Gene synthesis allows biologists to source genes from farther away in the tree of life

Abstract

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. 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. 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.

A novel d-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae

“…However, as well as eliminating PCR bias, an added benefit of gene synthesis is that its codon usage can be optimized for a specific host. Despite the expense, the use of such optimized genes is growing in popularity as evidenced by the twenty percent of sequences deposited at Addgene being composed of codon optimized genes 42 . Although some XI enzymes have been successfully expressed in S. cerevisiae allowing more or less efficient d -xylose metabolism, the screening for XIs with significant expression in yeast has proved difficult and often require a suite of optimizations 8 , 14 , 15 , 43 .…”

A roadmap for metagenomic enzyme discovery

“…Moreover, gene synthesis enables complete codon optimization to match codon usage preferences of the heterologous host, which is particularly useful for expression of metagenomic sequences from taxonomically distant, uncultivated organisms. 213 Even with constructs that are properly designed, many heterologous expression experiments still fail. From our personal experience, the activity of some biosynthetic enzymes is only detectable through the expression of complete BGCs rather than expressing genes individually from a cluster.…”

Development and evaluation of recombinant GRA8 protein for the serodiagnosis of Toxoplasma gondii infection in goats

“…However, the transfer of gene sequences between organisms may not be successful, leading to low level protein expression because of differences in codon usage [ 20 , 21 ]. Recently, synthetic gene synthesis has been used to design and create genes without an existing DNA template [ 22 ]. In addition, gene synthesis tools do not require access to a pathogen, thus preventing the exposure of research staff to harmful living parasites [ 23 ].…”