Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii

Friedrich Fauser; Josep Vilarrasa-Blasi; Masayuki Onishi; Silvia Ramundo; Weronika Patena; Matthew Millican; Jacqueline Osaki; Charlotte Philp; Matthew Nemeth; Patrice A Salomé; Xiaobo Li; Setsuko Wakao; Rick G Kim; Yuval Kaye; Arthur R Grossman; Krishna K Niyogi; Sabeeha S Merchant; Sean R Cutler; Peter Walter; José R Dinneny; Martin C Jonikas; Robert E Jinkerson

doi:10.1038/s41588-022-01052-9

Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii

Nat Genet. 2022 May;54(5):705-714. doi: 10.1038/s41588-022-01052-9. Epub 2022 May 5.

Authors

Friedrich Fauser^#^{1

2}, Josep Vilarrasa-Blasi^#^{2

3}, Masayuki Onishi^{4

5}, Silvia Ramundo⁶, Weronika Patena^{1

2}, Matthew Millican², Jacqueline Osaki², Charlotte Philp², Matthew Nemeth², Patrice A Salomé⁷, Xiaobo Li^{1

2

8}, Setsuko Wakao^{9

10}, Rick G Kim², Yuval Kaye², Arthur R Grossman², Krishna K Niyogi^{9

10

11}, Sabeeha S Merchant^{7

12}, Sean R Cutler¹³, Peter Walter⁶, José R Dinneny^{14

15}, Martin C Jonikas^{16

17}, Robert E Jinkerson^{18

19

20}

Affiliations

¹ Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
² Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA.
³ Department of Biology, Stanford University, Stanford, CA, USA.
⁴ Department of Biology, Duke University, Durham, NC, USA.
⁵ Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
⁶ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
⁷ Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.
⁸ School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.
⁹ Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
¹⁰ Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹¹ Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
¹² Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
¹³ Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.
¹⁴ Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA. dinneny@stanford.edu.
¹⁵ Department of Biology, Stanford University, Stanford, CA, USA. dinneny@stanford.edu.
¹⁶ Department of Molecular Biology, Princeton University, Princeton, NJ, USA. mjonikas@princeton.edu.
¹⁷ Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA. mjonikas@princeton.edu.
¹⁸ Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA. robert.jinkerson@ucr.edu.
¹⁹ Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA. robert.jinkerson@ucr.edu.
²⁰ Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA. robert.jinkerson@ucr.edu.

^# Contributed equally.

Abstract

Most genes in photosynthetic organisms remain functionally uncharacterized. Here, using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, we determined the phenotypes of more than 58,000 mutants under more than 121 different environmental growth conditions and chemical treatments. A total of 59% of genes are represented by at least one mutant that showed a phenotype, providing clues to the functions of thousands of genes. Mutant phenotypic profiles place uncharacterized genes into functional pathways such as DNA repair, photosynthesis, the CO₂-concentrating mechanism and ciliogenesis. We illustrate the value of this resource by validating phenotypes and gene functions, including three new components of an actin cytoskeleton defense pathway. The data also inform phenotype discovery in land plants; mutants in Arabidopsis thaliana genes exhibit phenotypes similar to those we observed in their Chlamydomonas homologs. We anticipate that this resource will guide the functional characterization of genes across the tree of life.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

Arabidopsis* / genetics
Chlamydomonas reinhardtii* / genetics
Eukaryota
Phenotype
Photosynthesis / genetics

Abstract

Publication types

MeSH terms

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