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Essential role of γ‐clade RNA‐dependent RNA polymerases in rice development and yield‐related traits is linked to their atypical polymerase activities regulating specific genomic regions
Author(s) -
Jha Vikram,
Narjala Anushree,
Basu Debjani,
T. N. Sujith,
Pachamuthu Kannan,
Chenna Swetha,
Nair Ashwin,
Shivaprasad Padubidri V.
Publication year - 2021
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.17700
Subject(s) - biology , rna , genetics , gene , rna silencing , clade , gene silencing , small rna , polymerase , rna polymerase , non coding rna , rna interference , rna dependent rna polymerase , phylogenetics
Summary RNA‐dependent RNA polymerases (RDR) generate double‐stranded (ds)RNA triggers for RNA silencing across eukaryotes. Among the three clades, α‐clade and β‐clade members are key components of RNA silencing and mediators of stress responses across eukaryotes. However, γ‐clade members are unusual in that they are represented in phylogenetically distant plants and fungi, and their functions are unknown. Using genetic, bioinformatic and biochemical methods, we show that γ‐clade RDRs from Oryza sativa L. are involved in plant development as well as regulation of expression of coding and noncoding RNAs. Overexpression of γ‐clade RDRs in transgenic rice and tobacco plants resulted in robust growth phenotype, whereas their silencing in rice displayed strong inhibition of growth. Small (s)RNA and RNA‐seq analysis of OsRDR3 mis‐expression lines suggested that it is specifically involved in the regulation of repeat‐rich regions in the genome. Biochemical analysis confirmed that OsRDR3 has robust polymerase activities on both single stranded (ss)RNA and ssDNA templates similar to the activities reported for α‐clade RDRs such as AtRDR6. Our results provide the first evidence of the importance of γ‐clade RDRs in plant development, their atypical biochemical activities and their contribution to the regulation of gene expression.