 | 309 | 188 | 216 | 225 | 187 | 180 | 157 | 140 | 117 | 125 | 113 | 659 | 775 | 738 | 709 | 702 | 607 | 726 | 737 | 699 | 642 | 630 | 670 |
01:36:21 | 23.3 | 9 | 9 | 9 | 8 | 9 | 9 | 9 | 9 | 9 | 8 | 8 | 8 | 347 | 295 | 170 | 197 | 224 | 180 | 168 | 157 | 148 | 114 | 109 | 100 | 668 | 722 | 733 | 678 | 664 | 580 | 666 | 700 | 633 | 655 | 598 | 647 |
01:41:21 | 23.3 | 9 | 10 | 10 | 9 | 10 | 9 | 8 | 9 | 9 | 9 | 10 | 10 | 313 | 298 | 178 | 186 | 225 | 189 | 159 | 148 | 133 | 117 | 123 | 97 | 635 | 683 | 699 | 652 | 651 | 577 | 679 | 729 | 647 | 604 | 585 | 607 |
01:46:21 | 23.3 | 9 | 8 | 9 | 10 | 8 | 8 | 10 | 8 | 9 | 10 | 10 | 11 | 302 | 293 | 160 | 181 | 220 | 170 | 167 | 144 | 130 | 120 | 113 | 109 | 660 | 713 | 701 | 622 | 640 | 574 | 657 | 650 | 621 | 607 | 579 | 606 |
01:51:21 | 23.3 | 11 | 10 | 9 | 9 | 9 | 9 | 9 | 8 | 9 | 10 | 8 | 9 | 296 | 283 | 164 | 160 | 216 | 172 | 149 | 145 | 119 | 98 | 113 | 106 | 603 | 676 | 662 | 610 | 624 | 564 | 641 | 673 | 607 | 582 | 550 | 597 |
01:56:21 | 23.3 | 9 | 8 | 8 | 10 | 9 | 8 | 9 | 10 | 9 | 10 | 10 | 10 | 283 | 257 | 147 | 161 | 194 | 159 | 139 | 138 | 123 | 108 | 115 | 108 | 609 | 656 | 660 | 610 | 594 | 540 | 651 | 625 | 590 | 564 | 550 | 584 |
02:01:21 | 23.3 | 8 | 9 | 9 | 9 | 9 | 9 | 9 | 10 | 9 | 11 | 9 | 9 | 282 | 264 | 150 | 169 | 178 | 162 | 141 | 133 | 119 | 94 | 118 | 102 | 598 | 652 | 626 | 627 | 586 | 524 | 618 | 630 | 575 | 561 | 551 | 598 |
Of all 4 measurements, the average was taken an is summarized in the chart below.
Interpretation of Luminescence Assay
As expected the control sample (UT) did not show any luminescence in the presence of the NanoLuc substrate.
eBAK1 coexpressed with eEFR showed a strong increase in luminescence. However, the highest levels were recorded in samples without the bacterial epitope elf18. This was unexpected as the epitope elf18 is the known elicitor to induce ligand-dependent interaction between the EFR receptor and its coreceptor BAK1 in A. thaliana. We later repeated the assay with the EFR ectodomain to get more data. Presence of the bacterial epitope elf18 did not lead to an increase in fluorescence levels again.
eBAK1 coexpressed with eCORE showed an increase in luminescence, although the effect was much smaller when compared with eEFR. The results again suggest, that addition of the bacterial elicitor csp22, which initiates interaciton between CORE and BAK1 does not increase the luminescence levels as samples without csp22 added showed greater luminescence than samples which were treated with this bacterial epitope.
These results led us to the conclusion that our plasmids get expressed. It further has been shown that the NanoBit parts fused to the receptors are able to interact and reconstitute their functionality as a funcitonal NanoLuc protein which catalyzes the reaction of furimazine to furimamide, which gives a luminescent output. In our case, however, receptor-specific bacterial epitopes did not increase luminescence levels when the receptors were expressed in S. cerevisiae.
Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Illegal PstI site found at 848
Illegal PstI site found at 893 - 12INCOMPATIBLE WITH RFC[12]Illegal PstI site found at 848
Illegal PstI site found at 893 - 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 1278
- 23INCOMPATIBLE WITH RFC[23]Illegal PstI site found at 848
Illegal PstI site found at 893 - 25INCOMPATIBLE WITH RFC[25]Illegal PstI site found at 848
Illegal PstI site found at 893 - 1000COMPATIBLE WITH RFC[1000]