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SeedTransNet: a directional translational network revealing regulatory patterns during seed maturation and germination
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands.
Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
Department of Molecular Plant Physiology, Utrecht University, Utrecht, Netherlands.
Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands.
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2023 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 74, no 7, p. 2416-2432Article in journal (Refereed) Published
Abstract [en]

Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.

Place, publisher, year, edition, pages
Oxford University Press, 2023. Vol. 74, no 7, p. 2416-2432
Keywords [en]
Arabidopsis thaliana, mRNA regulation, ribosome, seed germination, seed maturation, translatome profiling
National Category
Botany
Identifiers
URN: urn:nbn:se:umu:diva-209153DOI: 10.1093/jxb/erac394ISI: 000885655900001PubMedID: 36208446Scopus ID: 2-s2.0-85160085758OAI: oai:DiVA.org:umu-209153DiVA, id: diva2:1770900
Funder
Bio4EnergySwedish National Infrastructure for Computing (SNIC)Available from: 2023-06-20 Created: 2023-06-20 Last updated: 2023-06-20Bibliographically approved

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Bai, BingMähler, NiklasHanson, Johannes

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