|
|
| (73 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| == Background ==
| | #REDIRECT: [[Mycoplasma mycoides JCVI-syn1.0 Decoded]] |
| | |
| 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==
| |
| #Find closest natural relatives
| |
| #Identify syntenic discontinuities (this is where the new JCVI code should reside | |
| #Decode new sequence
| |
| ##Identify coding scheme
| |
| ###Probably using natural codon triplet encoding given that:
| |
| ####1x4 encoding = 4 letters
| |
| ####2x4 encoding = 16 letters
| |
| ####3x4 encoding = 64 letters
| |
| ###Given that there are 20ish natural amino acids, some of the codons will be appropriated for additional letters and symbols
| |
| ####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
| |
| ##Decode email address
| |
| #Valid email address
| |
| | |
| == Closest natural relatives ==
| |
| | |
| {| width="200" cellspacing="1" cellpadding="1" border="1"
| |
| |-
| |
| | 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
| |
| |-
| |
| | [[Image:Screen_Shot_2012-03-22_at_6.23.29_AM.png|400px]]
| |
| | [[Image:Screen_Shot_2012-03-22_at_6.26.34_AM.png|400px]]
| |
| |}
| |
| | |
| ==[[GEvo]] Analyses: high-resolution detection of syntenic discontinuities==
| |
| ===Genitalium===
| |
| [[File:Screen Shot 2012-03-22 at 6.32.40 AM.png|thumb|center|800px|[[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]]
| |
| | |
| [[File:Screen Shot 2012-03-22 at 6.38.08 AM.png|thumb|center|800px|[[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/cnm" "org/nrg" "net", "cvi" (jcvi)
| |
| ***Nothing: could be wrong code
| |
| | |
| ===Mycoides===
| |
| [[File:Screen shot 2012-03-22 at 9.12.01 AM.png|thumb|center|800px|GEvo whole genome analysis of Mycoplasma mycoides JCVI-syn1.0 v. Mycoplasma mycoides subsp. capri strain GM12. Results may be regenerated at http://genomevolution.org/r/4mxd]]
| |
| | |
| | |
| | |
| {| width="200" cellspacing="1" cellpadding="1" border="1"
| |
| |-
| |
| | Region
| |
| | Notes
| |
| |-
| |
| | [[File:Screen shot 2012-03-22 at 9.31.04 AM.png|thumb|center|800px|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
| |
| |-
| |
| | [[File:Screen shot 2012-03-22 at 9.38.58 AM.png|thumb|center|800px|http://genomevolution.org/r/4mxq]]
| |
| | http://genomevolution.org/CoGe//SeqView.pl?dsid=59166&chr=contig_sMmYCp235-1&start=389504&stop=390368&gstid=1. 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). This sequence does not match anything in K12 MG1655. Its sequence, when 6-frame translated, yields one frame that contains several "CVI" amino acid sequences. This sequence hasn't been seen in other aa sequences from this genome. Obvious email/web address [[JCVI potential code sequence | did not jump out]].
| |
| |-
| |
| | [[File:Screen shot 2012-03-22 at 1.15.13 PM.png|thumb|center|800px|http://genomevolution.org/r/4myz]]
| |
| | http://genomevolution.org/CoGe//SeqView.pl?dsid=59166&chr=contig_sMmYCp235-1&start=565568&stop=566608&gstid=1 . Did not match anything in E. coli. No obvious words.
| |
| |}
| |