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

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. DinnenyMartin C. Jonikas, Robert E. Jinkerson

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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.

Original language	English (US)
Pages (from-to)	705-714
Number of pages	10
Journal	Nature Genetics
Volume	54
Issue number	5
DOIs	https://doi.org/10.1038/s41588-022-01052-9
State	Published - May 2022

All Science Journal Classification (ASJC) codes

Genetics

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Fauser, F., Vilarrasa-Blasi, J., Onishi, M., Ramundo, S., Patena, W., Millican, M., Osaki, J., Philp, C., Nemeth, M., Salomé, P. A., Li, X., Wakao, S., Kim, R. G., Kaye, Y., Grossman, A. R., Niyogi, K. K., Merchant, S. S., Cutler, S. R., Walter, P., ... Jinkerson, R. E. (2022). Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii. Nature Genetics, 54(5), 705-714. https://doi.org/10.1038/s41588-022-01052-9

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title = "Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii",

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.",

author = "Friedrich Fauser and Josep Vilarrasa-Blasi and Masayuki Onishi and Silvia Ramundo and Weronika Patena and Matthew Millican and Jacqueline Osaki and Charlotte Philp and Matthew Nemeth and Salom{\'e}, {Patrice A.} and Xiaobo Li and Setsuko Wakao and Kim, {Rick G.} and Yuval Kaye and Grossman, {Arthur R.} and Niyogi, {Krishna K.} and Merchant, {Sabeeha S.} and Cutler, {Sean R.} and Peter Walter and Dinneny, {Jos{\'e} R.} and Jonikas, {Martin C.} and Jinkerson, {Robert E.}",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = may,

doi = "10.1038/s41588-022-01052-9",

language = "English (US)",

volume = "54",

pages = "705--714",

journal = "Nature Genetics",

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Fauser, F, Vilarrasa-Blasi, J, Onishi, M, Ramundo, S, Patena, W, Millican, M, Osaki, J, Philp, C, Nemeth, M, Salomé, PA, Li, X, Wakao, S, Kim, RG, Kaye, Y, Grossman, AR, Niyogi, KK, Merchant, SS, Cutler, SR, Walter, P, Dinneny, JR, Jonikas, MC & Jinkerson, RE 2022, 'Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii', Nature Genetics, vol. 54, no. 5, pp. 705-714. https://doi.org/10.1038/s41588-022-01052-9

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T1 - Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii

AU - Fauser, Friedrich

AU - Vilarrasa-Blasi, Josep

AU - Onishi, Masayuki

AU - Ramundo, Silvia

AU - Patena, Weronika

AU - Millican, Matthew

AU - Osaki, Jacqueline

AU - Philp, Charlotte

AU - Nemeth, Matthew

AU - Salomé, Patrice A.

AU - Li, Xiaobo

AU - Wakao, Setsuko

AU - Kim, Rick G.

AU - Kaye, Yuval

AU - Grossman, Arthur R.

AU - Niyogi, Krishna K.

AU - Merchant, Sabeeha S.

AU - Cutler, Sean R.

AU - Walter, Peter

AU - Dinneny, José R.

AU - Jonikas, Martin C.

AU - Jinkerson, Robert E.

PY - 2022/5

Y1 - 2022/5

N2 - 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.

AB - 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.

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JO - Nature Genetics

JF - Nature Genetics

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Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii

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