Evidence map›Paper›PMID 27989805›Full record

ArticleMetabolic engineering2016

Engineering a functional 1-deoxy-D-xylulose 5-phosphate (DXP) pathway in Saccharomyces cerevisiae.

James Kirby, Kevin L Dietzel, Gale Wichmann, Rossana Chan, Eugene Antipov, Nathan Moss, Edward E K Baidoo, Peter Jackson, Sara P Gaucher, Shayin Gottlieb and 8 more

Open access · greenAbstract read
In one paragraph

Article in Metabolic engineering, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.

0numbers the graph read from it
0cells of the map it votes in
24citing papers in PubMed
3.8field-weighted citation impact, top 6% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

24 citing papers in PubMed, 63 citations in OpenAlex.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Article
  6. Balancing Cell Growth and Product Synthesis for Efficient Microbial Cell Factories.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
    Review
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Review
  13. Review
  14. Review
  15. Diversifying Isoprenoid PlatformsFrontiers in microbiology · 2021
    Review
  16. Article
  17. Modular engineering for microbial production of carotenoids.Metabolic engineering communications · 2020
    Review
  18. Review
  19. Review
  20. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors at 5 institutions in 2 countries.

James KirbyCalifornia Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA.
Kevin L DietzelAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Gale WichmannAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Rossana ChanCalifornia Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA.
Eugene AntipovAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Nathan MossAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Edward E K BaidooJoint BioEnergy Institute, Emeryville, CA 94608, USA.
Peter JacksonAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Sara P GaucherAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Shayin GottliebAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Jeremy LaBargeAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Tina MahatdejkulAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Kristy M HawkinsAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Sheela MuleyAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Jack D NewmanAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
Pinghua LiuDepartment of Chemistry, Boston University, Boston, MA 02215, USA.
Jay D KeaslingCalifornia Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA; Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA 94702, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94702, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé, DK2970 Hørsholm, Denmark.
Lishan ZhaoAmyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA. Electronic address: zhao@amyris.com.
Amyris (United States) · USJoint BioEnergy Institute · USBoston University · USQB3 · USUniversity of California, Berkeley · US

Funding

Mechanistic studies of enzymes in isoprenoid biosynthesisR01GM093903 · NIGMS · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI LIU, PINGHUA · 2010 to 2014
$1.5M
NIGMS NIH HHS R01 GM093903
6 · The paper itself

Abstract

Isoprenoids are used in many commercial applications and much work has gone into engineering microbial hosts for their production. Isoprenoids are produced either from acetyl-CoA via the mevalonate pathway or from pyruvate and glyceraldehyde 3-phosphate via the 1-deoxy-D-xylulose 5-phosphate (DXP) pathway. Saccharomyces cerevisiae exclusively utilizes the mevalonate pathway to synthesize native isoprenoids and in fact the alternative DXP pathway has never been found or successfully reconstructed in the eukaryotic cytosol. There are, however, several advantages to isoprenoid synthesis via the DXP pathway, such as a higher theoretical yield, and it has long been a goal to transplant the pathway into yeast. In this work, we investigate and address barriers to DXP pathway functionality in S. cerevisiae using a combination of synthetic biology, biochemistry and metabolomics. We report, for the first time, functional expression of the DXP pathway in S. cerevisiae. Under low aeration conditions, an engineered strain relying solely on the DXP pathway for isoprenoid biosynthesis achieved an endpoint biomass 80% of that of the same strain using the mevalonate pathway.

Indexed as

Metabolic EngineeringPentosephosphatesSaccharomyces cerevisiaeTerpenes1-deoxylulose 5-phosphatePentosephosphatesTerpenesMEP pathwaymetabolic engineeringterpeneyeast

Identifiers

PMID27989805
PMCPMC5718835
OpenAlexW2540731211

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.