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

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 116; no. 6; pp. 2374 - 2383
• Main Authors: Strenkert, Daniela, Schmollinger, Stefan, Gallaher, Sean D., Salomé, Patrice A., Purvine, Samuel O., Nicora, Carrie D., Mettler-Altmann, Tabea, Soubeyrand, Eric, Weber, Andreas P. M., Lipton, Mary S., Basset, Gilles J., Merchant, Sabeeha S.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 05.02.2019; National Academy of Sciences, Washington, DC (United States)
• Series: PNAS Plus
• Subjects: Aeration; Algae; BASIC BIOLOGICAL SCIENCES; Biological Sciences; Cell Division; Changing environments; Chlamydomonas - genetics; Chlamydomonas - metabolism; Chlamydomonas reinhardtii; chloroplast; DNA Replication; Fermentation; Ferredoxin; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes; Genomes; Genomics - methods; Glycolysis; histone expression; Light intensity; Luminous intensity; Metabolism; Metabolites; Metabolome; Metabolomics - methods; NAD - metabolism; Night; Oxidation-Reduction; photo-bioreactor; Photosynthesis - genetics; Pigments; Plant communities; Plant populations; PNAS Plus; Proteins; Proteome; Proteomes; Proteomics - methods; Signal Transduction; systems biology; Transcriptome; systems biology; cell division; photobioreactor; chloroplast; histone expression
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1815238116

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.