MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops

Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20–24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.

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MicroRNA840 accelerates leaf senescence by targeting the overlapping 3’UTRs of PPR and WHIRLY3 in Arabidopsis thaliana

10.1101/2020.10.23.353052 ◽

2020 ◽

Author(s):

Ren Yujun ◽

Wang Wanzhen ◽

Lan Wei ◽

Schenke Dirk ◽

Cai Daguang ◽

...

Keyword(s):

Stress Responses ◽

Transcript Level ◽

Transcriptional Gene Silencing ◽

Loss Of Function ◽

Knockout Mutant ◽

Plant Senescence ◽

Senescent Phenotype ◽

Post Transcriptional Gene Silencing

AbstractMicroRNAs (miRNAs) negatively regulate gene expression by cleaving the target mRNA and/or impairing its translation, thereby playing a crucial role in plant development and environmental stress responses. In Arabidopsis, MIR840 is located within the overlapping 3’UTR of PPR and WHIRLY3 (WHY3), both being predicted targets of miR840. Gain- and loss-of-function of miR840 in Arabidopsis resulted in opposite senescent phenotypes. Highest expression of pri-miR840 is observed at senescence initiation, and is negatively correlated with a significant reduction of PPR transcripts but not of WHY3. Although WHY3 transcript levels were not significantly affected by miR840 overexpression, its protein synthesis was strongly reduced. Mutating the cleavage sites or replacing the target sequences abolishes the miR840-mediated degradation of PPR transcripts and inhibition of WHY3 translation. In support for this, concurrent knock-down of both PPR and WHY3 in the WT resulted in the senescent phenotype resembling that of the miR840-overexpressing mutant. This indicates that both PRR and WHY3 are targets in the miR840-regulated senescent pathway. Moreover, single knockout mutant of PPR or WHY3 shows a convergent up-regulated subset of senescence-associated genes, which are also found among those induced by miR840 overexpression. Our data provide evidences for a regulatory role of miR840 in plant senescence.HighlightMicroRNA840 (miR840) has a unique miRNA-target configuration regulating PPR and WHIRLY3 genes in Arabidopsis. MiR840 is highly expressed at the onset of plant senescent stage. Both PPR and WHIRLY3 transcripts are specifically targeted in vivo within their 3’UTR region by mature miR840 or its star strand in vivo. Interestingly, PPR expression is mainly repressed on mRNA transcript level by cleavage, while WHIRLY3 is predominantly translationally inhibited. We conclude that miR840 enhances plant senescence via post transcriptional gene silencing of PPR and WHIRLY3, which appear to be novel negative joint regulators of plant senescence.Footnote: The author(s) responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the intructions for Authors is: Ying Miao ([email protected])

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Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants

Cells ◽

10.3390/cells10051187 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1187

Author(s):

Michael Wassenegger ◽

Athanasios Dalakouras

Keyword(s):

Dna Methylation ◽

Rna Interference ◽

Gene Silencing ◽

Plant Cells ◽

Transcriptional Gene Silencing ◽

Rnai Machinery ◽

Double Stranded Rna ◽

Post Transcriptional Gene Silencing ◽

Cumulative Amount

Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene Silencing (PTGS) and RNA-directed DNA Methylation (RdDM), and the latter has the potential to trigger Transcriptional Gene Silencing (TGS). Over the last three decades, the employment of viroid-based systems has immensely contributed to our understanding of both of these RNAi facets. In this review, we highlight the role of Pospiviroidae in the discovery of RdDM, expound the gradual elucidation through the years of the diverse array of RdDM’s mechanistic details and propose a revised RdDM model based on the cumulative amount of evidence from viroid and non-viroid systems.

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MicroRNAs in Cardiac Autophagy: Small Molecules and Big Role

Cells ◽

10.3390/cells7080104 ◽

2018 ◽

Vol 7 (8) ◽

pp. 104 ◽

Cited By ~ 22

Author(s):

Teng Sun ◽

Meng-Yang Li ◽

Pei-Feng Li ◽

Ji-Min Cao

Keyword(s):

Cardiac Fibrosis ◽

Heart Diseases ◽

Critical Role ◽

Transcriptional Gene Silencing ◽

Close Link ◽

Post Transcriptional Gene Silencing ◽

Evolutionarily Conserved ◽

Cardiac Disorders ◽

Cellular Components

Autophagy, which is an evolutionarily conserved process according to the lysosomal degradation of cellular components, plays a critical role in maintaining cell homeostasis. Autophagy and mitochondria autophagy (mitophagy) contribute to the preservation of cardiac homeostasis in physiological settings. However, impaired or excessive autophagy is related to a variety of diseases. Recently, a close link between autophagy and cardiac disorders, including myocardial infarction, cardiac hypertrophy, cardiomyopathy, cardiac fibrosis, and heart failure, has been demonstrated. MicroRNAs (miRNAs) are a class of small non-coding RNAs with a length of approximately 21–22 nucleotides (nt), which are distributed widely in viruses, plants, protists, and animals. They function in mediating the post-transcriptional gene silencing. A growing number of studies have demonstrated that miRNAs regulate cardiac autophagy by suppressing the expression of autophagy-related genes in a targeted manner, which are involved in the pathogenesis of heart diseases. This review summarizes the role of microRNAs in cardiac autophagy and related cardiac disorders. Furthermore, we mainly focused on the autophagy regulation pathways, which consisted of miRNAs and their targeted genes.

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Comparative reactions of recombinant papaya ringspot viruses with chimeric coat protein (CP) genes and wild-type viruses on CP-transgenic papaya

Journal of General Virology ◽

10.1099/0022-1317-82-11-2827 ◽

2001 ◽

Vol 82 (11) ◽

pp. 2827-2836 ◽

Cited By ~ 32

Author(s):

Chu-Hui Chiang ◽

Ju-Jung Wang ◽

Fuh-Jyh Jan ◽

Shyi-Dong Yeh ◽

Dennis Gonsalves

Keyword(s):

Coat Protein ◽

Sequence Similarity ◽

Transcriptional Gene Silencing ◽

Papaya Ringspot Virus ◽

Wild Type ◽

Coding Region ◽

Transgenic Papaya ◽

Cp Gene ◽

Post Transcriptional Gene Silencing

Transgenic papaya cultivars SunUp and Rainbow express the coat protein (CP) gene of the mild mutant of papaya ringspot virus (PRSV) HA. Both cultivars are resistant to PRSV HA and other Hawaii isolates through homology-dependent resistance via post-transcriptional gene silencing. However, Rainbow, which is hemizygous for the CP gene, is susceptible to PRSV isolates from outside Hawaii, while the CP-homozygous SunUp is resistant to most isolates but susceptible to the YK isolate from Taiwan. To investigate the role of CP sequence similarity in overcoming the resistance of Rainbow, PRSV HA recombinants with various CP segments of the YK isolate were constructed and evaluated on Rainbow, SunUp and non-transgenic papaya. Non-transgenic papaya were severely infected by all recombinants, but Rainbow plants developed a variety of symptoms. On Rainbow, a recombinant with the entire CP gene of YK caused severe symptoms, while recombinants with only partial YK CP sequences produced a range of milder symptoms. Interestingly, a recombinant with a YK segment from the 5′ region of the CP gene caused very mild, transient symptoms, whereas recombinants with YK segments from the middle and 3′ parts of the CP gene caused prominent and lasting symptoms. SunUp was resistant to all but two recombinants, which contained the entire CP gene or the central and 3′-end regions of the CP gene and the 3′ non-coding region of YK, and the resulting symptoms were mild. It is concluded that the position of the heterologous sequences in the recombinants influences their pathogenicity on Rainbow.

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An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection

10.1101/2021.03.05.432875 ◽

2021 ◽

Author(s):

Ganna Reshetnyak ◽

Jonathan M. Jacobs ◽

Florence Auguy ◽

Coline Sciallano ◽

Lisa Claude ◽

...

Keyword(s):

Gene Silencing ◽

Stress Responses ◽

Small Rnas ◽

Early Stage ◽

Kinase Domain ◽

Transcriptional Gene Silencing ◽

Small Interfering Rnas ◽

Post Transcriptional Gene Silencing ◽

Virulent Strains ◽

Microbe Interactions

ABSTRACTNon-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences often encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and some xisRNA loci coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.

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Role of inverted DNA repeats in transcriptional and post-transcriptional gene silencing

Plant Gene Silencing ◽

10.1007/978-94-011-4183-3_9 ◽

2000 ◽

pp. 123-140 ◽

Cited By ~ 2

Author(s):

Mariëlle W. M. Muskens ◽

Adriënne P. A. Vissers ◽

Joseph N. M. Mol ◽

Jan M. Kooter

Keyword(s):

Gene Silencing ◽

Transcriptional Gene Silencing ◽

Dna Repeats ◽

Post Transcriptional Gene Silencing

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Fungal Production and Manipulation of Plant Hormones

Current Medicinal Chemistry ◽

10.2174/0929867324666170314150827 ◽

2018 ◽

Vol 25 (2) ◽

pp. 253-267 ◽

Cited By ~ 8

Author(s):

Sandra Fonseca ◽

Dhanya Radhakrishnan ◽

Kalika Prasad ◽

Andrea Chini

Keyword(s):

Stress Responses ◽

Current Knowledge ◽

Critical Role ◽

Plant Defence ◽

Pathogenic Fungi ◽

Plant Responses ◽

Defensive Strategies ◽

Hormone Balance ◽

Living Organisms

Living organisms are part of a highly interconnected web of interactions, characterised by species nurturing, competing, parasitizing and preying on one another. Plants have evolved cooperative as well as defensive strategies to interact with neighbour organisms. Among these, the plant-fungus associations are very diverse, ranging from pathogenic to mutualistic. Our current knowledge of plant-fungus interactions suggests a sophisticated coevolution to ensure dynamic plant responses to evolving fungal mutualistic/pathogenic strategies. The plant-fungus communication relies on a rich chemical language. To manipulate the plant defence mechanisms, fungi produce and secrete several classes of biomolecules, whose modeof- action is largely unknown. Upon perception of the fungi, plants produce phytohormones and a battery of secondary metabolites that serve as defence mechanism against invaders or to promote mutualistic associations. These mutualistic chemical signals can be co-opted by pathogenic fungi for their own benefit. Among the plant molecules regulating plant-fungus interaction, phytohormones play a critical role since they modulate various aspects of plant development, defences and stress responses. Intriguingly, fungi can also produce phytohormones, although the actual role of fungalproduced phytohormones in plant-fungus interactions is poorly understood. Here, we discuss the recent advances in fungal production of phytohormone, their putative role as endogenous fungal signals and how fungi manipulate plant hormone balance to their benefits.

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MicroRNAs as Emerging Regulators of Signaling in the Tumor Microenvironment

Cancers ◽

10.3390/cancers12040911 ◽

2020 ◽

Vol 12 (4) ◽

pp. 911 ◽

Cited By ~ 5

Author(s):

Shahzad Nawaz Syed ◽

Bernhard Brüne

Keyword(s):

Tumor Microenvironment ◽

Signaling Pathways ◽

Target Identification ◽

Cancer Therapeutics ◽

Protein Translation ◽

Transcriptional Gene Silencing ◽

Post Transcriptional Gene Silencing ◽

Cancer Initiation ◽

Regulate Protein

A myriad of signaling molecules in a heuristic network of the tumor microenvironment (TME) pose a challenge and an opportunity for novel therapeutic target identification in human cancers. MicroRNAs (miRs), due to their ability to affect signaling pathways at various levels, take a prominent space in the quest of novel cancer therapeutics. The role of miRs in cancer initiation, progression, as well as in chemoresistance, is being increasingly investigated. The canonical function of miRs is to target mRNAs for post-transcriptional gene silencing, which has a great implication in first-order regulation of signaling pathways. However, several reports suggest that miRs also perform non-canonical functions, partly due to their characteristic non-coding small RNA nature. Examples emerge when they act as ligands for toll-like receptors or perform second-order functions, e.g., to regulate protein translation and interactions. This review is a compendium of recent advancements in understanding the role of miRs in cancer signaling and focuses on the role of miRs as novel regulators of the signaling pathway in the TME.

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The potential role of epigenetic modifications in the heritability of multiple sclerosis

Multiple Sclerosis Journal ◽

10.1177/1352458514520911 ◽

2014 ◽

Vol 20 (2) ◽

pp. 135-140 ◽

Cited By ~ 20

Author(s):

Yuan Zhou ◽

Steve Simpson ◽

Adele F Holloway ◽

Jac Charlesworth ◽

Ingrid van der Mei ◽

...

Keyword(s):

Multiple Sclerosis ◽

Potential Role ◽

Transcriptional Gene Silencing ◽

Epigenetic Changes ◽

Missing Heritability ◽

Significant Component ◽

Post Transcriptional Gene Silencing ◽

Genetic And Environmental Factors ◽

Ms Pathogenesis

It is now well established that both genetic and environmental factors contribute to and interact in the development of multiple sclerosis (MS). However, the currently described causal genetic variants do not explain the majority of the heritability of MS, resulting in ‘missing heritability’. Epigenetic mechanisms, which principally include DNA methylation, histone modifications and microRNA-mediated post-transcriptional gene silencing, may contribute a significant component of this missing heritability. As the development of MS is a dynamic process potentially starting with inflammation, then demyelination, remyelination and neurodegeneration, we have reviewed the dynamic epigenetic changes in these aspects of MS pathogenesis and describe how environmental risk factors may interact with epigenetic changes to manifest in disease.

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Function of Chloroplasts in Plant Stress Responses

International Journal of Molecular Sciences ◽

10.3390/ijms222413464 ◽

2021 ◽

Vol 22 (24) ◽

pp. 13464

Author(s):

Yun Song ◽

Li Feng ◽

Mohammed Abdul Muhsen Alyafei ◽

Abdul Jaleel ◽

Maozhi Ren

Keyword(s):

Stress Responses ◽

Plant Stress ◽

Environmental Stresses ◽

Stress Conditions ◽

Oxygenic Photosynthesis ◽

Central Position ◽

Plant Responses ◽

Primary Metabolism ◽

Diverse Range ◽

Biotic Stresses

The chloroplast has a central position in oxygenic photosynthesis and primary metabolism. In addition to these functions, the chloroplast has recently emerged as a pivotal regulator of plant responses to abiotic and biotic stress conditions. Chloroplasts have their own independent genomes and gene-expression machinery and synthesize phytohormones and a diverse range of secondary metabolites, a significant portion of which contribute the plant response to adverse conditions. Furthermore, chloroplasts communicate with the nucleus through retrograde signaling, for instance, reactive oxygen signaling. All of the above facilitate the chloroplast’s exquisite flexibility in responding to environmental stresses. In this review, we summarize recent findings on the involvement of chloroplasts in plant regulatory responses to various abiotic and biotic stresses including heat, chilling, salinity, drought, high light environmental stress conditions, and pathogen invasions. This review will enrich the better understanding of interactions between chloroplast and environmental stresses, and will lay the foundation for genetically enhancing plant-stress acclimatization.

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