Tuning Beforehand: A Foresight on RNA Interference (RNAi) and In Vitro-Derived dsRNAs to Enhance Crop Resilience to Biotic and Abiotic Stresses

Crop yield is severely affected by biotic and abiotic stresses. Plants adapt to these stresses mainly through gene expression reprogramming at the transcriptional and post-transcriptional levels. Recently, the exogenous application of double-stranded RNAs (dsRNAs) and RNA interference (RNAi) technology has emerged as a sustainable and publicly acceptable alternative to genetic transformation, hence, small RNAs (micro-RNAs and small interfering RNAs) have an important role in combating biotic and abiotic stresses in plants. RNAi limits the transcript level by either suppressing transcription (transcriptional gene silencing) or activating sequence-specific RNA degradation (post-transcriptional gene silencing). Using RNAi tools and their respective targets in abiotic stress responses in many crops is well documented. Many miRNAs families are reported in plant tolerance response or adaptation to drought, salinity, and temperature stresses. In biotic stress, the spray-induced gene silencing (SIGS) provides an intelligent method of using dsRNA as a trigger to silence target genes in pests and pathogens without producing side effects such as those caused by chemical pesticides. In this review, we focus on the potential of SIGS as the most recent application of RNAi in agriculture and point out the trends, challenges, and risks of production technologies. Additionally, we provide insights into the potential applications of exogenous RNAi against biotic stresses. We also review the current status of RNAi/miRNA tools and their respective targets on abiotic stress and the most common responsive miRNA families triggered by stress conditions in different crop species.

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Signal Integration by Cyclin-Dependent Kinase 8 (CDK8) Module and Other Mediator Subunits in Biotic and Abiotic Stress Responses

International Journal of Molecular Sciences ◽

10.3390/ijms22010354 ◽

2020 ◽

Vol 22 (1) ◽

pp. 354

Author(s):

Leelyn Chong ◽

Xiaoning Shi ◽

Yingfang Zhu

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Abiotic Stresses ◽

Current Knowledge ◽

Signal Integration ◽

Cyclin Dependent Kinase ◽

Biotic And Abiotic Stress ◽

Biotic And Abiotic Stresses ◽

Adverse Conditions ◽

Plant Transcriptome

Environmental stresses have driven plants to develop various mechanisms to acclimate in adverse conditions. Extensive studies have demonstrated that a significant reprogramming occurs in the plant transcriptome in response to biotic and abiotic stresses. The highly conserved and large multi-subunit transcriptional co-activator of eukaryotes, known as the Mediator, has been reported to play a substantial role in the regulation of important genes that help plants respond to environmental perturbances. CDK8 module is a relatively new component of the Mediator complex that has been shown to contribute to plants’ defense, development, and stress responses. Previous studies reported that CDK8 module predominantly acts as a transcriptional repressor in eukaryotic cells by reversibly associating with core Mediator. However, growing evidence has demonstrated that depending on the type of biotic and abiotic stress, the CDK8 module may perform a contrasting regulatory role. This review will summarize the current knowledge of CDK8 module as well as other previously documented Mediator subunits in plant cell signaling under stress conditions.

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Balancing trade-offs between biotic and abiotic stress responses through leaf age-dependent variation in stress hormone cross-talk

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1817233116 ◽

2019 ◽

Vol 116 (6) ◽

pp. 2364-2373 ◽

Cited By ~ 51

Author(s):

Matthias L. Berens ◽

Katarzyna W. Wolinska ◽

Stijn Spaepen ◽

Jörg Ziegler ◽

Tatsuya Nobori ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Tolerance ◽

Stress Responses ◽

Abiotic Stresses ◽

Abiotic Stress Tolerance ◽

Leaf Age ◽

Biotic And Abiotic Stress ◽

Biotic And Abiotic Stresses ◽

Trade Offs ◽

Age Dependent

In nature, plants must respond to multiple stresses simultaneously, which likely demands cross-talk between stress-response pathways to minimize fitness costs. Here we provide genetic evidence that biotic and abiotic stress responses are differentially prioritized inArabidopsis thalianaleaves of different ages to maintain growth and reproduction under combined biotic and abiotic stresses. Abiotic stresses, such as high salinity and drought, blunted immune responses in older rosette leaves through the phytohormone abscisic acid signaling, whereas this antagonistic effect was blocked in younger rosette leaves byPBS3, a signaling component of the defense phytohormone salicylic acid. Plants lackingPBS3exhibited enhanced abiotic stress tolerance at the cost of decreased fitness under combined biotic and abiotic stresses. Together with this role,PBS3is also indispensable for the establishment of salt stress- and leaf age-dependent phyllosphere bacterial communities. Collectively, our work reveals a mechanism that balances trade-offs upon conflicting stresses at the organism level and identifies a genetic intersection among plant immunity, leaf microbiota, and abiotic stress tolerance.

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MicroRNA and cDNA-Microarray as Potential Targets against Abiotic Stress Response in Plants: Advances and Prospects

Agronomy ◽

10.3390/agronomy12010011 ◽

2021 ◽

Vol 12 (1) ◽

pp. 11

Author(s):

Tariq Pervaiz ◽

Muhammad Waqas Amjid ◽

Ashraf El-kereamy ◽

Shi-Hui Niu ◽

Harry X. Wu

Keyword(s):

Abiotic Stress ◽

Cdna Microarray ◽

Stress Responses ◽

Abiotic Stresses ◽

Abiotic Stress Tolerance ◽

Expression Patterns ◽

Machine Learning Algorithms ◽

Current Status ◽

Developmental Cycle ◽

Altered Expression

Abiotic stresses, such as temperature (heat and cold), salinity, and drought negatively affect plant productivity; hence, the molecular responses of abiotic stresses need to be investigated. Numerous molecular and genetic engineering studies have made substantial contributions and revealed that abiotic stresses are the key factors associated with production losses in plants. In response to abiotic stresses, altered expression patterns of miRNAs have been reported, and, as a result, cDNA-microarray and microRNA (miRNA) have been used to identify genes and their expression patterns against environmental adversities in plants. MicroRNA plays a significant role in environmental stresses, plant growth and development, and regulation of various biological and metabolic activities. MicroRNAs have been studied for over a decade to identify those susceptible to environmental stimuli, characterize expression patterns, and recognize their involvement in stress responses and tolerance. Recent findings have been reported that plants assign miRNAs as critical post-transcriptional regulators of gene expression in a sequence-specific manner to adapt to multiple abiotic stresses during their growth and developmental cycle. In this study, we reviewed the current status and described the application of cDNA-microarray and miRNA to understand the abiotic stress responses and different approaches used in plants to survive against different stresses. Despite the accessibility to suitable miRNAs, there is a lack of simple ways to identify miRNA and the application of cDNA-microarray. The elucidation of miRNA responses to abiotic stresses may lead to developing technologies for the early detection of plant environmental stressors. The miRNAs and cDNA-microarrays are powerful tools to enhance abiotic stress tolerance in plants through multiple advanced sequencing and bioinformatics techniques, including miRNA-regulated network, miRNA target prediction, miRNA identification, expression profile, features (disease or stress, biomarkers) association, tools based on machine learning algorithms, NGS, and tools specific for plants. Such technologies were established to identify miRNA and their target gene network prediction, emphasizing current achievements, impediments, and future perspectives. Furthermore, there is also a need to identify and classify new functional genes that may play a role in stress resistance, since many plant genes constitute an unexplained fraction.

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Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview

Metabolites ◽

10.3390/metabo11070445 ◽

2021 ◽

Vol 11 (7) ◽

pp. 445

Author(s):

Morena M. Tinte ◽

Kekeletso H. Chele ◽

Justin J. J. van der Hooft ◽

Fidele Tugizimana

Keyword(s):

Machine Learning ◽

Abiotic Stress ◽

Stress Responses ◽

Abiotic Stresses ◽

Industrial Revolution ◽

Chemical Space ◽

Big Data Analytics ◽

Plant Responses ◽

Next Generation ◽

Computational Tools

Plants are constantly challenged by changing environmental conditions that include abiotic stresses. These are limiting their development and productivity and are subsequently threatening our food security, especially when considering the pressure of the increasing global population. Thus, there is an urgent need for the next generation of crops with high productivity and resilience to climate change. The dawn of a new era characterized by the emergence of fourth industrial revolution (4IR) technologies has redefined the ideological boundaries of research and applications in plant sciences. Recent technological advances and machine learning (ML)-based computational tools and omics data analysis approaches are allowing scientists to derive comprehensive metabolic descriptions and models for the target plant species under specific conditions. Such accurate metabolic descriptions are imperatively essential for devising a roadmap for the next generation of crops that are resilient to environmental deterioration. By synthesizing the recent literature and collating data on metabolomics studies on plant responses to abiotic stresses, in the context of the 4IR era, we point out the opportunities and challenges offered by omics science, analytical intelligence, computational tools and big data analytics. Specifically, we highlight technological advancements in (plant) metabolomics workflows and the use of machine learning and computational tools to decipher the dynamics in the chemical space that define plant responses to abiotic stress conditions.

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Whole-Genome DNA Methylation Analysis in Hydrogen Peroxide Overproducing Transgenic Tobacco Resistant to Biotic and Abiotic Stresses

Plants ◽

10.3390/plants10010178 ◽

2021 ◽

Vol 10 (1) ◽

pp. 178

Author(s):

Ana L. Villagómez-Aranda ◽

Luis F. García-Ortega ◽

Irineo Torres-Pacheco ◽

Ramón G. Guevara-González

Keyword(s):

Hydrogen Peroxide ◽

Dna Methylation ◽

Transgenic Tobacco ◽

Stress Responses ◽

Abiotic Stresses ◽

Methylation Status ◽

Physiological Adaptation ◽

Whole Genome ◽

Sequencing Analysis ◽

Biotic And Abiotic Stresses

Epigenetic regulation is a key component of stress responses, acclimatization and adaptation processes in plants. DNA methylation is a stable mark plausible for the inheritance of epigenetic traits, such that it is a potential scheme for plant breeding. However, the effect of modulators of stress responses, as hydrogen peroxide (H2O2), in the methylome status has not been elucidated. A transgenic tobacco model to the CchGLP gene displayed high H2O2 endogen levels correlated with biotic and abiotic stresses resistance. The present study aimed to determine the DNA methylation status changes in the transgenic model to obtain more information about the molecular mechanism involved in resistance phenotypes. The Whole-genome bisulfite sequencing analysis revealed a minimal impact of overall levels and distribution of methylation. A total of 9432 differential methylated sites were identified in distinct genome regions, most of them in CHG context, with a trend to hypomethylation. Of these, 1117 sites corresponded to genes, from which 83 were also differentially expressed in the plants. Several genes were associated with respiration, energy, and calcium signaling. The data obtained highlighted the relevance of the H2O2 in the homeostasis of the system in stress conditions, affecting at methylation level and suggesting an association of the H2O2 in the physiological adaptation to stress functional linkages may be regulated in part by DNA methylation.

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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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Overcoming biotic and abiotic stresses in the Solanaceae through grafting: current status and future perspectives

Biological Agriculture & Horticulture ◽

10.1080/01448765.2014.964317 ◽

2014 ◽

Vol 30 (4) ◽

pp. 272-287 ◽

Cited By ~ 25

Author(s):

J.D.H. Keatinge ◽

L.-J. Lin ◽

A.W. Ebert ◽

W.Y. Chen ◽

J.d'A. Hughes ◽

...

Keyword(s):

Abiotic Stresses ◽

Current Status ◽

Future Perspectives ◽

Biotic And Abiotic Stresses

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WRKY Proteins: Signaling and Regulation of Expression during Abiotic Stress Responses

The Scientific World JOURNAL ◽

10.1155/2015/807560 ◽

2015 ◽

Vol 2015 ◽

pp. 1-17 ◽

Cited By ~ 121

Author(s):

Aditya Banerjee ◽

Aryadeep Roychoudhury

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Biotic Stress ◽

Abiotic Stresses ◽

Abiotic Stress Tolerance ◽

Plant Signaling ◽

Biological Functions ◽

Abiotic And Biotic Stress ◽

Regulation Of Expression ◽

Wrky Proteins

WRKY proteins are emerging players in plant signaling and have been thoroughly reported to play important roles in plants under biotic stress like pathogen attack. However, recent advances in this field do reveal the enormous significance of these proteins in eliciting responses induced by abiotic stresses. WRKY proteins act as major transcription factors, either as positive or negative regulators. Specific WRKY factors which help in the expression of a cluster of stress-responsive genes are being targeted and genetically modified to induce improved abiotic stress tolerance in plants. The knowledge regarding the signaling cascade leading to the activation of the WRKY proteins, their interaction with other proteins of the signaling pathway, and the downstream genes activated by them are altogether vital for justified targeting of theWRKYgenes. WRKY proteins have also been considered to generate tolerance against multiple abiotic stresses with possible roles in mediating a cross talk between abiotic and biotic stress responses. In this review, we have reckoned the diverse signaling pattern and biological functions of WRKY proteins throughout the plant kingdom along with the growing prospects in this field of research.

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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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FOXO regulates RNA interference in Drosophila and protects from RNA virus infection

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1517124112 ◽

2015 ◽

Vol 112 (47) ◽

pp. 14587-14592 ◽

Cited By ~ 33

Author(s):

Michael J. Spellberg ◽

Michael T. Marr

Keyword(s):

Rna Interference ◽

Virus Infection ◽

Gene Silencing ◽

Small Rna ◽

Stress Responses ◽

Posttranscriptional Regulation ◽

Rna Virus ◽

Regulation Of Gene Expression ◽

Cellular Physiology ◽

Metabolic Conditions

Small RNA pathways are important players in posttranscriptional regulation of gene expression. These pathways play important roles in all aspects of cellular physiology from development to fertility to innate immunity. However, almost nothing is known about the regulation of the central genes in these pathways. The forkhead box O (FOXO) family of transcription factors is a conserved family of DNA-binding proteins that responds to a diverse set of cellular signals. FOXOs are crucial regulators of cellular homeostasis that have a conserved role in modulating organismal aging and fitness. Here, we show that Drosophila FOXO (dFOXO) regulates the expression of core small RNA pathway genes. In addition, we find increased dFOXO activity results in an increase in RNA interference (RNAi) efficacy, establishing a direct link between cellular physiology and RNAi. Consistent with these findings, dFOXO activity is stimulated by viral infection and is required for effective innate immune response to RNA virus infection. Our study reveals an unanticipated connection among dFOXO, stress responses, and the efficacy of small RNA-mediated gene silencing and suggests that organisms can tune their gene silencing in response to environmental and metabolic conditions.

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