Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure
| Autor: | Dennis M. Mishler, Peng Geng, Jeffrey E. Barrick, Sean P. Leonard |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
Transposable element Genetic Vectors Biomedical Engineering Computational biology Biology 01 natural sciences Biochemistry Genetics and Molecular Biology (miscellaneous) Genome Genomic Instability Evolution Molecular Synthetic biology 03 medical and health sciences RNA interference 010608 biotechnology Escherichia coli Clustered Regularly Interspaced Short Palindromic Repeats Gene Repetitive Sequences Nucleic Acid 030304 developmental biology 0303 health sciences CRISPR interference Acinetobacter 030306 microbiology General Medicine Metabolic Engineering Mutation DNA methylation DNA Transposable Elements RNA Interference Synthetic Biology CRISPR-Cas Systems Mobile genetic elements Selfish DNA Genome Bacterial Plasmids |
| Zdroj: | ACS Synthetic Biology. 8:521-531 |
| ISSN: | 2161-5063 |
| Popis: | Mobile genetic elements drive evolution by disrupting genes and rearranging genomes. Eukaryotes have evolved epigenetic mechanisms, including DNA methylation and RNA interference, that silence mobile elements and thereby preserve the integrity of their genomes. We created an artificial reprogrammable epigenetic system based on CRISPR interference to give engineered bacteria a similar line of defense against transposons and other selfish elements in their genomes. We demonstrate that this CRISPR interference against mobile elements (CRISPRi-ME) approach can be used to simultaneously repress two different transposon families in Escherichia coli, thereby increasing the evolutionary stability of costly protein expression. We further show that silencing a transposon in Acinetobacter baylyi ADP1 reduces mutation rates by a factor of five, nearly as much as deleting all copies of this element from its genome. By deploying CRISPRi-ME on a broad-host-range vector we have created a generalizable platform for stabilizing the genomes of engineered bacterial cells for applications in metabolic engineering and synthetic biology.SignificanceEngineered cells often cease to function or lose productivity when mutations arise in their genomes. Mobile DNA elements, such as transposons, are major sources of these inactivating mutations. Eukaryotic genomes have evolved flexible epigenetic defenses against mobile DNA that help them to maintain genome integrity, but bacteria do not possess comparable silencing systems. We developed a synthetic control system based on CRISPR interference that can be used to give bacterial cells a reprogrammable line of defense against selfish DNA elements in their genomes. We show that this system effectively represses multicopy transposons and multiple families of transposons. Limiting selfish DNA proliferation within a genome in this way improves the reliability of genetically engineered functions in replicating bacterial cell populations. |
| Databáze: | OpenAIRE |
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