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miRNA plant

Yanfei Ding, Shaohua Gong, Yi Wang, Feijuan Wang, Hexigeduleng Bao, Junwei Sun, Chong Cai, Keke Yi, Zhixiang Chen, Cheng Zhu
MicroRNAs (miRNAs) are 20- to 24-nucleotide small non-coding RNAs that regulate gene expression in eukaryotic organisms. Several plant miRNAs, such as miR166, have vital roles in plant growth, development and responses to environmental stresses. One such environmental stress encountered by crop plants is exposure to cadmium (Cd), an element highly toxic to most organisms, including humans and plants. In this study, we analyzed the role of miR166 in Cd accumulation and tolerance in rice (Oryza sativa). The expression levels of miR166 in both root and leaf tissues were significantly higher in the reproductive stage than in the seedling stage in rice...
June 20, 2018: Plant Physiology
Beibei Chen, Jinhui Chen, Qingzhang Du, Daling Zhou, Longxin Wang, Jianbo Xie, Ying Li, Deqiang Zhang
MicroRNAs (miRNAs) function as key regulators of complex traits, but how genetic alterations in miRNA biogenesis genes (miRBGs) affect quantitative variation has not been elucidated. We conducted transcript analyses and association genetics to investigate how miRBGs, miRNA genes (MIRNAs) and their respective targets contribute to secondary growth in a natural population of 435 Populus tomentosa individuals. This analysis identified 29 843 common single-nucleotide polymorphisms (SNPs; frequency > 0.10) within 682 genes (80 miRBGs, 152 MIRNAs, and 457 miRNA targets)...
June 19, 2018: New Phytologist
Yun Lu, Wei Gao, Lu-Qi Huang
miRNA (microRNA) is a kind of important endogenous non-coding small RNA, which mainly regulates the expression of target gene at the post-transcriptional level by splicing and translation inhibition and it plays an important role in the synthesis of plant secondary metabolites, especially for medicinal plants, the secondary metabolites are mostly active ingredients, which are the basis of medicinal effects. It is of great significance to study the biosynthetic pathways and complex regulatory networks of secondary metabolites of medicinal plants...
May 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Raghuram Badmi, Arsheed Hussain Sheikh, Prakash Kumar Bhagat, Deepanjali Verma, Stanzin Noryang, Alok Krishna Sinha
Signalling pathways play vital roles as determinants of almost all the molecular processes inside a eukaryotic cell. They are more often considered to be the link between extracellular and intracellular environmental cues. Gene silencing pathways have emerged to be involved in regulation of stress responses and developmental processes. However, very little is known about the crosstalk between signalling and silencing pathways and their influence on each other. The present work describes the effects of general protein kinase inhibitors and specific mitogen activated protein kinase (MAPK) pathway inhibitors on the components of microRNA pathway in rice...
June 6, 2018: Plant Physiology and Biochemistry: PPB
Milda Mickute, Milda Nainyte, Lina Vasiliauskaite, Alexandra Plotnikova, Viktoras Masevicius, Saulius Klimašauskas, Giedrius Vilkaitis
S-adenosyl-L-methionine-dependent 2'-O-methylati-on of the 3'-terminal nucleotide plays important roles in biogenesis of eukaryotic small non-coding RNAs, such as siRNAs, miRNAs and Piwi-interacting RNAs (piRNAs). Here we demonstrate that, in contrast to Mg2+/Mn2+-dependent plant and bacterial homologues, the Drosophila DmHen1 and human HsHEN1 piRNA methyltransferases require cobalt cations for their enzymatic activity in vitro. We also show for the first time the capacity of the animal Hen1 to catalyse the transfer of a variety of extended chemical groups from synthetic analogues of the AdoMet cofactor onto a wide range (22-80 nt) of single-stranded RNAs permitting their 3'-terminal functionalization and labelling...
June 13, 2018: Nucleic Acids Research
Zhanghui Dong, Jianhong Zhang, Qingzhu Zhu, Lifen Zhao, Shuxiang Sui, Zengshu Li, Yanli Zhang, Hu Wang, Dongliang Tian, Yankun Zhao
Drought stress is one of the most important abiotic stresses. Cotton is classified as drought tolerant crop but the regulatory mechanism is unknown. MicroRNAs (miRNAs) have been implicated important roles in stress responses in many plants. However, the study of miRNAs in cotton responsive to drought stress is limited, especially in early-maturing cotton. In this study, we performed deep sequencing of small RNAs to identify known and novel miRNAs involved in the regulation of drought stress and understand the expression profile of miRNAs in early-maturing cotton...
March 2018: Genes & Genomics
Greta Nölke, Mirna Barsoum, Marcel Houdelet, Elsa Arcalís, Fritz Kreuzaler, Rainer Fischer, Stefan Schillberg
Increasing the productivity of crops is a major challenge in agricultural research. Given that photosynthetic carbon assimilation is necessary for plant growth, enhancing the efficiency of photosynthesis is one strategy to boost agricultural productivity. We attempted to increase the photosynthetic efficiency and biomass of tobacco plants by expressing individual components of the Chlamydomonas reinhardtii carbon concentration mechanism (CCM) and integrating them into the chloroplast. Independent transgenic varieties were generated accumulating the carbonic anhydrase CAH3 in the thylakoid lumen or the bicarbonate transporter LCIA in the inner chloroplast membrane...
June 11, 2018: Biotechnology Journal
Saiqi Yang, Olena Poretska, Tobias Sieberer
Plants show an indeterminate mode of growth by the activity of organ forming stem cell niches in apically positioned meristems. The correct formation and activity of these meristems are a prerequisite for their adaptive development and also allow the maintenance of organogenesis under adverse circumstances such as wounding. Mutation of the putative Arabidopsis thaliana glutamate carboxypeptidase ALTERED MERISTEM PROGRAM1 (AMP1) results in Arabidopsis plants with enlarged shoot apical meristems, supernumerary stem cell pools and higher leaf formation rate...
June 8, 2018: Plant Physiology
Wen Zhou, Bin Li, Lin Li, Wen Ma, Yuanchu Liu, Shuchao Feng, Zhezhi Wang
Dioscorea zingiberensis (Dioscoreceae) is the main plant source of diosgenin (steroidal sapogenins), the precursor for the production of steroid hormones in the pharmaceutical industry. Despite its large economic value, genomic information of this Dioscorea genus is currently unavailable. Here, we present an initial survey of the D. zingiberensis genome performed by next-generation sequencing technology together with a genome size investigation inferred by flow cytometry. The whole genome survey of D. zingiberensis generated 31...
June 8, 2018: Genome Génome / Conseil National de Recherches Canada
Jinhua Zuo, Yunxiang Wang, Benzhong Zhu, Yunbo Luo, Qing Wang, Lipu Gao
DNA methylation is an essential feature of epigenetic regulation and plays a role in various physiological and biochemical processes at CG, CHG, and CHH sites in plants. LeERF1 is an ethylene response factor (ERF) found in tomatoes which plays an important role in ethylene signal transduction. To explore the characteristics of DNA methylation in the ethylene pathway, sense-/antisense-LeERF1 transgenic tomato fruit were chosen for deep sequencing and bioinformatics parsing. The methylation type with the greatest distribution was CG, (71...
May 21, 2018: Genes
Joanna Miskiewicz, Marta Szachniuk
A small non-coding molecule of microRNA (19⁻24 nt) controls almost every biological process, including cellular and physiological, of various organisms’ lives. The amount of microRNA (miRNA) produced within an organism is highly correlated to the organism’s key processes, and determines whether the system works properly or not. A crucial factor in plant biogenesis of miRNA is the Dicer Like 1 (DCL1) enzyme. Its responsibility is to perform the cleavages in the miRNA maturation process...
June 6, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Jonas Defoort, Yves Van de Peer, Vanessa Vermeirssen
Gene regulatory networks (GRNs) consist of different molecular interactions that closely work together to establish proper gene expression in time and space. Especially in higher eukaryotes, many questions remain on how these interactions collectively coordinate gene regulation. We study high quality GRNs consisting of undirected protein-protein, genetic and homologous interactions, and directed protein-DNA, regulatory and miRNA-mRNA interactions in the worm Caenorhabditis elegans and the plant Arabidopsis thaliana...
June 5, 2018: Nucleic Acids Research
Xuelian Zheng, Lijia Yang, Qian Li, Linyi Ji, Aiting Tang, Lili Zang, Kejun Deng, Jianping Zhou, Yong Zhang
MiRNA-induced gene silencing (MIGS) technology is a special kind of RNA interference technology that uses miR173 to mediate the production of trans -acting siRNA (ta-siRNA) to achieve target gene silencing. This technique has successfully mediated the silencing of interested genes in plants such as Arabidopsis, tobacco, petunia, etc. In order to establish the MIGS technology system in monocots such as rice, we constructed the MIGS backbone vectors pZHY930, pZHY931, pZHY932, and pZHY933 with different with promoters to regulate the expression of miR173 and miR173_ts...
2018: Frontiers in Plant Science
Grazia M Borrelli, Elisabetta Mazzucotelli, Daniela Marone, Cristina Crosatti, Vania Michelotti, Giampiero Valè, Anna M Mastrangelo
NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels...
June 4, 2018: International Journal of Molecular Sciences
Hugo F Hofhuis, Renze Heidstra
Recent findings highlight three instances in which major aspects of plant development are controlled by dosage-dependent protein levels. In the shoot apical meristem the mobile transcription factor WUS displays an intricate function with respect to target regulation that involves WUS dosage, binding site affinity and protein dimerization. The size of the root meristem is controlled by dosage-dependent PLT protein activity. Recent identification of targets and feedbacks provide new insights and entry into possible mechanisms of dosage read-out...
May 28, 2018: Current Opinion in Plant Biology
Haron Salih, Wenfang Gong, Mtawa Andrew Prosper Mkulama, Xiong-Ming DU
WD40 repeat proteins are largely distributed across the plant kingdom and played an important role in diverse biological activities. In this work, we performed genome-wide identification, characterization and expression level analysis of WD40 genes in cotton. A total of 579, 318 and 313 WD40 genes were found in Gossypium hirsutum, Gossypium arboreum and Gossypium raimondii, respectively. Based on phylogenetic tree analyses, WD40 genes were divided into 11 groups with high similarities in exon/intron features and protein domains within the group...
May 31, 2018: Genome Génome / Conseil National de Recherches Canada
Taichiro Iki, Cléry Antoine, Nicolas Bologna, Alexis Sarazin, Christopher Brosnan, Nathan Pumplin, Frédéric H T Allain, Olivier Voinnet
In eukaryotes, the RNase-III Dicer often produces length/sequence microRNA (miRNA) variants, called "isomiRs", owing to intrinsic structural/sequence determinants of miRNA precursors (pre-miRNAs). Here, we combined biophysics, genetics and biochemistry to study Arabidopsis miR168, the key feedback-regulator of the central plant silencing effector protein ARGONAUTE1 (AGO1). We identified a motif conserved among plant pre-miR168 orthologs that enables flexible internal base-pairing underlying at least three metastable structural configurations...
May 24, 2018: Molecular Plant
Yuanxiu Lin, Leiyu Jiang, Qing Chen, Yali Li, Yunting Zhang, Ya Luo, Yong Zhang, Bo Sun, Xiaorong Wang, Haoru Tang
Anthocyanins are water-soluble pigments in plants. They confer both economical and healthy profits for humans. To gain a deeper insight into the regulation of anthocyanins biosynthesis in octoploid strawberry (Fragaria × ananassa; Fa), a widely-consumed economically important fruit, we performed comparative transcriptomic analysis of red- and white-fleshed strawberry cultivars in two ripening stages. In total, 365,455 non-redundant transcripts were assembled from the RNA sequencing (RNAseq) data. Of this collection, 377 were annotated as putative anthocyanins related transcripts...
May 25, 2018: Plant & Cell Physiology
Shuxin Zhang, Yongchao Dou, Shengjun Li, Guodong Ren, David Chevalier, Chi Zhang, Bin Yu
DAWDLE (DDL) is a conserved forkhead-associated (FHA) domain-containing protein with essential roles in plant development and immunity. It acts in the biogenesis of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which regulate gene expression at the transcriptional and/or post-transcriptional levels. However, the functional mechanism of DDL and its impact on exogenous siRNAs remain elusive. Here we report that DDL is required for the biogenesis of siRNAs derived from sense transgenes and inverted-repeat transgenes...
May 21, 2018: Plant Physiology
Zhaoyun Wang, Yeqiang Xia, Siyuan Lin, Yanru Wang, Baohuan Guo, Xiaoning Song, Shaochen Ding, Liyu Zheng, Ruiying Feng, Shulin Chen, Yalin Bao, Cong Sheng, Xin Zhang, Jianguo Wu, Dongdong Niu, Hailing Jin, Hongwei Zhao
Exploring the regulatory mechanism played by endogenous rice miRNAs in defense responses against the blast disease is of great significance in both resistant variety breeding and disease control management. We identified rice defense-related miRNAs by comparing rice miRNA expression patterns before and after Magnaporthe oryzae strain Guy11 infection. We discovered that osa-miR164a expression reduced upon Guy11 infection at both early and late stages, which was perfectly associated with the induced expression of its target gene, OsNAC60...
May 18, 2018: Plant Journal: for Cell and Molecular Biology
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