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

Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics

Morgan N. Price, Grant M. Zane, Jennifer V. Kuehl, Ryan A. Melnyk, Judy D. Wall, Adam M. Deutschbauer, Adam P. Arkin
doi: https://doi.org/10.1101/192971
Morgan N. Price
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Grant M. Zane
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jennifer V. Kuehl
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ryan A. Melnyk
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Judy D. Wall
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adam M. Deutschbauer
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adam P. Arkin
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. We studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge. Using genome-wide mutant fitness data, we identified novel enzymes that fill 9 of the 11 gaps and hence explain the biosynthesis of methionine, threonine, serine, or histidine by bacteria from six genera. We also found that the sulfate-reducing bacterium Desulfovibrio vulgaris synthesizes homocysteine (which is a precursor to methionine) by using DUF39, NIL/ferredoxin, and COG2122 proteins, and that homoserine is not an intermediate in this pathway. Our results suggest that most free-living bacteria can likely make all 20 amino acids and illustrate how high-throughput genetics can uncover previously-unknown amino acid biosynthesis genes.

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 4.0 International license.
Back to top
PreviousNext
Posted September 23, 2017.
Download PDF

Supplementary Material

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.
Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics
(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
Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics
Morgan N. Price, Grant M. Zane, Jennifer V. Kuehl, Ryan A. Melnyk, Judy D. Wall, Adam M. Deutschbauer, Adam P. Arkin
bioRxiv 192971; doi: https://doi.org/10.1101/192971
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics
Morgan N. Price, Grant M. Zane, Jennifer V. Kuehl, Ryan A. Melnyk, Judy D. Wall, Adam M. Deutschbauer, Adam P. Arkin
bioRxiv 192971; doi: https://doi.org/10.1101/192971

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

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4842)
  • Biochemistry (10769)
  • Bioengineering (8030)
  • Bioinformatics (27240)
  • Biophysics (13952)
  • Cancer Biology (11102)
  • Cell Biology (16022)
  • Clinical Trials (138)
  • Developmental Biology (8766)
  • Ecology (13261)
  • Epidemiology (2067)
  • Evolutionary Biology (17336)
  • Genetics (11675)
  • Genomics (15900)
  • Immunology (11010)
  • Microbiology (26028)
  • Molecular Biology (10623)
  • Neuroscience (56436)
  • Paleontology (417)
  • Pathology (1729)
  • Pharmacology and Toxicology (2999)
  • Physiology (4538)
  • Plant Biology (9613)
  • Scientific Communication and Education (1612)
  • Synthetic Biology (2681)
  • Systems Biology (6967)
  • Zoology (1508)