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Title: Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality

Abstract

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. Inmore » 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.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ORCiD logo; ORCiD logo
Publication Date:
Research Org.:
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Swiss Federal Inst. of Technology in Zurich (ETH Zurich) (Switzerland)
Sponsoring Org.:
USDOE Office of Science (SC); Swiss Federal Inst. of Technology in Zurich (ETH Zurich) (Switzerland); Swiss National Science Foundation (Switzerland)
OSTI Identifier:
1504504
Alternate Identifier(s):
OSTI ID: 1625030
Grant/Contract Number:  
AC02-05CH11231; ETH-08 16-1; 31003A_166476
Resource Type:
Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 116 Journal Issue: 16; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Caulobacter crescentus; chemical genome synthesis; genome rewriting; synonymous recoding; de novo DNA synthesis

Citation Formats

Venetz, Jonathan E., Del Medico, Luca, Wölfle, Alexander, Schächle, Philipp, Bucher, Yves, Appert, Donat, Tschan, Flavia, Flores-Tinoco, Carlos E., van Kooten, Mariëlle, Guennoun, Rym, Deutsch, Samuel, Christen, Matthias, and Christen, Beat. Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality. United States: N. p., 2019. Web. doi:10.1073/pnas.1818259116.
Venetz, Jonathan E., Del Medico, Luca, Wölfle, Alexander, Schächle, Philipp, Bucher, Yves, Appert, Donat, Tschan, Flavia, Flores-Tinoco, Carlos E., van Kooten, Mariëlle, Guennoun, Rym, Deutsch, Samuel, Christen, Matthias, & Christen, Beat. Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality. United States. doi:10.1073/pnas.1818259116.
Venetz, Jonathan E., Del Medico, Luca, Wölfle, Alexander, Schächle, Philipp, Bucher, Yves, Appert, Donat, Tschan, Flavia, Flores-Tinoco, Carlos E., van Kooten, Mariëlle, Guennoun, Rym, Deutsch, Samuel, Christen, Matthias, and Christen, Beat. Mon . "Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality". United States. doi:10.1073/pnas.1818259116.
@article{osti_1504504,
title = {Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality},
author = {Venetz, Jonathan E. and Del Medico, Luca and Wölfle, Alexander and Schächle, Philipp and Bucher, Yves and Appert, Donat and Tschan, Flavia and Flores-Tinoco, Carlos E. and van Kooten, Mariëlle and Guennoun, Rym and Deutsch, Samuel and Christen, Matthias and Christen, Beat},
abstractNote = {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.},
doi = {10.1073/pnas.1818259116},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 16,
volume = 116,
place = {United States},
year = {2019},
month = {4}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1073/pnas.1818259116

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Cited by: 10 works
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