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Systematic characterization of gene function in a photosynthetic organism

View ORCID ProfileJosep Vilarrasa-Blasi, View ORCID ProfileFriedrich Fauser, View ORCID ProfileMasayuki Onishi, View ORCID ProfileSilvia Ramundo, View ORCID ProfileWeronika Patena, Matthew Millican, Jacqueline Osaki, Charlotte Philp, Matthew Nemeth, Patrice A. Salomé, View ORCID ProfileXiaobo Li, Setsuko Wakao, Rick G. Kim, Yuval Kaye, View ORCID ProfileArthur R. Grossman, View ORCID ProfileKrishna K. Niyogi, View ORCID ProfileSabeeha Merchant, View ORCID ProfileSean Cutler, View ORCID ProfilePeter Walter, View ORCID ProfileJosé R. Dinneny, View ORCID ProfileMartin C. Jonikas, View ORCID ProfileRobert E. Jinkerson
doi: https://doi.org/10.1101/2020.12.11.420950
Josep Vilarrasa-Blasi
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
6Department of Biology, Stanford University, Stanford, CA, USA
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Friedrich Fauser
1Department of Molecular Biology, Princeton University, Princeton, NJ, USA
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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Masayuki Onishi
5Department of Biology, Duke University, Durham, NC, USA
7Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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Silvia Ramundo
8Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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Weronika Patena
1Department of Molecular Biology, Princeton University, Princeton, NJ, USA
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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Matthew Millican
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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Jacqueline Osaki
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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Charlotte Philp
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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Matthew Nemeth
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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Patrice A. Salomé
9Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
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Xiaobo Li
1Department of Molecular Biology, Princeton University, Princeton, NJ, USA
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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Setsuko Wakao
10Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
11Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Rick G. Kim
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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Yuval Kaye
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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Arthur R. Grossman
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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Krishna K. Niyogi
10Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
11Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
12Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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Sabeeha Merchant
9Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
13Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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Sean Cutler
3Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
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Peter Walter
8Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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José R. Dinneny
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
6Department of Biology, Stanford University, Stanford, CA, USA
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Martin C. Jonikas
1Department of Molecular Biology, Princeton University, Princeton, NJ, USA
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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Robert E. Jinkerson
2Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
3Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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  • For correspondence: robert.jinkerson@ucr.edu
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Abstract

Photosynthetic organisms are essential for human life, yet most of their genes remain functionally uncharacterized. Single-celled photosynthetic model systems have the potential to accelerate our ability to connect genes to functions. 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. 78% 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 allow us to place known and previously 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 novel phenotypes and gene functions, including the discovery of three novel components of a defense pathway that counteracts actin cytoskeleton inhibitors released by other organisms. The data also inform phenotype discovery in land plants: mutants in Arabidopsis thaliana genes exhibit similar phenotypes 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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵⊠ e-mail: dinneny{at}stanford.edu, mjonikas{at}princeton.edu, robert.jinkerson{at}ucr.edu

  • https://www.chlamylibrary.org/download

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Systematic characterization of gene function in a photosynthetic organism
Josep Vilarrasa-Blasi, Friedrich Fauser, 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 Merchant, Sean Cutler, Peter Walter, José R. Dinneny, Martin C. Jonikas, Robert E. Jinkerson
bioRxiv 2020.12.11.420950; doi: https://doi.org/10.1101/2020.12.11.420950
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Systematic characterization of gene function in a photosynthetic organism
Josep Vilarrasa-Blasi, Friedrich Fauser, 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 Merchant, Sean Cutler, Peter Walter, José R. Dinneny, Martin C. Jonikas, Robert E. Jinkerson
bioRxiv 2020.12.11.420950; doi: https://doi.org/10.1101/2020.12.11.420950

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