Coding

Part:BBa_K2255006:Design

Designed by: Hussein Daher   Group: iGEM17_Aix-Marseille   (2017-08-28)
Revision as of 16:36, 26 September 2017 by Kamy (Talk | contribs) (→‎Design Notes)


EPS-Depolymerase (Rfc25)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Erwinia amylovora is gram-negative bacterium in the family Enterobacteria. This bacterium have a similar path of infection as Xylella Fastidiosa, Erwinia amylovora makes its entry into its host xylem synthesis the extracellular polysaccharides (EPS) occluding the xylem vessels of the plant.

This information narrowed my research in the direction of determining enzymes capable of degrading the biofilm of Xylella fastidiosa rendering it more susceptible to antibiotic, naturally present phages or the natural defence of the plant.

First step was to run a blast using the EPS-Depolymerase from Erwinia amylovora (Q9G072_9CAUD) to see if an EPS-Depolymerase was present in phages against Xylella fastidiosa, but alas the results where negative but a potential candidate arose.

Putative tail fiber protein/putative EPS Depolymerase (DIBBI_029) is an enzyme of 852 amino acids, from the organism Xanthomonas phage vB_XveM_DIBBI which contain two function one structural and one pectin lyase. Multiple articles showed that some phages that work on Xanthomonas can work on Xylella fastidiosa and Vis versa. However, we can't be sure if the gene chosen can work because of the lack of documentation.

T--Aix-Marseille--DEPS-explication-1.png

The protein is 852 amino acid which translate to 2556 nucleobases, quite big making it difficult to work with so a process of trimming was done. Seeing as the domain we are interested in pectin lyase start from the 139th to 426th amino acid it is possible to remove the excess amino acids without harming the functionality and specificity of the enzyme. A Blast against NR was done to see if this domain is highly conserved and if the excess were not aligned with the the query sequence DIBBI_029. We found a majority of the alignment started with a gap of 78 amino acids in N-terminus and 266 amino acids in C-terminus so we obted to reduce the size of the protein to 510 amino acids a 342 amino acid reduction.

T--Aix-Marseille--DEPS-explication-2.png


Giving us the sequence present:

MQIQEPDGFKYIGRVPSFAALVSVVPEKAGERVIVSGHVAGNDYGGGVFVARAGSVAINDGGTIMPVNNNFYWQRLVEDPGTLDVTHFGAKRDGVTDCATAC LAMWNYTQSLGAGGSMIGIQFPAGEFAVSNIDISANYVGNFRLVGKGVVTTFGYFPATRIKLIGADNQAAFKVQARRSEIANLQIYGQYEVKANTRGFFKNT CVSGQYVHGVNWRSTYTGGPIFDLMDTLDTKFSEFYASYVYGGVIYGVPSGSESGSWDHLTAIELSNFNVQRCYGKQAFDLQKSGQSFIYNGWIEKTDFPGD LSNGQWIIQGLSMEDCVNPLDLTFTRAQLSQINLQGTSALRYDNPDKSRLLSTYEMGRNRVEAYGAQFFGSLSYDYLSSHYRLSNATDKAAWFNLGKMIVTN QNDASRIRFFGANGQASVPSDQGAFDSNNFGGGECLLTLRRVPGTGTRQDCAIEVHGNSPIADIRISRPYENDVEIYVQLKPQCGFVNVSLETSTNSRFDSG

Our primary cloning medium is the plasmid pSB1C3, we chose RFC 25 as the prefix and suffix for the sequence and the E.coli promoter

To purify the protein we added a histidine tag at 3’, which enable a chromatography on a nickel column. The prefix and suffix are special sequence designed with restriction sites to flank both ends of the sequence we are trying to modify. the prefix hold two restriction sites for EcoRI and xbaI, the suffix holds SpeI and PstI.

The sequence was retro translated to obtain the genomic sequence with the E.coli bias. ATGCAGATTCAGGAACCGGATGGCTTTAAATATATTGGCCGCGTGCCGAGCTTTGCGGCGCTGGTGAGCGTGGTGCCGGAAAAAGCGGGCGAACGCGTGATT GTGAGCGGCCATGTGGCGGGCAACGATTATGGCGGCGGCGTGTTTGTGGCGCGCGCGGGCAGCGTGGCGATTAACGATGGCGGCACCATTATGCCGGTGAAC AACAACTTTTATTGGCAGCGCCTGGTGGAAGATCCGGGCACCCTGGATGTGACCCATTTTGGCGCGAAACGCGATGGCGTGACCGATTGCGCGACCGCGTGC CTGGCGATGTGGAACTATACCCAGAGCCTGGGCGCGGGCGGCAGCATGATTGGCATTCAGTTTCCGGCGGGCGAATTTGCGGTGAGCAACATTGATATTAGC GCGAACTATGTGGGCAACTTTCGCCTGGTGGGCAAAGGCGTGGTGACCACCTTTGGCTATTTTCCGGCGACCCGCATTAAACTGATTGGCGCGGATAACCAG GCGGCGTTTAAAGTGCAGGCGCGCCGCAGCGAAATTGCGAACCTGCAGATTTATGGCCAGTATGAAGTGAAAGCGAACACCCGCGGCTTTTTTAAAAACACC TGCGTGAGCGGCCAGTATGTGCATGGCGTGAACTGGCGCAGCACCTATACCGGCGGCCCGATTTTTGATCTGATGGATACCCTGGATACCAAATTTAGCGAA TTTTATGCGAGCTATGTGTATGGCGGCGTGATTTATGGCGTGCCGAGCGGCAGCGAAAGCGGCAGCTGGGATCATCTGACCGCGATTGAACTGAGCAACTTT AACGTGCAGCGCTGCTATGGCAAACAGGCGTTTGATCTGCAGAAAAGCGGCCAGAGCTTTATTTATAACGGCTGGATTGAAAAAACCGATTTTCCGGGCGAT CTGAGCAACGGCCAGTGGATTATTCAGGGCCTGAGCATGGAAGATTGCGTGAACCCGCTGGATCTGACCTTTACCCGCGCGCAGCTGAGCCAGATTAACCTG CAGGGCACCAGCGCGCTGCGCTATGATAACCCGGATAAAAGCCGCCTGCTGAGCACCTATGAAATGGGCCGCAACCGCGTGGAAGCGTATGGCGCGCAGTTT TTTGGCAGCCTGAGCTATGATTATCTGAGCAGCCATTATCGCCTGAGCAACGCGACCGATAAAGCGGCGTGGTTTAACCTGGGCAAAATGATTGTGACCAAC CAGAACGATGCGAGCCGCATTCGCTTTTTTGGCGCGAACGGCCAGGCGAGCGTGCCGAGCGATCAGGGCGCGTTTGATAGCAACAACTTTGGCGGCGGCGAA TGCCTGCTGACCCTGCGCCGCGTGCCGGGCACCGGCACCCGCCAGGATTGCGCGATTGAAGTGCATGGCAACAGCCCGATTGCGGATATTCGCATTAGCCGC CCGTATGAAAACGATGTGGAAATTTATGTGCAGCTGAAACCGCAGTGCGGCTTTGTGAACGTGAGCCTGGAAACCAGCACCAACAGCCGCTTTGATAGCGGC

However, this sequence had three restriction sites for the endonuclease PSTI which is in conflict with the endonuclease we will be using to modify and insert the gene in the plasmid. Keeping these sites will cleave the gene in three separate places losing all functionality. The three sites found on the 555th, 855th and 1020th position with the conserved sequence of CTGCAG, CTG code for a leucine and CAG code for a glutamine. Thankfully, the genomic code is redundant so we can modify nucleobases without changing the protein translated. We chose to change the G of CTG to an A giving us CTA this modification did not produce any restriction sites critical to our work eliminating the restriction site for PSTI.

Resulting in the sequence as present

ATGCAGATTCAGGAACCGGATGGCTTTAAATATATTGGCCGCGTGCCGAGCTTTGCGGCGCTGGTGAGCGTGGTGCCGGAAAAA GCGGGCGAACGCGTGATTGTGAGCGGCCATGTGGCGGGCAACGATTATGGCGGCGGCGTGTTTGTGGCGCGCGCGGGCAGCGTG GCGATTAACGATGGCGGCACCATTATGCCGGTGAACAACAACTTTTATTGGCAGCGCCTGGTGGAAGATCCGGGCACCCTGGAT GTGACCCATTTTGGCGCGAAACGCGATGGCGTGACCGATTGCGCGACCGCGTGCCTGGCGATGTGGAACTATACCCAGAGCCTG GGCGCGGGCGGCAGCATGATTGGCATTCAGTTTCCGGCGGGCGAATTTGCGGTGAGCAACATTGATATTAGCGCGAACTATGTG GGCAACTTTCGCCTGGTGGGCAAAGGCGTGGTGACCACCTTTGGCTATTTTCCGGCGACCCGCATTAAACTGATTGGCGCGGAT AACCAGGCGGCGTTTAAAGTGCAGGCGCGCCGCAGCGAAATTGCGAACCTACAGATTTATGGCCAGTATGAAGTGAAAGCGAAC ACCCGCGGCTTTTTTAAAAACACCTGCGTGAGCGGCCAGTATGTGCATGGCGTGAACTGGCGCAGCACCTATACCGGCGGCCCG ATTTTTGATCTGATGGATACCCTGGATACCAAATTTAGCGAATTTTATGCGAGCTATGTGTATGGCGGCGTGATTTATGGCGTG CCGAGCGGCAGCGAAAGCGGCAGCTGGGATCATCTGACCGCGATTGAACTGAGCAACTTTAACGTGCAGCGCTGCTATGGCAAA CAGGCGTTTGATCTACAGAAAAGCGGCCAGAGCTTTATTTATAACGGCTGGATTGAAAAAACCGATTTTCCGGGCGATCTGAGC AACGGCCAGTGGATTATTCAGGGCCTGAGCATGGAAGATTGCGTGAACCCGCTGGATCTGACCTTTACCCGCGCGCAGCTGAGC CAGATTAACCTACAGGGCACCAGCGCGCTGCGCTATGATAACCCGGATAAAAGCCGCCTGCTGAGCACCTATGAAATGGGCCGC AACCGCGTGGAAGCGTATGGCGCGCAGTTTTTTGGCAGCCTGAGCTATGATTATCTGAGCAGCCATTATCGCCTGAGCAACGCG ACCGATAAAGCGGCGTGGTTTAACCTGGGCAAAATGATTGTGACCAACCAGAACGATGCGAGCCGCATTCGCTTTTTTGGCGCG AACGGCCAGGCGAGCGTGCCGAGCGATCAGGGCGCGTTTGATAGCAACAACTTTGGCGGCGGCGAATGCCTGCTGACCCTGCGC CGCGTGCCGGGCACCGGCACCCGCCAGGATTGCGCGATTGAAGTGCATGGCAACAGCCCGATTGCGGATATTCGCATTAGCCGC CCGTATGAAAACGATGTGGAAATTTATGTGCAGCTGAAACCGCAGTGCGGCTTTGTGAACGTGAGCCTGGAAACCAGCACCAAC AGCCGCTTTGATAGCGGC

If all well and done, we should be able to clone the gene and recuperate the protein with a Molecular weight of 55.81 kD that is 510 amino acids without taking into account the histidine tag.

Source

Genomic sequence from the phage vB_XveM_DIBBI

References