Coding

Part:BBa_K1150006

Designed by: Freiburg 2013   Group: iGEM13_Freiburg   (2013-09-16)
Revision as of 00:48, 9 October 2013 by TU Munich (Talk | contribs) (→‎Sequence and Features)

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UVR8

UVR8
Function UVB receptor
Use in Mammalians and plants
RFC standard RFC 25
Backbone pSB1C3
Organism Arabidopsis thaliana
Source AG Weber, Freiburg
Submitted by [http://2013.igem.org/Team:Freiburg Freiburg 2013]

Sunlight is essential for plants: Not only as an energy source but also as information for their growth cycle. Therefore they need receptors to detect different light wavelengths. Ultraviolet B (UVB) light can be perceived with photoreceptor UV resistance Locus 8 (UVR8) [1]. This receptor derives from Arapidopsis thaliana and contains its core domain (amino acids 12-381) [2]. The receptor reacts best to light of the wavelength 311 nm.

Biology and Usage

In the absence of UVB light UVR8 forms homodimers. This is its closed configuration. When UVB light is perceived UVR8 monomerizes and changes into its open configuration. UVR8 is then able to recruit COP1 [2]. This interaction is disrupted when UVB radiation stops. Plants use this mechanism to perceive UVB light and respond with photomorphogenesis or react to UVB induced stress [3].

Freiburg 2013 used this part to engineer a UVB light induced mechanism to activate gene expression. You need a combination of these BioBricks: Cas9-UVR8, COP1-VP16, RNAimer

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 37
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI site found at 52


Protein data table for BioBrick BBa_K1150006 automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)
 ATGGCCGGCGCTCCTCCT ... GTCGATGGAACCGGT
 ORF from nucleotide position -8 to 1116 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 
301 		MAGAPPRKVLIISAGASHSVALLSGDIVCSWGRGEDGQLGHGDAEDRPSPTQLSALDGHQIVSVTCGADHTVAYSQSGMEVYSWGWGDFGRLGHGNSSDL
FTPLPIKALHGIRIKQIACGDSHCLAVTMEGEVQSWGRNQNGQLGLGDTEDSLVPQKIQAFEGIRIKMVAAGAEHTAAVTEDGDLYGWGWGRYGNLGLGD
RTDRLVPERVTSTGGEKMSMVACGWRHTISVSYSGALYTYGWSKYGQLGHGDLEDHLIPHKLEALSNSFISQISGGWRHTMALTSDGKLYGWGWNKFGQV
GVGNNLDQCSPVQVRFPDDQKVVQVSCGWRHTLAVTERNNVFAWGRGTNGQLGIGESVDRNFPKIIEALSVDGTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
None of the supported features appeared in the sequence
Amino acid composition:
Ala (A)25 (6.7%)
Arg (R)18 (4.8%)
Asn (N)12 (3.2%)
Asp (D)23 (6.1%)
Cys (C)7 (1.9%)
Gln (Q)18 (4.8%)
Glu (E)16 (4.3%)
Gly (G)56 (14.9%)
His (H)14 (3.7%)
Ile (I)18 (4.8%)
Leu (L)30 (8.0%)
Lys (K)12 (3.2%)
Met (M)7 (1.9%)
Phe (F)8 (2.1%)
Pro (P)12 (3.2%)
Ser (S)31 (8.3%)
Thr (T)19 (5.1%)
Trp (W)13 (3.5%)
Tyr (Y)9 (2.4%)
Val (V)27 (7.2%)
Amino acid counting
Total number:375
Positively charged (Arg+Lys):30 (8.0%)
Negatively charged (Asp+Glu):39 (10.4%)
Aromatic (Phe+His+Try+Tyr):44 (11.7%)
Biochemical parameters
Atomic composition:C1765H2720N512O543S14
Molecular mass [Da]:40249.0
Theoretical pI:5.84
Extinction coefficient at 280 nm [M-1 cm-1]:84910 / 85348 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):good (0.72)good (0.75)good (0.68)good (0.77)excellent (0.81)good (0.69)
Alignments (obtained from PredictProtein.org)
   There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours.
Predictions (obtained from PredictProtein.org)
   There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours.
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation.
If you have any questions, comments or suggestions, please leave us a comment.

References

[1] Rizzini L., Favory J.-J., Cloix C., Faggionato D., O'Hara A., Kaiserli E., Baumeister R., Schäfer E., Nagy F., Jenkins G. I., Ulm R. (2011). Perception of UV-B by the Arabidopsis UVR8 protein. Science 332

[2] Müller K., Engesser R., Schulz S., Steinberg T., Tomakidi P., Weber C. C., Ulm R., Timmer J., Zurbriggen M. D., Weber W. (2013). Multi-chromatic control of mammalian gene expression and signaling. Nucleic Acids Research Vol. 41, No. 12

[3] Favory J.-J., Stec A., Gruber H., Rizzini L., Oravecz A., Funk M., Albert A., Cloix C., Jenkins G. I., Oakeley E. J., Seidlitz H. K., Nagy F., Ulm R. (2009). Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. The EMBO Journal 28, 591-600

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