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

Abstract

The unicellular green algaChlamydomonas reinhardtiidisplays 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 thatChlamydomonasexhibits 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 genesPSBS,LHCSR1, andLHCSR3show an acute response to lights-on at dawn under abrupt dark-to-light transitions, whileLHCSR3genes 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.

Authors:

Strenkert, Daniela ;

• Search DOE PAGES for author "Strenkert, Daniela"
• Search DOE PAGES for ORCID "0000-0002-3420-1332"

Schmollinger, Stefan; Gallaher, Sean D. ;

• Search DOE PAGES for author "Gallaher, Sean D."
• Search DOE PAGES for ORCID "0000-0002-9773-6051"

Salomé, Patrice A. ;

• Search DOE PAGES for author "Salomé, Patrice A."
• Search DOE PAGES for ORCID "0000-0003-4452-9064"

Purvine, Samuel O. ;

• Search DOE PAGES for author "Purvine, Samuel O."
• Search DOE PAGES for ORCID "0000-0002-2257-2400"

Nicora, Carrie D. ;

• Search DOE PAGES for author "Nicora, Carrie D."
• Search DOE PAGES for ORCID "0000-0003-2461-9548"

Mettler-Altmann, Tabea ;

• Search DOE PAGES for author "Mettler-Altmann, Tabea"
• Search DOE PAGES for ORCID "0000-0002-9161-4889"

Soubeyrand, Eric ;

• Search DOE PAGES for author "Soubeyrand, Eric"
• Search DOE PAGES for ORCID "0000-0003-2970-3183"

Weber, Andreas P. M.; Lipton, Mary S.; Basset, Gilles J. ;

• Search DOE PAGES for author "Basset, Gilles J."
• Search DOE PAGES for ORCID "0000-0001-5275-9797"

Merchant, Sabeeha S.

Publication Date:

Fri Jan 18 00:00:00 EST 2019

Research Org.:

Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:

1491412

Alternate Identifier(s):

OSTI ID: 1501660; OSTI ID: 1561906

Report Number(s):

PNNL-SA-140230
Journal ID: ISSN 0027-8424

Grant/Contract Number:  

FC02-02ER63421; AC05-76RL01830; AC02-05CH11231

Resource Type:

Published Article

Journal Name:

Proceedings of the National Academy of Sciences of the United States of America

Additional Journal Information:

Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 116 Journal Issue: 6; Journal ID: ISSN 0027-8424

Publisher:

National Academy of Sciences, Washington, DC (United States)

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; photo-bioreactor; systems biology; cell division; histone expression; chloroplast