Jcvi code

Background

Rumor has it that there is a code in one of the synthetic genomes by JCVI. Supposedly, this code contains an email address.

Synthetic JCVI genomes in CoGe

• synthetic Mycoplasma genitalium strain JCVI-1.0: http://genomevolution.org/CoGe/OrganismView.pl?oid=35986
• synthetic Mycoplasma mycoides JCVI-syn1.0: http://genomevolution.org/CoGe/OrganismView.pl?oid=35385

Methods

1. Find closest natural relatives
2. Identify syntenic discontinuities (this is where the new JCVI code should reside
3. Decode new sequence
   1. Identify coding scheme
      1. Probably using natural codon triplet encoding given that:
         1. 1x4 encoding = 4 letters
         2. 2x4 encoding = 16 letters
         3. 3x4 encoding = 64 letters
      2. Given that there are 20ish natural amino acids, some of the codons will be appropriated for additional letters and symbols
         1. An example for students of expanded codon encoding (using neighboring codons for additional letters): http://nature.ca/genome/05/051/0511/0511_m205_e.cfm
   2. Decode email address
4. Valid email address

Closest natural relatives

Syntenic dotplot of synthetic Mycoplasma genitalium strain JCVI-1.0 (y-axis) v. Mycoplasma genitalium strain G37 (x-axis) http://genomevolution.org/r/4mx1	Syntenic dotplot of synthetic Mycoplasma mycoides JCVI-syn1.0 (y-axis) v. Mycoplasma mycoides subsp. capri strain GM12 (x-axis) http://genomevolution.org/r/4mx2

GEvo Analyses: high-resolution detection of syntenic discontinuities

Genitalium

GEvo whole genome analysis of Mycoplasma genitalium strain JCVI-1.0 v. Mycoplasma genitalium strain G37. Results may be regenerated at: http://genomevolution.org/r/4mwy

GEvo analysis of syntenic discontinuity ofMycoplasma genitalium strain JCVI-1.0 v. Mycoplasma genitalium strain G37. http://genomevolution.org/r/4mx3

• Disrupted WT gene: MG_408 , NP_073081.1 , pmsR
  • methionine sulfoxide reductase A
  • this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form a fusion protein of this enzyme with MsrB provides protection against oxidative stress in Neisseria gonorrhoeae this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form
• Inserted gene: ABY79711.1 , MGATCC33530_0530
  • bifunctional AAC/APH (AAC(6'): 6'-aminoglycoside N-acetyltransferase and APH(2'): 2-aminoglycoside phosphotransferase
  • Aminoglycoside antibiotic resistance is largely the result of the production of enzymes that covalently modify the drugs including kinases (Aph) with structural and functional similarity to protein and lipid kinases. One of the most important aminoglycoside resistance enzymes is Aac(6')-Aph(2), a bifunctional enzyme with both aminoglycoside acetyltransferase and kinase activities.
• Extract sequence: http://genomevolution.org/CoGe//SeqView.pl?featid=143193835_1&dsid=63956&chr=1&start=&upstream=-227770&downstream=228068&rc=0&dsgid=15768
  • Perform 6-frame translation (using above link)
  • search for anything that might match "com/" "org" "net"

Mycoides

Whole genome GEvo analysis: http://genomevolution.org/r/4mx4 (need higher res monitor to take a screen shot that show discontinuities.)