Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Definitive demonstration by synthesis of genome annotation completeness

Paul R. Jaschke, Gabrielle A Dotson, Kay Hung, Diane Liu, Drew Endy
doi: https://doi.org/10.1101/455428
Paul R. Jaschke
1Bioengineering Department, Stanford University, Stanford, CA, USA
2Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: paul.jaschke@mq.edu.au endy@stanford.edu
Gabrielle A Dotson
1Bioengineering Department, Stanford University, Stanford, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kay Hung
1Bioengineering Department, Stanford University, Stanford, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Diane Liu
1Bioengineering Department, Stanford University, Stanford, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Drew Endy
1Bioengineering Department, Stanford University, Stanford, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: paul.jaschke@mq.edu.au endy@stanford.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Bacteriophage øX174 was the first DNA genome to be sequenced. The genome is well studied by classical methods and is known to encode 11 essential genes. At least 23 closely-related Bullavirinae genome sequences are now available. We identified 315 potential open reading frames (ORFs) within the genome via bioinformatic analysis, and a subset of 82 highly-conserved ORFs that have no known gene products or functions. Using genome scale design and synthesis we made a mutant genome in which all 11 essential genes are simultaneously disrupted, leaving intact only the 82 conserved-but-cryptic ORFs. The resulting genome is not viable, as expected. Cell-free gene expression followed by mass spectrometry revealed only a single peptide expressed from both the cryptic-ORF and wild-type genomes, suggesting a potential new gene. A second synthetic genome in which 71 conserved cryptic ORFs were simultaneously disrupted is viable but with ~50% reduced fitness relative to the wild type. However, rather than finding any new genes, repeated evolutionary adaptation revealed a single point mutation modulating translation of gene H, a known essential gene, that fully suppressed the fitness defect. Taken together, we conclude that the annotation of ORFs for the øX174 genome is formally complete. Sequencing and bioinformatics followed by synthesis-enabled reverse genomics, proteomics, and evolutionary adaptation can definitely establish the sufficiency and completeness of natural genome annotations.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
Back to top
PreviousNext
Posted October 28, 2018.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Definitive demonstration by synthesis of genome annotation completeness
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Definitive demonstration by synthesis of genome annotation completeness
Paul R. Jaschke, Gabrielle A Dotson, Kay Hung, Diane Liu, Drew Endy
bioRxiv 455428; doi: https://doi.org/10.1101/455428
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Definitive demonstration by synthesis of genome annotation completeness
Paul R. Jaschke, Gabrielle A Dotson, Kay Hung, Diane Liu, Drew Endy
bioRxiv 455428; doi: https://doi.org/10.1101/455428

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Synthetic Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4091)
  • Biochemistry (8772)
  • Bioengineering (6487)
  • Bioinformatics (23356)
  • Biophysics (11756)
  • Cancer Biology (9154)
  • Cell Biology (13257)
  • Clinical Trials (138)
  • Developmental Biology (7418)
  • Ecology (11376)
  • Epidemiology (2066)
  • Evolutionary Biology (15095)
  • Genetics (10403)
  • Genomics (14014)
  • Immunology (9126)
  • Microbiology (22070)
  • Molecular Biology (8783)
  • Neuroscience (47395)
  • Paleontology (350)
  • Pathology (1421)
  • Pharmacology and Toxicology (2482)
  • Physiology (3705)
  • Plant Biology (8054)
  • Scientific Communication and Education (1433)
  • Synthetic Biology (2211)
  • Systems Biology (6017)
  • Zoology (1250)