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Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism

Journal Article · · mSystems
 [1];  [1];  [2];  [1];  [3];  [3];  [4];  [5];
  1. Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  2. QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, California, USA
  3. DOE Joint Genome Institute, Walnut Creek, California, USA
  4. Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA, Department of Bioengineering, University of California, Berkeley, California, USA
  5. Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA, Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
+ Show Author Affiliations

Deoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants’ abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of metabolism. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways.

Sponsoring Organization:
USDOE
Grant/Contract Number:
NONE; AC02-05CH11231
OSTI ID:
1493373
Alternate ID(s):
OSTI ID: 1508059
Journal Information:
mSystems, Journal Name: mSystems Journal Issue: 1 Vol. 4; ISSN 2379-5077
Publisher:
American Society for MicrobiologyCopyright Statement
Country of Publication:
United States
Language:
English

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