Evidence map›Paper›PMID 41272269›Full record

ArticleCommunications biology2025

A multi-omic characterization of the physiological responses to salt stress in Scenedesmus obliquus UTEX393.

Colin P S Kruse, Sara Calhoun, Bishoy Kamel, Scott J Edmundson, Omar Holguin, Phillip M Mach, Zaid McKie-Krisberg, Leo Baumgart, Ian K Blaby, Benjamin Bowen and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Communications biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Exogenous putrescine enhances salt tolerance inFrontiers in plant science · 2025
    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

29 authors.

Colin P S KruseBioscience Division, Los Alamos National Laboratory, Genomics and Bioanalytics Group (B-GEN), Los Alamos, NM, USA. krusec@lanl.gov.ORCID http://orcid.org/0000-0001-7070-8889
Sara CalhounUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-2942-1338
Bishoy KamelUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-2934-3827
Scott J EdmundsonPacific Northwest National Laboratory, Marine and Coastal Research Laboratory, Sequim, WA, USA.ORCID http://orcid.org/0000-0002-4763-6917
Omar HolguinDepartment of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, USA.
Phillip M MachBioscience Division, Los Alamos National Laboratory, Genomics and Bioanalytics Group (B-GEN), Los Alamos, NM, USA.
Zaid McKie-KrisbergDepartment of Biology, Brooklyn College of City University of New York, New York, NY, USA.
Leo BaumgartUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-2773-5897
Ian K BlabyUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-1631-3154
Benjamin BowenUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-1368-3958
Cindy ChenUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-7539-103X
Yuliya KundeBioscience Division, Los Alamos National Laboratory, Genomics and Bioanalytics Group (B-GEN), Los Alamos, NM, USA.
Jane GrimwoodUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-8356-8325
Anna LipzenUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-2293-9329
Katherine LouieUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-6787-7558
Ritesh MewalalUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Cheryl D GleasnerBioscience Division, Los Alamos National Laboratory, Genomics and Bioanalytics Group (B-GEN), Los Alamos, NM, USA.
Trent NorthenUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-8404-3259
Jayson TalagArizona Genomics Institute, University of Arizona, Tucson, AZ, USA.
Daniel TreenUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-8896-0000
Yu ZhangUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-4495-3447
Andrew GutknechtPacific Northwest National Laboratory, Marine and Coastal Research Laboratory, Sequim, WA, USA.
Ronan C O'MalleyUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-4907-0339
Trevor G GlarosBioscience Division, Los Alamos National Laboratory, Genomics and Bioanalytics Group (B-GEN), Los Alamos, NM, USA.
Juergen PolleDepartment of Biology, Brooklyn College of City University of New York, New York, NY, USA.
James UmenEnterprise Institute for Renewable Fuels, Donald Danforth Plant Science Center, St. Louis, MO, USA.ORCID http://orcid.org/0000-0003-4094-9045
Michael HuesemannPacific Northwest National Laboratory, Marine and Coastal Research Laboratory, Sequim, WA, USA.
Igor V GrigorievUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-3136-8903
Shawn R StarkenburgBioscience Division, Los Alamos National Laboratory, Genomics and Bioanalytics Group (B-GEN), Los Alamos, NM, USA. shawns@lanl.gov.ORCID http://orcid.org/0000-0002-8564-1274

Funding

DOE | Office of Energy Efficiency & Renewable Energy | Bioenergy Technologies Office (BETO) NL0032266DOE | Office of Science (SC) DE-AC02-05CH11231
6 · The paper itself

Abstract

Scenedesmus obliquus UTEX393 is a promising microalgal candidate for sustainable biomanufacturing but its limited halotolerance hinders large-scale cultivation in saline environments. To investigate the molecular basis of salt stress responses, we conducted a comprehensive multi-omic analysis integrating genomics, transcriptomics, proteomics, lipidomics, metabolomics, and DNA affinity purification sequencing (DAP-seq). An improved nuclear genome assembly and annotation yielded 19,017 gene models and a 97% BUSCO completeness score, enabling construction of a genome-scale metabolic model. Comparing 15 ppt salinity stress to 5 ppt control, growth and productivity were significantly reduced, accompanied by widespread transcriptomic and proteomic changes. Transcriptomic analysis revealed downregulation of photosynthetic machinery and energy conservation genes, and upregulation of stress-responsive elements such as expansins, flavodoxins, and osmoprotectants. Lipidomic profiling showed accumulation of triacylglycerols (TAGs) and degradation of galactosyl lipids, consistent with a shift toward lipid biosynthesis to mitigate redox imbalance. Depletion of key polar metabolites and branched-chain amino acids suggested a rerouting of central carbon metabolism under stress. DAP-seq identified key transcription factors, including LHY1 and SPL12, that target central metabolic enzymes involved in redox balancing, such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and malate dehydrogenase (MDH). These findings establish a regulatory-metabolic framework linking redox stress to lipid accumulation and reveal potential engineering targets to enhance salt tolerance. Overall, the multi-omic analysis supports the "overflow" hypothesis, where impaired photosynthesis results in excess reducing equivalents being diverted into TAG synthesis and highlights transcriptional regulators as candidates for improving algal robustness in brackish environments.

Indexed as

Salt StressScenedesmusGene Expression ProfilingLipidomicsMetabolomicsMultiomicsProteomicsTranscriptome

Identifiers

PMID41272269
PMCPMC12638912

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.