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

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.

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Publication Details

Journal
Communications Biology
Published
2025-11-21
DOI
https://doi.org/10.1038/s42003-025-09016-5
Citations
3
Primary Topic
Algal biology and biofuel production
Type
article
Field-Weighted Citation Impact
1.09

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article

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

Sara Calhoun, Scott Edmundson, Shawn R. Starkenburg, Zaid McKie‐Krisberg et al.
3 citations
Communications Biology
Algal biology and biofuel production
1.09
article

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

Sara Calhoun, Scott Edmundson, Shawn R. Starkenburg, Zaid McKie‐Krisberg, Igor V. Grigoriev, Cindy Chen, Ritesh Mewalal, Jayson Talag, Juergen Polle, Yu Zhang, Omar Holguin, Daniel Treen, Anna Lipzen, Ronan C. O’Malley, Ian K. Blaby, Trent R. Northen, Benjamin P. Bowen, Leo Baumgart, Michael H. Huesemann, Jane Grimwood, Bishoy Kamel, James Umen, Phillip M. Mach, Colin P. S. Kruse, Katherine Louie, Yuliya A. Kunde, Cheryl D. Gleasner, Trevor Glaros, Andrew Gutknecht
article en
3 citations

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.

Communications BiologyVol. 8(1)
New Mexico State University (US), Los Alamos National Laboratory (US), University of Arizona (US), Pacific Northwest National Laboratory (US), Lawrence Berkeley National Laboratory (US), City University of New York (US), Joint Genome Institute (US), Donald Danforth Plant Science Center (US), Los Alamos National Security (United States) (US), HudsonAlpha Institute for Biotechnology (US), New York City College of Technology (US), Brooklyn College (US), University of California, Berkeley (US)
U.S. Department of Energy, New Mexico State University, Joint Genome Institute, Office of Science, Office of Energy Efficiency and Renewable Energy, Bioenergy Technologies Office, Office of Energy Efficiency, Lawrence Berkeley National Laboratory, Los Alamos National Laboratory, Pacific Northwest National Laboratory
Openalex Percentile: Top 21%
Algal biology and biofuel production
1.09
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