Multiomics resolution of molecular events during a day in the life of Chlamydomonas
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...
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Published in | Proceedings of the National Academy of Sciences - PNAS Vol. 116; no. 6; pp. 2374 - 2383 |
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Main Authors | , , , , , , , , , , , |
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 | |
Online Access | Get full text |
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Summary: | 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. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 FC02-02ER63421; AC05-76RL01830; AC02-05CH11231 PNNL-SA-140230 USDOE Office of Science (SC), Biological and Environmental Research (BER) 2Present addresses: Department of Plant and Microbial Biology and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720. Author contributions: D.S. and S.S.M. designed research; D.S., S.S., S.D.G., P.A.S., S.O.P., C.D.N., T.M.-A., E.S., and G.J.B. performed research; S.D.G., S.O.P., C.D.N., T.M.-A., E.S., A.P.M.W., M.S.L., and G.J.B. contributed new reagents/analytic tools; D.S., S.S., S.D.G., P.A.S., S.O.P., C.D.N., T.M.-A., E.S., A.P.M.W., M.S.L., G.J.B., and S.S.M. analyzed data; and D.S., P.A.S., and S.S.M. wrote the paper. 1Present address: Horticultural Sciences Department, University of Florida, Gainesville, FL 32611. Reviewers: A.A., UMR Marbec; and M.G.-C., University of Geneva. Contributed by Sabeeha S. Merchant, November 26, 2018 (sent for review September 7, 2018; reviewed by Ariane Atteia and Michel Goldschmidt-Clermont) |
ISSN: | 0027-8424 1091-6490 |
DOI: | 10.1073/pnas.1815238116 |