Synthetic Gene DataBase
 

Synthetic Gene 18


 
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Field NameNatural GeneSynthetic Gene
SGDB Gene ID1418
GenBank AccessionU78724
GenBank GI1699002
Gene NameEBA-175pSRII (EBA-175)
Gene Length (bp)18481
SpeciesPlasmodium falciparumMus musculus
Strains3D7VM92 (melanoma cells)
CDSggaagaaatacttcatctaataacgaagttttaagtaattgtagggaaaaaaggaaagga
atgaaatgggattgtaaaaagaaaaatgatagaagcaactatgtatgtattcctgatcgt
agaatccaattatgcattgttaatcttagcattattaaaacatatacaaaagagaccatg
aaggatcatttcattgaagcctctaaaaaagaatctcaacttttgcttaaaaaaaatgat
aacaaatataattctaaattttgtaatgatttgaagaatagttttttagattatggacat
cttgctatgggaaatgatatggattttggaggttattcaactaaggcagaaaacaaaatt
caagaagtttttaaaggggctcatggggaaataagtgaacataaaattaaaaattttaga
aaaaaatggtggaatgaatttagagagaaactttgggaagctatgttatctgagcataaa
aataatataaataattgtaaaaatattccccaagaagaattacaaattactcaatggata
aaagaatggcatggagaatttttgcttgaaagagataatagatcaaaattgccaaaaagt
aaatgtaaaaataatacattatatgaagcatgtgagaaggaatgtattgatccatgtatg
aaatatagagattggattattagaagtaaatttgaatggcatacgttatcgaaagaatat
gaaactcaaaaagttccaaaggaaaatgcggaaaattatttaatcaaaatttcagaaaac
aagaatgatgctaaagtaagtttattattgaataattgtgatgctgaatattcaaaatat
tgtgattgtaaacatactactactctcgttaaaagcgttttaaatggtaacgacaataca
attaaggaaaagcgtgaacatattgatttagatgatttttctaaatttggatgtgataaa
aattccgttgatacaaacacaaaggtgtgggaatgtaaaaaaccttataaattatccact
aaagatgtatgtgtacctccgaggaggcaagaattatgtcttggaaacattgatagaata
tacgataaaaacctattaatgataaaagagcatattcttgctattgcaatatatgaatca
agaatattgaaacgaaaatataagaataaagatgataaagaagtttgtaaaatcataaat
aaaactttcgctgatataagagatattataggaggtactgattattggaatgatttgagc
aatagaaaattagtaggaaaaattaacacaaattcaaattatgttcacaggaataaacaa
aatgataagctttttcgtgatgagtggtggaaagttattaaaaaagatgtatggaatgtg
atatcatgggtattcaaggataaaactgtttgtaaagaagatgatattgaaaatatacca
caattcttcagatggtttagtgaatggggtgatgattattgccaggataaaacaaaaatg
atagagactctgaaggttgaatgcaaagaaaaaccttgtgaagatgacaattgtaaacgt
aaatgtaattcatataaagaatggatatcaaaaaaaaaagaagagtataataaacaagcc
aaacaataccaagaatatcaaaaaggaaataattacaaaatgtattctgaatttaaatct
ataaaaccagaagtttatttaaagaaatactcggaaaaatgttctaacctaaatttcgaa
gatgaatttaaggaagaattacattcagattataaaaataaatgtacgatgtgtccagaa
gtaaaggatgtaccaatttctataataagaaataatgaacaaacttcg
5' End
3' End
NotesNo wild-type sequence for EBA-175 was mentioned in the paper, so a similar record from GenBank (U78724) was included for reference.CAI values were calculated with highly expressed human genes defined in Haas 1996 as the reference set. No synthetic gene sequence published. The authors were emailed on 9/6/5. But the email was invalid.
Expression VectorVR1020VR1020
Assay MethodsSDS-PAGE and Western BlotSDS-PAGE and Western Blot
ResultsDetectable protein expressionSignificant higher expression compared with native gene
Protein Functionerythrocyte-binding protein (EBA-175 Region II), binds to its erythrocyte receptor sialic acids on glycophorin A
Recoding PurposeTo improve expression
Synthesized ByAuthors
Recoding MethodHuman most abundant codons (from CUTG) were used for every amino acid except Ser (UCC rather than
AGC).
Publication Author(s)Narum, D. L.; Kumar, S.; Rogers, W. O.; Fuhrmann, S. R.; Liang, H.; Oakley, M.; Taye, A.; Sim, B. K.; Hoffman, S. L.
Corresponding AuthorStephen L. Hoffman
Corresponding AddressEntreMed, Inc., Rockville, Maryland, USA.
Publication Year2001
Publication TitleCodon optimization of gene fragments encoding Plasmodium falciparum merzoite proteins enhances DNA vaccine protein expression and immunogenicity in mice
AbstractIn contrast to conventional vaccines, DNA and other subunit vaccines exclusively utilize host cell molecules for transcription and translation of proteins. The adenine plus thymine content of Plasmodium falciparum gene sequences (approximately 80%) is much greater than that of Homo sapiens (approximately 59%); consequently, codon usage is markedly different. We hypothesized that modifying codon usage of P. falciparum genes encoded by DNA vaccines from that used by the parasite to those resembling mammalian codon usage would lead to increased P. falciparum protein expression in vitro in mouse cells and increased antibody responses in DNA-vaccinated mice. We synthesized gene fragments encoding the receptor-binding domain of the 175-kDa P. falciparum erythrocyte-binding protein (EBA-175 region II) and the 42-kDa C-terminal processed fragment of the P. falciparum merozoite surface protein 1 (MSP-1(42)) using the most frequently occurring codon in mammals to code for each amino acid, and inserted the synthetic genes in DNA vaccine plasmids. In in vitro transient-expression assays, plasmids containing codon-optimized synthetic gene fragments (pS plasmids) showed greater than fourfold increased protein expression in mouse cells compared to those containing native gene fragments (pN plasmids). In mice immunized with 0.5, 5.0, or 50 microg of the DNA plasmids, the dose of DNA required to induce equivalent antibody titers was 10- to 100-fold lower for pS than for pN plasmids. These data demonstrate that optimizing codon usage in DNA vaccines can improve protein expression and consequently the immunogenicity of gene fragments in DNA vaccines for organisms whose codon usage differs substantially from that of mammals.
JournalInfect Immun. 69(12): 7250-3.
SummaryTwo malaria vaccine candidate antigens were fully codon optimized for expression in mammalian cells using human codon preference determined based on CUTG data. Both synthetic genes exhibited significant stronger expression than their wild-type counterparts.
Comments
Discussion http://www.evolvingcode.net/forum/viewtopic.php?t=527
PubMed ID11705894
Submitter NameWu, Gang
Submitter AddressDepartment of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
Entry ConfirmationNo
 
 

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