Biological Roles of RNA Processing and its Regulations in Plants

Editorial

10 January 2024

Editorial: Plant RNA processing: discovery, mechanism and function

Lili Hao

Ming Chen

Dayong Li

and

Diego Lijavetzky

1,390 views

0 citations

Editors

Lili Hao

National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS)

Ming Chen

Zhejiang University

Dayong Li

Beijing Vegetable Research Center

Diego Lijavetzky

National Scientific and Technical Research Council (CONICET)

Impact

Review

19 January 2023

microRNA production in Arabidopsis

Ning Ding

and

Bailong Zhang

MIR genes are transcribed by POL II and regulated by multiple cotranscriptional regulators (such as mediator, DCL1 complex, TREX-2, ect.). The C-terminus of POL II can be phosphorylated by kinases during the transcription process. Pri-miRNA is processed at the dicing bodies (DCL1, HYL1 and SE). Pre-miRNA is subsequently processed by DCL1 into an imperfect miRNA/miRNA* duplexes. HEN1 methylates the 3’ end of the miRNA/miRNA*. Mature miRNAs are loaded into AGO1 protein in the nucleus. MiRISCs are exported into the cytoplasm through a CRM1 (EXPO1)/NES-dependent manner via the TREX-2/NUP1 facilitation pathway. EMA1 and TRN1 can negatively and positively regulate miRNA loading, respectively. Translocation of miRNAs from the nucleus to the cytoplasm directs target transcript cleavage and translation repression. AGO1 mediates cleavage of miRNA targets sequences, and followed by degradation of cleaved fragments. Translation repression occurs on membrane-bound polysomes (MBPs), and requires endoplasmic reticulum (ER)-localized AMP1. Degradation of miRNA begins with the removal of the methyl group at the 3’ end by the SDN1 family of 3’-5’ exonucleases, followed at 3’ end uridylation by the nucleotidyl transferases HESO1 and/or URT1. In addition, SDN1 and HESO1/URT1 can act on both AGO-bound miRNAs and free miRNAs in the cytoplasm. Free miRNAs are also degraded by SDN1 directly. For the target mRNAs cleaved by miRISC, RICE1 is responsible for degrading the uridylated target mRNA 5’ fragment. The 5’-3’ exonuclease XRN4 can degrade the 3’ fragment of target RNA.

In plants, microRNAs (miRNAs) associate with ARGONAUTE (AGO) proteins and act as sequence-specific repressors of target gene expression, at the post-transcriptional level through target transcript cleavage and/or translational inhibition. MiRNAs are mainly transcribed by DNA-dependent RNA polymerase II (POL II) and processed by DICER LIKE1 (DCL1) complex into 21∼22 nucleotide (nt) long. Although the main molecular framework of miRNA biogenesis and modes of action have been established, there are still new requirements continually emerging in the recent years. The studies on the involvement factors in miRNA biogenesis indicate that miRNA biogenesis is not accomplished separately step by step, but is closely linked and dynamically regulated with each other. In this article, we will summarize the current knowledge on miRNA biogenesis, including MIR gene transcription, primary miRNA (pri-miRNA) processing, miRNA AGO1 loading and nuclear export; and miRNA metabolism including methylation, uridylation and turnover. We will describe how miRNAs are produced and how the different steps are regulated. We hope to raise awareness that the linkage between different steps and the subcellular regulation are becoming important for the understanding of plant miRNA biogenesis and modes of action.

6,768 views

14 citations

Original Research

04 October 2022

Identification of long non-coding RNAs involved in floral scent of Rosa hybrida

Shaochuan Shi

, 3 more and

Zhao Zhang

Long non-coding RNAs (lncRNAs) were found to play important roles in transcriptional, post-transcriptional, and epigenetic gene regulation in various biological processes. However, lncRNAs and their regulatory roles remain poorly studied in horticultural plants. Rose is economically important not only for their wide use as garden and cut flowers but also as important sources of natural fragrance for perfume and cosmetics industry, but presently little was known about the regulatory mechanism of the floral scent production. In this paper, a RNA-Seq analysis with strand-specific libraries, was performed to rose flowers in different flowering stages. The scented variety ‘Tianmidemeng’ (Rosa hybrida) was used as plant material. A total of 13,957 lncRNAs were identified by mining the RNA-Seq data, including 10,887 annotated lncRNAs and 3070 novel lncRNAs. Among them, 10,075 lncRNAs were predicted to possess a total of 29,622 target genes, including 54 synthase genes and 24 transcription factors related to floral scent synthesis. 425 lncRNAs were differentially expressed during the flowering process, among which 19 were differentially expressed among all the three flowering stages. Using weighted correlation network analysis (WGCNA), we correlate the differentially-expressed lncRNAs to synthesis of individual floral scent compounds. Furthermore, regulatory function of one of candidate lncRNAs for floral scent synthesis was verified using VIGS method in the rose. In this study, we were able to show that lncRNAs may play important roles in floral scent production in the rose. This study also improves our understanding of how plants regulate their secondary metabolism by lncRNAs.

2,579 views

12 citations

Original Research

23 November 2022

ZmnMAT1, a nuclear-encoded type I maturase, is required for the splicing of mitochondrial Nad1 intron 1 and Nad4 intron 2

Kaijian Fan

, 8 more and

Yunjun Liu

1,588 views

0 citations

Rice mitochondrial RNA editing in well-watered (CK) and drought-treated (DT) fields. (A) RNA editing efficiencies of upland (U) and lowland (L) rice at 426 informative sites in well-watered (CK) and drought-treated (DT) fields. The dots within gray rectangle on top mark the significant difference in editing efficiency between rice upland (U) lowland (L) or treatments. (B) Proportion of increased, decreased, and unchanged editing efficiencies of genotype-site combinations at each mitochondrial gene.

Original Research

19 July 2022

Pentatricopeptide Repeat Gene-Mediated Mitochondrial RNA Editing Impacts on Rice Drought Tolerance

Zhi Luo

, 8 more and

Lijun Luo

Mitochondrial RNA editing plays crucial roles in the plant development and environmental adaptation. Pentatricopeptide repeat (PPR) genes, which are involved in the regulating mitochondrial RNA editing, are potential gene resources in the improvement of rice drought tolerance. In this study, we investigated genome-wide mitochondrial RNA editing in response to drought between upland and lowland rice. Responses of mitochondrial RNA editing to drought exhibit site-specific and genotype-specific patterns. We detected 22 and 57 ecotype-differentiated editing sites under well-watered and drought-treated conditions, respectively. Interestingly, the RNA editing efficiency was positively correlated with many agronomic traits, while it was negatively correlated with drought tolerance. We further selected two mitochondrial-localized PPR proteins, PPR035 and PPR406, to validate their functions in drought tolerance. PPR035 regulated RNA editing at rps4-926 and orfX-406, while PPR406 regulated RNA editing at orfX-355. The defectiveness in RNA editing at these sites had no apparent penalties in rice respiration and vegetative growth. Meanwhile, the knockout mutants of ppr035 and ppr406 show enhanced drought- and salt tolerance. PPR035 and PPR406 were under the balancing selection in upland rice and highly differentiated between upland and lowland rice ecotypes. The upland-dominant haplotypes of PPR035 and PPR406 shall contribute to the better drought tolerance in upland rice. They have great prospective in the improvement of rice drought tolerance.