BBa_K1968022 1 BBa_K1968022 weLOV1 fluorescent protein Phytobrick 2016-10-13T11:00:00Z 2016-10-17T11:02:37Z Based ont he ilov sequence from BBa_K660004. weLOV1 codes for the same protein sequence as iLOV (BBa_K660004) but holds a different codon optimization than its predecesor. iLOV is a modified LOV2 domain from a blue light receptor phototropin (Briggs et al. 2007) with a reported excitation peak around 476nm and a measurable emission range between 510 and 550 nm. Coding sequences can sometimes be troublesome to work with, especially if these are not codon optimized for the selected organism. Since the team was going to work with four different organisms (E. coli, Rhodococcus justt, Penicillium roqueforti, Synechocystis sp. PCC6803) as an alternative to synthesizing the optimized version for each organism a different approach was discussed and implemented. By trying to design a sequence based on all four codon preference tables, one could hypothetically generate a sequence able to express well in all four hosts. Perhaps this might not be the most ideal sequence, but, one that could potentially help avoid some DNA synthesis costs. Two sequences were predicted under different algorithms: weLOV1 (BBa_K1968022) and weLOV2 (BBa_K1968023). The algorithm for the first one was as follows: Parting from the first aminoacid, the ideal codon was decided by 1) Obtaining the abundances for the respective coding codons in all four organisms. 2) Calculating the Euclidean distance between those abundances. 3) The codon with the minimum distance between abundance would then be selected as the appropriate triplet. This was done for all aminoacids from the iLOV protein. In an effort to mitigate selecting codons that not only had the smallest Euclidean distance between abundances, but also a low abundance; values with higher abundance were preferred. iLOV was selected because of its many advantages that could make it a better option than the most widely used green fluorescent protein. Its gene size is only 336 base pairs; most of the other fluorescent proteins available are at least twice as big. Its size, its reported superior photostability as well as its ability to fluoresce under anaerobic conditions make it an interesting reporter to be used across multiple organisms (Christie et al. 2012). Briggs, W.R. et al., 2007. Phototropins and Their LOV Domains: Versatile Plant Blue-Light Receptors. Journal of Integrative Plant Biology, 49(1), pp.4???10. Christie, J.M. et al., 2012. Structural Tuning of the Fluorescent Protein iLOV for Improved Photostability. Journal of Biological Chemistry, 287(26) false false _2435_ 9146 9146 9 No part sequence false Coding sequences can sometimes be troublesome to work with, especially if these are not codon optimized for the selected organism. Since the team was going to work with four different organisms (E. coli, Rhodococcus justt, Penicillium roqueforti, Synechocystis sp. PCC6803) as an alternative to synthesizing the optimized version for each organism a different approach was discussed and implemented. Designed under the Phytobrick standard. false Ricardo Camilo Ch??vez Mart??nez annotation2505965 1 Phytobrick Adapter Site C range2505965 1 1 4 annotation2505966 1 weLOV1 range2505966 1 2 337 annotation2505980 1 Phytobrick Adapter Site D range2505980 1 338 341 BBa_K1968022_sequence 1 aatgatagagaagaacttcgtaataacagatccaaggctaccagataacccaataatattcgcatcagatggattcctagagctaacagagtactcaagggaggagatactaggaaggaacgcaaggttcctacagggaccagagacagatcaggcaacagtacagaagataagggatgcaataagggatcagagggagacaacagtacagctaataaactacacaaagtcaggaaagaagttctggaacctactacatctacagccagtaagggatcagaagggagagctacagtacttcataggagtacagctagatggatcagatcatgtatagaggt igem2sbol 1 iGEM to SBOL conversion Conversion of the iGEM parts registry to SBOL2.1 Chris J. Myers James Alastair McLaughlin 2017-03-06T15:00:00.000Z