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Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2374-2383. doi: 10.1073/pnas.1815238116. Epub 2019 Jan 18.

Multiomics resolution of molecular events during a day in the life of Chlamydomonas.

Author information

1
Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095.
2
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095.
3
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), US Department of Energy, Richland, WA 99352.
4
Biological Sciences Divison, PNNL, US Department of Energy, Richland, WA 99352.
5
Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich Heine University, 40225 Düsseldorf, Germany.
6
Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588.
7
Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095; sabeeha@chem.ucla.edu.

Abstract

The unicellular green alga Chlamydomonas reinhardtii displays metabolic flexibility in response to a changing environment. We analyzed expression patterns of its three genomes in cells grown under light-dark cycles. Nearly 85% of transcribed genes show differential expression, with different sets of transcripts being up-regulated over the course of the day to coordinate cellular growth before undergoing cell division. Parallel measurements of select metabolites and pigments, physiological parameters, and a subset of proteins allow us to infer metabolic events and to evaluate the impact of the transcriptome on the proteome. Among the findings are the observations that Chlamydomonas exhibits lower respiratory activity at night compared with the day; multiple fermentation pathways, some oxygen-sensitive, are expressed at night in aerated cultures; we propose that the ferredoxin, FDX9, is potentially the electron donor to hydrogenases. The light stress-responsive genes PSBS, LHCSR1, and LHCSR3 show an acute response to lights-on at dawn under abrupt dark-to-light transitions, while LHCSR3 genes also exhibit a later, second burst in expression in the middle of the day dependent on light intensity. Each response to light (acute and sustained) can be selectively activated under specific conditions. Our expression dataset, complemented with coexpression networks and metabolite profiling, should constitute an excellent resource for the algal and plant communities.

KEYWORDS:

cell division; chloroplast; histone expression; photobioreactor; systems biology

PMID:
30659148
PMCID:
PMC6369806
DOI:
10.1073/pnas.1815238116
[Indexed for MEDLINE]
Free PMC Article

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