Gene synthesis enables creation and modification of genetic sequences at an unprecedented pace, offering enormous potential for new biological functionality but also increasing the need for biosurveillance. In this paper, we introduce a bioinformatics technique for determining whether a gene is natural or synthetic based solely on nucleotide sequence. Show Codon Frequencies Reverse Translate a Protein Import or Create a Codon Usage Table Change Codons in a Coding Sequence (CDS) Based on a Codon Usage Table. This technique, grounded in codon theory and machine learning, can correctly classify genes with 97.7% accuracy on a novel data set. We then classify ∼19,000 unique genes from the Addgene non-profit plasmid repository to investigate whether natural and synthetic genes have differential use in heterologous expression. A program to back-translate a protein sequence to a nucleotide sequence. Phylogenetic analysis of distance between source and expression organisms reveals that researchers are using synthesis to source genes from more genetically-distant organisms, particularly for longer genes. We provide empirical evidence that gene synthesis is leading biologists to sample more broadly across the diversity of life, and we provide a foundational tool for the biosurveillance community.īiologists and bioengineers often transfer genes across organisms to test genetic hypotheses or to endow their favorite model organisms with novel traits or functionality 1, 2. In the first industrial example of recombinant DNA technology, Eli Lilly and Genentech expressed a synthetic gene encoding human insulin in the model bacterium Escherichia coli for drug manufacturing 3. Soon afterwards, biologists began sourcing genes encoding thermostable polymerases 4 from thermophilic bacteria and the well-known green fluorescent protein (GFP) 5 from the jellyfish as research tools. More recent biological research focused on mammalian models has featured considerable introduction of bacterial genes, notably the targeted genome editing tool CRISPR-Cas9 6– 8 and tools for optogenetics 9, 10. The growing field of synthetic biology also drives gene transfer because the genome sequences of non-model organisms present a treasure trove of potentially novel and orthogonal genes for testing in model organisms 11, 12. Using DNA synthesis to transfer synthetic gene sequences from one organism to another may succeed where transferring natural gene sequences would fail. This tool can aid in optimizing GC content and repetitive sequences, improving mRNA stability, and avoiding restriction enzyme recognition sites, thus improving transcription or translation efficiency.īelow are some examples illustrating various functionalities of our codon optimization tool: 1.Although natural genes have the potential for direct transfer from one organism to another because of the universality of the genetic code, many such sequences would express poorly when moved into a new organism because of differences in codon usage, GC content, or the presence of expression-limiting regulatory elements 13, 14. Our tool can be used for optimizing sequences with extreme GC content and simple repeats for highly efficient gene synthesis and DNA cloning applications.Ĭodon optimization can additionally be used to enhance cloning efficiency of a gene of interest. Additionally, it allows you to avoid cleavage sites of selected restriction enzymes while codon optimizing your target sequence. It includes a comprehensive list of species and is seamlessly incorporated into our online vector design platform enabling you to optimize your GOIs while designing vectors. VectorBuilder’s codon optimization tool is designed to help you achieve the optimal codon adaptation index (CAI) for your GOI in any organism of your choice. The gel scanning assay revealed that the amount of TrMgTx was the largest in the supernatant after inducing with 0.5 methanol for 72 h (71 ± 13 mg/L) (). This tool can optimize the codon adaptation index ( CAI), taking advantage of the host organism’s codon bias to produce the same amino acid sequence at a higher efficiency. For optimization of methanol induction, biomass production of a TrMgTx clone was induced with 0.5, 1, and 1.5 MeOH, using a medium of pH 6. This can lead to decreased translation when a gene is placed into a different host species. Most amino acids can be translated from multiple codons, but codon bias reflects the preference for one codon over another and varies between species. VectorBuilder’s Codon Optimization tool is in-built into the Design Studio and can be used independently here. Codon optimization is a useful tool when expressing genes heterologously (in a different host organism), if problems occur when cloning a gene, or when optimizing gene expression level.
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