. 2021 Jun 10;184(12):3333-3348.e19.

doi: 10.1016/j.cell.2021.04.024. Epub 2021 May 18.

Innovation, conservation, and repurposing of gene function in root cell type development

Kaisa Kajala¹, Mona Gouran², Lidor Shaar-Moshe³, G Alex Mason³, Joel Rodriguez-Medina⁴, Dorota Kawa³, Germain Pauluzzi⁵, Mauricio Reynoso⁶, Alex Canto-Pastor³, Concepcion Manzano³, Vincent Lau⁷, Mariana A S Artur⁸, Donnelly A West⁹, Sharon B Gray³, Alexander T Borowsky⁵, Bryshal P Moore¹⁰, Andrew I Yao¹¹, Kevin W Morimoto³, Marko Bajic¹², Elide Formentin¹³, Niba A Nirmal³, Alan Rodriguez³, Asher Pasha⁷, Roger B Deal¹², Daniel J Kliebenstein¹⁴, Torgeir R Hvidsten¹⁵, Nicholas J Provart⁷, Neelima R Sinha¹⁶, Daniel E Runcie¹⁴, Julia Bailey-Serres¹⁷, Siobhan M Brady¹⁸

Affiliations

¹ Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA; Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands.
² Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA; Plant Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA.
³ Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA.
⁴ Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA; Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA 95616, USA.
⁵ Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
⁶ Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; IBBM, FCE-UNLP CONICET, La Plata 1900, Argentina.
⁷ Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada.
⁸ Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands.
⁹ Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA 95616, USA; Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA.
¹⁰ Fort Valley State University, Fort Valley, GA 31030, USA.
¹¹ Department of Biomedical Engineering and Genome Center, University of California, Davis, Davis, CA 95616, USA.
¹² Department of Biology, Emory University, Atlanta, GA 30322, USA.
¹³ Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, University of Padova, Padova, Italy.
¹⁴ Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA.
¹⁵ Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway.
¹⁶ Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA.
¹⁷ Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands; Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
¹⁸ Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA. Electronic address: sbrady@ucdavis.edu.

PMID: 34010619
DOI: 10.1016/j.cell.2021.04.024

Free article

Innovation, conservation, and repurposing of gene function in root cell type development

Kaisa Kajala et al. Cell. 2021.

Free article

. 2021 Jun 10;184(12):3333-3348.e19.

doi: 10.1016/j.cell.2021.04.024. Epub 2021 May 18.

Authors

Affiliations

¹ Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA; Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands.
² Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA; Plant Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA.
³ Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA.
⁴ Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA; Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA 95616, USA.
⁵ Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
⁶ Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; IBBM, FCE-UNLP CONICET, La Plata 1900, Argentina.
⁷ Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada.
⁸ Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands.
⁹ Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA 95616, USA; Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA.
¹⁰ Fort Valley State University, Fort Valley, GA 31030, USA.
¹¹ Department of Biomedical Engineering and Genome Center, University of California, Davis, Davis, CA 95616, USA.
¹² Department of Biology, Emory University, Atlanta, GA 30322, USA.
¹³ Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, University of Padova, Padova, Italy.
¹⁴ Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA.
¹⁵ Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway.
¹⁶ Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA.
¹⁷ Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands; Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
¹⁸ Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA. Electronic address: sbrady@ucdavis.edu.

PMID: 34010619
DOI: 10.1016/j.cell.2021.04.024

Erratum in

Innovation, conservation, and repurposing of gene function in root cell type development.
Kajala K, Gouran M, Shaar-Moshe L, Mason GA, Rodriguez-Medina J, Kawa D, Pauluzzi G, Reynoso M, Canto-Pastor A, Manzano C, Lau V, Artur MAS, West DA, Gray SB, Borowsky AT, Moore BP, Yao AI, Morimoto KW, Bajic M, Formentin E, Nirmal NA, Rodriguez A, Pasha A, Deal RB, Kliebenstein DJ, Hvidsten TR, Provart NJ, Sinha NR, Runcie DE, Bailey-Serres J, Brady SM. Kajala K, et al. Cell. 2021 Sep 16;184(19):5070. doi: 10.1016/j.cell.2021.08.032. Cell. 2021. PMID: 34534466 No abstract available.

Abstract

Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals.

Keywords: cell types; evolution; exodermis; gene regulation; rice; root development; tomato; translatomes; xylem.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Comment in

Plants upcycle gene functions to suit their roots.
Zhu F, Fernie AR. Zhu F, et al. Trends Plant Sci. 2021 Oct;26(10):996-998. doi: 10.1016/j.tplants.2021.07.006. Epub 2021 Jul 17. Trends Plant Sci. 2021. PMID: 34284955

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Innovation, conservation, and repurposing of gene function in root cell type development

Affiliations

Innovation, conservation, and repurposing of gene function in root cell type development

Authors

Affiliations

Erratum in

Abstract

Conflict of interest statement

Comment in

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Molecular Biology Databases