Team:Paris Bettencourt/Notebook/Drug Screening/Monday 10th June.html

Drug Screening

Day Number^suffix Month

Design of SirA, FdrA, and FdxC genes for synthesis

Mycobacterium tuberculosis
Reference: Pinto et al. 2007. Sulfite Reduction in Mycobacteria doi: 10.1128/JB.00487-07
Primers:
TBsirA F      GGAATTCCATATGTCCGCGAAGGAGAACCCC
TBsirA R      AAGGAAAAAAGCGGCCGCTCATCGCAGGTCGTCCTCCTCGGCCCGGAT We blasted the above primers used to clone sirA from M. tuberculosis into E. coli. We then extracted the sequence from genbank to retrieve the following sequence which includes the restriction sites introduced by Pinto et al.

Ggaattccat atgtccgcga aggagaaccc ccaaatgacc actgcacgtc ccgccaaggc tcgaaatgag ggccagtggg cgctgggaca tcgcgagcca ctcaacgcca acgaagagct gaagaaggcc ggcaacccgc tcgacgtgcg ggagcgcatc gaaaacatct acgccaaaca gggtttcgac agcatcgaca agaccgacct gcgagggcgc tttcgctggt ggggcctgta cacccagcgt gagcagggct acgacggcac ctggaccggt gacgacaaca tcgacaagct cgaggccaaa tacttcatga tgcgggtgcg ttgcgacggc ggcgcgctct cggctgccgc gctgcgcacg ctgggccaga tctcgacgga gttcgcgcgc gataccgccg atatctccga ccggcagaac gtgcaatacc actggatcga agtggaaaac gtccctgaaa tctggcgacg gttagacgat gtcggactgc agaccaccga ggcgtgcggt gactgcccgc gggtagtgct gggctcgccg ttggccggcg agtcgctcga cgaagtgctc gacccgacct gggcgatcga ggagatcgtg cgtcgctaca tcggcaagcc cgacttcgcc gacttgccgc gcaagtacaa gaccgccatc tctggcctgc aggacgtcgc gcacgagatc aacgacgtcg ccttcatcgg cgtcaaccat cccgagcacg gaccaggcct ggatctgtgg gtgggcggtg gactgtcgac caacccgatg ctggcccagc gggtcggcgc ctgggttcca ctgggcgaag tgcccgaggt gtgggcggcg gtcacctcgg tgtttcgcga ctacggctac cggcgactgc gcgccaaggc ccggctgaaa tttctgatca aagactgggg catagcgaag ttccgcgaag tgctcgaaac cgagtacctc aagcgtccgc tgatcgacgg tccggccccc gaaccggtca agcatccgat cgaccacgtc ggggtgcaac gactcaagaa cgggctcaac gccgtcggag tcgcccccat cgccgggcgg gtatcgggca ccatcctcac ggcggtcgcc gacctgatgg cgcgggccgg ttccgaccgg atccggttca ccccctacca gaagctggtc atcctcgaca ttccggacgc cttgctcgac gacttgatcg ccggtctgga cgcgctgggg ctgcagtcgc gcccgtcgca ttggcgccgg aacttgatgg cgtgcagcgg gattgagttc tgcaagttgt cattcgccga aacccgggtt cgagcacagc atttggtgcc cgagctggaa cgccggcttg aggacatcaa ctcgcagctc gacgtaccga tcaccgtcaa catcaacggc tgcccgaact catgtgcgcg aattcaaatc gccgacatcg gattcaaggg acagatgatc gacgacggac acggcggctc cgtcgaaggc ttccaggtgc atctgggcgg acacctcggc ctggatgccg gattcggccg caaactgcgc cagcacaagg tcaccagtga cgaactcggc gactacatcg accgggtggt gcgcaacttc gtcaaacacc gcagcgaagg tgaacgcttc gcgcagtggg tcatccgggc cgaggaggac gacctgcgat gagcggccgc ttttttcctt

This sequence was then inserted into Geneious. The PstI and EcoRI sites were manually removed and replaced with silent mutations. A NcoI site was inserted at the start codon and an extra glycine was added after the start codon for the NcoI site to function properly. We chose glycine as it is small an unlikely to interfere with either polar or non-polar domains within the protein. We used GGC as the codon as it is the highest used glycine codon in e. coli. We also added an AvrII site on the 3’ end of the site. We then added biobrick restriction sites on the ends of the sequence (EcoRI, XbaI, SpeI, PstI). This will allow us to clone into our expression vector pACYCDuet-1 with NcoI and AvrII enzymes and into a biobrick registry with EcoRI and PstI. The insertion into pACYCDuet-1 removes both protein tags and cuts out the second MCS resulting in vector pACYCDuet-TBsirA. The resulting sequence for TB SirA follows:

CATGGAATTCTAGACCATGGGCTCCGCGAAGGAGAACCCCCAAATGACCACTGCACGTCCCGCCAAGGCTCGAAATGAGGGCCAGTGGGCGCTGGGACATCGCGAGCCACTCAACGCCAACGAAGAGCTGAAGAAGGCCGGCAACCCGCTCGACGTGCGGGAGCGCATCGAAAACATCTACGCCAAACAGGGTTTCGACAGCATCGACAAGACCGACCTGCGAGGGCGCTTTCGCTGGTGGGGCCTGTACACCCAGCGTGAGCAGGGCTACGACGGCACCTGGACCGGTGACGACAACATCGACAAGCTCGAGGCCAAATACTTCATGATGCGGGTGCGTTGCGACGGCGGCGCGCTCTCGGCTGCCGCGCTGCGCACGCTGGGCCAGATCTCGACGGAGTTCGCGCGCGATACCGCCGATATCTCCGACCGGCAGAACGTGCAATACCACTGGATCGAAGTGGAAAACGTCCCTGAAATCTGGCGACGGTTAGACGATGTCGGACTTCAGACCACCGAGGCGTGCGGTGACTGCCCGCGGGTAGTGCTGGGCTCGCCGTTGGCCGGCGAGTCGCTCGACGAAGTGCTCGACCCGACCTGGGCGATCGAGGAGATCGTGCGTCGCTACATCGGCAAGCCCGACTTCGCCGACTTGCCGCGCAAGTACAAGACCGCCATCTCTGGCCTTCAGGACGTCGCGCACGAGATCAACGACGTCGCCTTCATCGGCGTCAACCATCCCGAGCACGGACCAGGCCTGGATCTGTGGGTGGGCGGTGGACTGTCGACCAACCCGATGCTGGCCCAGCGGGTCGGCGCCTGGGTTCCACTGGGCGAAGTGCCCGAGGTGTGGGCGGCGGTCACCTCGGTGTTTCGCGACTACGGCTACCGGCGACTGCGCGCCAAGGCCCGGCTGAAATTTCTGATCAAAGACTGGGGCATAGCGAAGTTCCGCGAAGTGCTCGAAACCGAGTACCTCAAGCGTCCGCTGATCGACGGTCCGGCCCCCGAACCGGTCAAGCATCCGATCGACCACGTCGGGGTGCAACGACTCAAGAACGGGCTCAACGCCGTCGGAGTCGCCCCCATCGCCGGGCGGGTATCGGGCACCATCCTCACGGCGGTCGCCGACCTGATGGCGCGGGCCGGTTCCGACCGGATCCGGTTCACCCCCTACCAGAAGCTGGTCATCCTCGACATTCCGGACGCCTTGCTCGACGACTTGATCGCCGGTCTGGACGCGCTGGGGCTTCAGTCGCGCCCGTCGCATTGGCGCCGGAACTTGATGGCGTGCAGCGGGATTGAGTTCTGCAAGTTGTCATTCGCCGAAACCCGGGTTCGAGCACAGCATTTGGTGCCCGAGCTGGAACGCCGGCTTGAGGACATCAACTCGCAGCTCGACGTACCGATCACCGTCAACATCAACGGCTGCCCGAACTCATGTGCGCGAGTTCAAATCGCCGACATCGGATTCAAGGGACAGATGATCGACGACGGACACGGCGGCTCCGTCGAAGGCTTCCAGGTGCATCTGGGCGGACACCTCGGCCTGGATGCCGGATTCGGCCGCAAACTGCGCCAGCACAAGGTCACCAGTGACGAACTCGGCGACTACATCGACCGGGTGGTGCGCAACTTCGTCAAACACCGCAGCGAAGGTGAACGCTTCGCGCAGTGGGTCATCCGGGCCGAGGAGGACGACCTGCGATGAGCGGCCGCCTAGGACTACTAGTCTGCAGTTTTTCCTT

Mycobacterium smegmatis
This reference also contains the cloning of sirA from T. smegmatis. We used the primers below taken from Pinto et al, blasted against the T. smegmatis genome and extracted the sirA sequence from genbank as above.
Primers:
smegsirA F      TACAGCTGATGCTCGAAGACGAGTACTTCAT
smegsirA R      CCCAAGCTTTCACGTTGCCTACCTCAAATCCGCTTCGTC

tacagctgat gctcgaagac gagtacttca tgctgcgcgt gcgctgcgat ggtggcgcgctgaccact gcagcgctgc gcacgctcgg cggcatctcg accgagttcg cgcgcgacac cgccgacatc tccgaccgcg agaacgtcca gtaccactgg atccaggtcg agaacatgcc cgagatctgg aagcgcctcg acgccgtcgg cctgcagacc accgaggcgt gcggcgactg cccgcgtgtg gtcctcggct cgccgctggc cggtgagtcc ctcgacgagg tgatcgacgg gacccccgcg atcgacgaga tcgtgcgccg ctacatcggc aagcccgagt actcgaacct gccgcgcaag ttcaagaccg cgatctcggg gcttcaggac gtggtccacg aggtcaacga cgtcgcgttc atcggcgtca accaccccga gcacggcccg ggcttcgacc tgtgggtcgg tggcggcctg tcgaccaacc cgatgctggc ccagcgcgtc ggggtgtggg tgccgctcga cgaggtgccc gacgtctggg agggcgtcgt cagcatcttc cgcgactacg gttaccggcg tctgcggtcg aaggcgcggc tgaagttcct gatcaaggac tggggcgtcg aaaagttcag ggaagtgctg gaaaccgagt acctcaagcg ccccctgatc gacggcccgg cacccgaacc ggtgacccgc cccatcgacc acgtcggtgt gcagaagctc aagaacggcc tcaacgccgt gggcgtcgcc ccgatcgcgg gtcgcgtctc gggcacgatc ctgaccaagg tggccgatct cgccgaggcc gccgggtccg accggatccg cttcacgccg taccagaagc tgatcatcct cgacgtgccc gacgacaaga tcgacgaact gcgcgctggc ctcgacgcgc tcggactgcc gtcgacgccg tcgcactggc gccgcaacct catggcgtgc acgggtatcg agttctgcaa gctgagcttc gccgagaccc gcaagcgtgc ccaggtgctg gttcccgagc tggagaaacg gctcgacgac atcaacgccc agctcgacgt gcccatcacg gtcaacatca acggctgccc caactcgtgc gcccgtatcc aggtcgccga catcgggttc aagggccaga tggtcgacga tggcaacggc cccgaggagg gtttccaggt gcatctgggc ggcagcctgg gcctggacag cgggttcggc cgcaagctgc gccagcacaa ggtgctctcg tccgagctcg gcgactacat cgagcgcgtc gtgcgcaact tcgtgaaaca acgcgaggac ggcgagcgtt tcgcccagtg ggccgtgcgg gccgacgaag cggatttgag gtaggcaacg tgaaagcttg gg

As above, the sequence was imported into geneious, the biobrick restriction sites were manually removed from the sequence and restriction sites were added to the 5’ and 3’ ends in the same fashion as TB sirA. This resulted in the following sequence for synthesis:

p { text-transform: lowercase; } TACAGAATTCTAGACCATGGGCCTCGAAGACGAGTACTTCATGCTGCGCGTGCGCTGCGATGGTGGCGCGCTGACCACTACAGCGCTGCGCACGCTCGGCGGCATCTCGACCGAGTTCGCGCGCGACACCGCCGACATCTCCGACCGCGAGAACGTCCAGTACCACTGGATCCAGGTCGAGAACATGCCCGAGATCTGGAAGCGCCTCGACGCCGTCGGCCTACAGACCACCGAGGCGTGCGGCGACTGCCCGCGTGTGGTCCTCGGCTCGCCGCTGGCCGGTGAGTCCCTCGACGAGGTGATCGACGGGACCCCCGCGATCGACGAGATCGTGCGCCGCTACATCGGCAAGCCCGAGTACTCGAACCTGCCGCGCAAGTTCAAGACCGCGATCTCGGGGCTTCAGGACGTGGTCCACGAGGTCAACGACGTCGCGTTCATCGGCGTCAACCACCCCGAGCACGGCCCGGGCTTCGACCTGTGGGTCGGTGGCGGCCTGTCGACCAACCCGATGCTGGCCCAGCGCGTCGGGGTGTGGGTGCCGCTCGACGAGGTGCCCGACGTCTGGGAGGGCGTCGTCAGCATCTTCCGCGACTACGGTTACCGGCGTCTGCGGTCGAAGGCGCGGCTGAAGTTCCTGATCAAGGACTGGGGCGTCGAAAAGTTCAGGGAAGTGCTGGAAACCGAGTACCTCAAGCGCCCCCTGATCGACGGCCCGGCACCCGAACCGGTGACCCGCCCCATCGACCACGTCGGTGTGCAGAAGCTCAAGAACGGCCTCAACGCCGTGGGCGTCGCCCCGATCGCGGGTCGCGTCTCGGGCACGATCCTGACCAAGGTGGCCGATCTCGCCGAGGCCGCCGGGTCCGACCGGATCCGCTTCACGCCGTACCAGAAGCTGATCATCCTCGACGTGCCCGACGACAAGATCGACGAACTGCGCGCTGGCCTCGACGCGCTCGGACTGCCGTCGACGCCGTCGCACTGGCGCCGCAACCTCATGGCGTGCACGGGTATCGAGTTCTGCAAGCTGAGCTTCGCCGAGACCCGCAAGCGTGCCCAGGTGCTGGTTCCCGAGCTGGAGAAACGGCTCGACGACATCAACGCCCAGCTCGACGTGCCCATCACGGTCAACATCAACGGCTGCCCCAACTCGTGCGCCCGTATCCAGGTCGCCGACATCGGGTTCAAGGGCCAGATGGTCGACGATGGCAACGGCCCCGAGGAGGGTTTCCAGGTGCATCTGGGCGGCAGCCTGGGCCTGGACAGCGGGTTCGGCCGCAAGCTGCGCCAGCACAAGGTGCTCTCGTCCGAGCTCGGCGACTACATCGAGCGCGTCGTGCGCAACTTCGTGAAACAACGCGAGGACGGCGAGCGTTTCGCCCAGTGGGCCGTGCGGGCCGACGAAGCGGATTTGAGGTAGGCAACGTGAAAGCCTAGGTACTAGTCTGCAGTGGG