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.

Find closest natural relatives
Identify syntenic discontinuities (this is where the new JCVI code should reside
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
Valid email address

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

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/cnm" "org/nrg" "net", "cvi" (jcvi)
  - Nothing: could be wrong code

Region	Notes
http://genomevolution.org/r/4mxl	Annotation talks about how a piece of e. coli made it into this area. Not the greener region (GC rich). When that sequence is extracted and blasted against E. coli, get a very high quality hit (95%). http://genomevolution.org/CoGe//CoGeBlast.pl?chr=contig_sMmYCp235-1&upstream=308819&downstream=309545&dsid=59166&rc=0&gstid=1
http://genomevolution.org/r/4mxq	Interesting region. There is an obvious "new thing" that is annotated as a hypothetical protein predicted by glimmer. Gene it replaces is a transposon (which wouldn't be missed). Its sequence (http://genomevolution.org/CoGe//SeqView.pl?dsid=59166&chr=contig_sMmYCp235-1&start=389374&stop=390574&gstid=1), when 6-frame translated, yields one frame that contains several "CVI" amino acid sequences. This sequence hasn't been seen in other aa sequences. Obvious email/web address did not jump out.