Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis

Autor: Joachim Kopka, Alexandre Augusto Pereira Firmino, Dirk Walther, Aleksandra Skirycz, Yin-Chen Hsieh, Kheloud El Eshraky, Bo-Eng Cheong, Olga Beine-Golovchuk, Ute Roessner, Federico Martinez-Seidel, Erika V. Jimenez-Posada, Michal Gorka
Jazyk: angličtina
Rok vydání: 2021
Předmět:
Ribosomal Proteins
0106 biological sciences
0301 basic medicine
Proteome
QH301-705.5
Acclimatization
Arabidopsis
Ribosome biogenesis
ribosome biogenesis
Biology
01 natural sciences
Ribosome
Catalysis
Article
substoichiometry
Inorganic Chemistry
03 medical and health sciences
Polysome
Cold acclimation
paralog subfunctionalization
Biology (General)
Physical and Theoretical Chemistry
QD1-999
Molecular Biology
Spectroscopy
remodeling
ribosomal code
Arabidopsis Proteins
Eukaryotic Large Ribosomal Subunit
Organic Chemistry
Translation (biology)
General Medicine
functional heterogeneity
Ribosomal RNA
stress-specialized ribosomes
Computer Science Applications
Cell biology
ribosome-associated proteins
Cold Temperature
Chemistry
030104 developmental biology
Ribosomes
Biogenesis
010606 plant biology & botany
Zdroj: International Journal of Molecular Sciences
International Journal of Molecular Sciences, Vol 22, Iss 6160, p 6160 (2021)
Volume 22
Issue 11
ISSN: 1422-0067
Popis: Ribosome biogenesis is essential for plants to successfully acclimate to low temperature. Without dedicated steps supervising the 60S large subunits (LSUs) maturation in the cytosol, e.g., Rei-like (REIL) factors, plants fail to accumulate dry weight and fail to grow at suboptimal low temperatures. Around REIL, the final 60S cytosolic maturation steps include proofreading and assembly of functional ribosomal centers such as the polypeptide exit tunnel and the P-Stalk, respectively. In consequence, these ribosomal substructures and their assembly, especially during low temperatures, might be changed and provoke the need for dedicated quality controls. To test this, we blocked ribosome maturation during cold acclimation using two independent reil double mutant genotypes and tested changes in their ribosomal proteomes. Additionally, we normalized our mutant datasets using as a blank the cold responsiveness of a wild-type Arabidopsis genotype. This allowed us to neglect any reil-specific effects that may happen due to the presence or absence of the factor during LSU cytosolic maturation, thus allowing us to test for cold-induced changes that happen in the early nucleolar biogenesis. As a result, we report that cold acclimation triggers a reprogramming in the structural ribosomal proteome. The reprogramming alters the abundance of specific RP families and/or paralogs in non-translational LSU and translational polysome fractions, a phenomenon known as substoichiometry. Next, we tested whether the cold-substoichiometry was spatially confined to specific regions of the complex. In terms of RP proteoforms, we report that remodeling of ribosomes after a cold stimulus is significantly constrained to the polypeptide exit tunnel (PET), i.e., REIL factor binding and functional site. In terms of RP transcripts, cold acclimation induces changes in RP families or paralogs that are significantly constrained to the P-Stalk and the ribosomal head. The three modulated substructures represent possible targets of mechanisms that may constrain translation by controlled ribosome heterogeneity. We propose that non-random ribosome heterogeneity controlled by specialized biogenesis mechanisms may contribute to a preferential or ultimately even rigorous selection of transcripts needed for rapid proteome shifts and successful acclimation.
Databáze: OpenAIRE
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