Evidence map›Paper›PMID 37537586›Full record

ArticleMicrobial cell factories2023

Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts.

Samuel T Coradetti, Paul A Adamczyk, Di Liu, Yuqian Gao, Peter B Otoupal, Gina M Geiselman, Bobbie-Jo M Webb-Robertson, Meagan C Burnet, Young-Mo Kim, Kristin E Burnum-Johnson and 2 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbial cell factories, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
2.2field-weighted citation impact, top 13% 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

4 citing papers in PubMed, 20 citations in OpenAlex.

  1. Article
  2. Article
  3. Review
  4. 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

12 authors at 2 institutions in 1 country.

Samuel T Coradetti *DOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
Paul A Adamczyk *DOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
Di LiuDOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
Yuqian GaoDOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
Peter B OtoupalDOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
Gina M GeiselmanDOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
Bobbie-Jo M Webb-RobertsonPacific Northwest National Laboratory, Richland, WA, USA.
Meagan C BurnetPacific Northwest National Laboratory, Richland, WA, USA.
Young-Mo KimDOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
Kristin E Burnum-JohnsonDOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
Jon MagnusonDOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
John M GladdenDOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA. jmgladden@lbl.gov.
Pacific Northwest National Laboratory · USSandia National Laboratories California · US

Funding

Agile BioFoundry DE-AC02-05CH11231Environmental Molecular Sciences Laboratory DE-AC05-76RL01830
6 · The paper itself

Abstract

Efficient conversion of pentose sugars remains a significant barrier to the replacement of petroleum-derived chemicals with plant biomass-derived bioproducts. While the oleaginous yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) has a relatively robust native metabolism of pentose sugars compared to other wild yeasts, faster assimilation of those sugars will be required for industrial utilization of pentoses. To increase the rate of pentose assimilation in R. toruloides, we leveraged previously reported high-throughput fitness data to identify potential regulators of pentose catabolism. Two genes were selected for further investigation, a putative transcription factor (RTO4_12978, Pnt1) and a homolog of a glucose transceptor involved in carbon catabolite repression (RTO4_11990). Overexpression of Pnt1 increased the specific growth rate approximately twofold early in cultures on xylose and increased the maximum specific growth by 18% while decreasing accumulation of arabitol and xylitol in fast-growing cultures. Improved growth dynamics on xylose translated to a 120% increase in the overall rate of xylose conversion to fatty alcohols in batch culture. Proteomic analysis confirmed that Pnt1 is a major regulator of pentose catabolism in R. toruloides. Deletion of RTO4_11990 increased the growth rate on xylose, but did not relieve carbon catabolite repression in the presence of glucose. Carbon catabolite repression signaling networks remain poorly characterized in R. toruloides and likely comprise a different set of proteins than those mainly characterized in ascomycete fungi.

Indexed as

ProteomicsXyloseGlucosePentosesRhodotorulaGlucosePentosesXyloseCarbon catabolite repressionFatty alcoholProteomicsRhodosporidium toruloidesTranscriptional regulationXylose metabolism

Identifiers

PMID37537586
PMCPMC10398944
OpenAlexW4385550772

What Socratic holds

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LicenceCC BY
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 Socratic graph.