期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 116, 期 16, 页码 8070-8079出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1818259116
关键词
Caulobacter crescentus; chemical genome synthesis; genome rewriting; synonymous recoding; de novo DNA synthesis
资金
- US Department of Energy Joint Genome Institute, Swiss Federal Institute of Technology (ETH) Zurich ETH Research Grant [CSP-2840, ETH-08 16-1, CSP-1593]
- Swiss National Science Foundation [31003A 166476]
- Office of Science of the US Department of Energy [DE-AC02-05CH11231]
- Swiss National Science Foundation (SNF) [31003A_166476] Funding Source: Swiss National Science Foundation (SNF)
Understanding how to program biological functions into artificial DNA sequences remains a key challenge in synthetic genomics. Here, we report the chemical synthesis and testing of Caulobacter ethensis-2.0 (C. eth-2.0), a rewritten bacterial genome composed of the most fundamental functions of a bacterial cell. We rebuilt the essential genome of Caulobacter crescentus through the process of chemical synthesis rewriting and studied the genetic information content at the level of its essential genes. Within the 785,701-bp genome, we used sequence rewriting to reduce the number of encoded genetic features from 6,290 to 799. Overall, we introduced 133,313 base substitutions, resulting in the rewriting of 123,562 codons. We tested the biological functionality of the genome design in C. crescentus by transposon mutagenesis. Our analysis revealed that 432 essential genes of C. eth-2.0, corresponding to 81.5% of the design, are equal in functionality to natural genes. These findings suggest that neither changing mRNA structure nor changing the codon context have significant influence on biological functionality of synthetic genomes. Discovery of 98 genes that lost their function identified essential genes with incorrect annotation, including a limited set of 27 genes where we uncovered noncoding control features embedded within protein-coding sequences. In sum, our results highlight the promise of chemical synthesis rewriting to decode fundamental genome functions and its utility toward the design of improved organisms for industrial purposes and health benefits.
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