Evidence map›Paper›PMID 37421944›Full record

ArticleCell chemical biology2023

Integration of metabolism and regulation reveals rapid adaptability to growth on non-native substrates.

Vikas D Trivedi, Sean F Sullivan, Debika Choudhury, Venkatesh Endalur Gopinarayanan, Taylor Hart, Nikhil U Nair

Abstract read
In one paragraph

Article in Cell chemical biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
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

2 citing papers in PubMed.

  1. Article
  2. Article
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

6 authors.

Vikas D TrivediDepartment of Chemical & Biological Engineering, Tufts University, Medford, MA, USA.
Sean F SullivanDepartment of Chemical & Biological Engineering, Tufts University, Medford, MA, USA.
Debika ChoudhuryDepartment of Chemical & Biological Engineering, Tufts University, Medford, MA, USA.
Venkatesh Endalur GopinarayananDepartment of Chemical & Biological Engineering, Tufts University, Medford, MA, USA.
Taylor HartDepartment of Chemical & Biological Engineering, Tufts University, Medford, MA, USA.
Nikhil U NairDepartment of Chemical & Biological Engineering, Tufts University, Medford, MA, USA. Electronic address: nikhil.nair@tufts.edu.

Funding

Metabolic engineering in humans: Altered gut microbes as a therapeutic platformDP2HD091798 · NICHD · TUFTS UNIVERSITY MEDFORD · PI NAIR, NIKHIL UNNI · 2016 to 2016
$2.3M
NICHD NIH HHS DP2 HD091798
6 · The paper itself

Abstract

Engineering synthetic heterotrophy is a key to the efficient bio-based valorization of renewable and waste substrates. Among these, engineering hemicellulosic pentose utilization has been well-explored in Saccharomyces cerevisiae (yeast) over several decades-yet the answer to what makes their utilization inherently recalcitrant remains elusive. Through implementation of a semi-synthetic regulon, we find that harmonizing cellular and engineering objectives are a key to obtaining highest growth rates and yields with minimal metabolic engineering effort. Concurrently, results indicate that "extrinsic" factors-specifically, upstream genes that direct flux of pentoses into central carbon metabolism-are rate-limiting. We also reveal that yeast metabolism is innately highly adaptable to rapid growth on non-native substrates and that systems metabolic engineering (i.e., functional genomics, network modeling, etc.) is largely unnecessary. Overall, this work provides an alternate, novel, holistic (and yet minimalistic) approach based on integrating non-native metabolic genes with a native regulon system.

Indexed as

PentosesSaccharomyces cerevisiaeFermentationMetabolic EngineeringPentosesbiomanufacturinginhibitorslignocellulosemetabolic engineeringpleiotropic effectsstress responsesustainabilitysynthetic biologysystems biologytranscriptomics

Identifiers

PMID37421944
PMCPMC10529486

What OpenQuestion holds

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Registered trials

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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.