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Different RNAi pathways in plants. 1) miRNA and tasi-RNA biogenesis regulating expression of MIRNA gene and TAS loci. With the help of DCL1 and HYL1, pri-miRNA is processed to short lived miRNA: miRNA* duplex in plants and are methylated by HEN1 within the nucleus. Thereafter, the miRNA is exported to the cytoplasm by HASTY and after maturation, methylated miRNA is incorporated into a RISC. In this complex, the miRNA is capable of targeting complementary RNAs for cleavage by AGO1, and also for translational repression. Similarly in second phase, trans-acting small interfering RNAs (ta-siRNA) duplexes can be set by miRNA-directed cleavage of the TAS transcript. One strand from each siRNA duplex is stably incorporated into RISC, and the other is degraded. siRNAs in RISCs guide cleavage of complementary RNAs. 2) Heterochromatic siRNAs, endogenous siRNAs/siRNAs from transgenes or viral RNA or DNA are generated through similar or partially overlapping pathways. Long double-stranded RNA, generated through the action of RNA-dependent RNA polymerases (RDRs), and iteratively processed by Dicer-like (DCL) proteins to yield multiple siRNA duplexes. One strand from each siRNA duplex is stably incorporated into a RISC, and the other is degraded. siRNAs in RISCs guide cleavage of complementary RNAs. Pol IV is involved in heterochromatic siRNA production in plants, either transcribing the genomic DNA to produce the singlestranded RNA or transcribing the double-stranded RNA to amplify the single-stranded RNA.
Source publication
Efficient control of plant pathogens affecting economically important crop species represents one of the major challenges for sustainable agriculture production. Though plant breeding has been the classical means of manipulating the plant genome to develop resistant cultivar for controlling plants diseases, the advent of genetic engineering provide...
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... RNA molecules provide specificity to guide vari- ous activities of RNAi machinery including RNA cleavage (El-bashir et al. 2001;Llave et al. 2002;Hily and Liu 2007), translational repression ( Doench et al. 2003) and methyla- tion of chromatin ( Volpe et al. 2002;Chan et al. 2004) are outlined in Fig. 1. The biogenesis of various RNA mole- cules and their roles in RNAi machinery along with other key players are briefly described in the following ...
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... regulates gene expression by microRNAs (miRNAs) (Jones-Rhoades et al. 2006) and trans-acting smRNAs (ta-smRNAs) (Vaucheret 2006). Both species predominantly direct cleavage of near-perfect complementary target mRNAs ( Vaucheret et al. 2004), but suppression of translation has also been observed ). The working of miRNA based RNAi path- way ( Fig. 1) emerged after the expression of a specific gene "MIRNA" which is predominantly found within genomic segments previously known as intergenic regions (IGRs) (Jones-Rhoades et al. 2006). The expression of this gene begins with Pol II transcription to yield a primary miRNA transcript (pri-miRNA) that is capable of forming the cha- ...
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... the passenger strand which results in the formation of an active RISC-loading complex. are predominantly mediated by transcript cleavage (Xie and Qi 2008). In addition, ta-siRNAs are also known to play signifi- cant role in RNAi pathway which arises from defined gene- tic loci (TAS loci) through miRNA-dependent biogenesis pathway (Vaucheret 2006) (Fig. 1). The expression of ta- siRNAs is initiated by Pol II transcription to yield TAS transcripts that contain miRNA target site(s). The miRNA- directed cleavage of TAS transcript is thought to generate critical features that are recognized by RDR6 (Allen et al. 2005). The cleaved TAS transcript is converted into dsRNA by RDR6, a process ...
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... acids, such as viruses and transgenes, through the action of siRNAs that direct the cleavage of homologous RNAs ( Lecellier and Voinnet 2004). Viruses engineered to contain an endogenous se- quence can trigger silencing of the endogene, which is termed 'virus-induced gene silencing' (VIGS) (Ruiz et al. 1998;Baulcombe 1999;Godge et al. 2008) (Fig. 1). This system involves a branched pathway that converges on the production of dsRNA. Depending on the nature of the transgene and the virus, dsRNA is either formed directly by intra-or intermolecular base pairing (hpRNA constructs, IR transgenes) or indirectly through antisense transgenes or replication intermediates (RNA viruses), or ...
Citations
... Plant genome manipulation is an emerging technique that holds promise for developing resistant cultivars, combating plant diseases, and gaining deeper insights into the intricate metabolism underlying desired phenotypes. Techniques such as the identification, mapping, and cloning of pest and disease-resistant genes, and their incorporation through introgression, pyramiding, and the development of transgenics (Mann et al. 2008;Sanghera et al. 2011) offer avenues for creating resilient crop varieties. ...
The conventional methods of addressing plant pathogens, such as crop protection and resistant varieties, have been complemented by advancements in plant-microbe interactions. The field has witnessed significant progress in genetic engineering, gene transfer technologies, and omics approaches such as transcriptomics, proteomics, and metabolomics. These advancements offer insights into plant metabolic pathways, key gene associations, and regulatory mechanisms. Plant genome manipulation, empowered by these technologies, is a key focus for researchers aiming to develop disease-resistant cultivars and gain a deeper understanding of complex metabolic processes. Recent breakthroughs in understanding small noncoding ribonucleic acids (sRNAs) have opened new avenues for RNA-mediated functions in plants. sRNAs, acting as regulatory molecules, trigger RNA interference (RNAi), a mechanism pivotal in gene expression regulation. The host RNAi machinery, with its well-defined structure, plays a crucial role in balancing plant immunity and growth. By suppressing specific genes before translation, RNAi disrupts target messenger RNA (mRNA) molecules. While sRNAs predominantly function endogenously, some can traverse organism boundaries, influencing gene expression in interacting organisms. This review focuses on recent discoveries elucidating the regulatory role of RNAi in plant-microbe interactions and its applications in managing plant diseases.
... RNA susturma veya RNAi, transkripsiyonu baskılayarak veya diziye özgü RNA'nın bozulmasıyla transkript miktarını düzenleyen yenilikçi mekanizmalardır. RNAi; transkripsiyon, mRNA stabilitesi veya translasyon seviyelerinde gen ekspresyonunun sekansa özgü inhibisyonu ile sonuçlanan çeşitli RNA temelli süreçleri ifade eden epigenetik bir mekanızmadır (Mann et al., 2008;Saraswat et al., 2017). Keşfi tıp alanında Nobel Ödülü aldıktan sonra, ortaya çıkan RNAi aracılı sistemler, tarımsal mahsul korumadaki ve üretimindeki uygulamalarla tarım üzerinde potan-siyel büyük etkiler göstermektedir (Zotti et al., 2018). ...
... RNA susturma tetiklendikten sonra, hareketli sinyal molekülleri, dsRNA'ların sentezi veya bunların ikincil siR-NA'lara bölünmesi yoluyla daha da artabilir (amplifikasyon). dsRNA'lar; RNA'ya bağlı RNA polimeraz (RDR) enziminin etkisiyle oluşturulur ve çoklu siRNA dublekslerini üretmek üzere Dicer-benzeri proteinler (DCL) tarafından defalarca işlenir (Şekil 3) (Mann et al., 2008;Rosa et al., 2018;Hung and Slotkin, 2021 (Mann et al., 2008). ...
... RNA susturma tetiklendikten sonra, hareketli sinyal molekülleri, dsRNA'ların sentezi veya bunların ikincil siR-NA'lara bölünmesi yoluyla daha da artabilir (amplifikasyon). dsRNA'lar; RNA'ya bağlı RNA polimeraz (RDR) enziminin etkisiyle oluşturulur ve çoklu siRNA dublekslerini üretmek üzere Dicer-benzeri proteinler (DCL) tarafından defalarca işlenir (Şekil 3) (Mann et al., 2008;Rosa et al., 2018;Hung and Slotkin, 2021 (Mann et al., 2008). ...
Birçok organizma, doğal ortamlarında meydana gelen değişikliklere
yanıt olarak yaşamlarını sürdürmelerini sağlayan başarılı adaptasyonlar
göstermektedir. Adaptasyonlar, canlıların değişen koşullarda yaşamlarını sürdürmelerinin yanı sıra göç, üreme ve beslenme davranışlarını da
kolaylaştırmaktadır (Bektaş ve Altıntaş, 2007; Aşçı vd., 2011.; Yoldaş ve
Erişmiş, 2021). Örneğin, dondurucu koşullarda organizmalar donma stresine, oksijen eksikliğine ve dehidrasyona maruz kaldıklarında, bu olumsuz etkilerden korunma antifriz proteinleri ve kriyoprotektanlar sayesinde
sağlanabilmektedir (Yoldaş ve Erişmiş, 2021).
Antifriz proteinleri buz kristalleri üzerindeki çarpıcı etkileriyle birlikte benzersiz özelliklere sahiptir. Bu proteinler akademik literatürde
yıllardır yer almalarıyla birlikte donmuş gıdalar ve kriyoprezervasyon
(dondurarak saklama) gibi teknik konularda sahip oldukları potansiyel
uygulamalarla popüler duruma gelmişlerdir (Clarke vd., 2002). Antifriz proteinleri (AFP), balıklar, böcekler, bitkiler ve bakterileri kapsayan
birçok farklı organizmayı 1°C’nin altındaki sıcaklıklarda donmaya karşı
korumakta ve bir inhibisyon mekanizması yoluyla büyümelerini düzenlemektedir (Clarke vd., 2002; Raymond ve DeVries, 1977). Buz kristallerine
doğrudan bağlanma özellikleri antifriz proteinlerin ortak noktası olsa da
onlar yapısal olarak farklı bir protein grubunda yer almaktadır (Clarke vd.,
2002).
Soğuğa dayanıklı canlılarda temel amaç, sıfırın altındaki sıcaklıklarda vücut sıvılarının sıvı halde kalmasına yardımcı olan belirli yapıda
proteinleri üretmektir. Genel olarak antifriz proteinleri AFP’ler olarak
adlandırılırlar, ancak antifriz glikoproteinler, antifriz polipeptidleri gibi
diğer terimler de bu antifriz proteinlerin yapısal özelliklerini belirtmek
için kullanılmaktadır (Raymond ve DeVries, 1977).
Kutuplardaki sularda yaşayan deniz teleostları, deniz suyu ile aynı
yaklaşık ±1,9 °C’lik bir vücut ısısına sahiptir. Ancak, vücut sıvıları deniz
suyuna karşı hipoozmotiktir ve yaklaşık ± 0,7 °C’ lik bir erime noktasına
sahiptir. Böylece kutupsal teleostlar 1°C’den fazla bir soğumaya maruz
kalabilmektedir. Bu durumda balıkların bir şekilde ölümcül bir donma yaşayacağı ön görülebilmektedir. Kutuplarda yaşayan balıklarda, vücut sıvılarında meydana gelen soğuma sonucu buz miktarının artışı ile meydana
gelmesi muhtemel bir donma, antifriz proteinleri sayesinde önlenmektedir. Bu benzersiz özellik sayesinde kutup balıkları, hücre zarı hasarı ile
bazı zararlı fiziksel ve kimyasal değişikliklerden korunmaktadır (Kumar
vd., 2014).
Günümüzde antifriz proteinler pek çok önemli alanda kullanılmaya
başlanmıştır ve gün geçtikçe bu proteinler daha da önem kazanmaktadır.
. Fen Bilimleri ve
... It is important to mention here that the nanotechnology has found promising potential in enhancing crop production and sustainability by improving shelf life, reducing toxicity and increasing the solubility of poorly water-soluble pesticides (Worrall et al. 2018;Kashyap et al. 2020). Use of RNAi technology as a method for disease suppression is a newly advancing avenue (Werner et al. 2020;Mann et al. 2008). This chapter, thus, aims to discuss the different antimicrobial compounds and their advances so far in managing the major diseases of wheat. ...
... The available management strategies are either environmentally hazardous or harmful to non-target organisms. Hence, efforts are being made to develop a better alternative as compared to the traditional methods, which has brought RNA interference (RNAi) technology to the forefront (Manske et al. 2017;Mann et al. 2008). RNAi technology has a quick knockdown effect on the target genes, and hence, has been used against a number of pests and pathogens. ...
The emergence of new strains of plant pathogenic organisms has caused serious limitations in our ability to control them, so desperately from time to time we need to review the use of antimicrobial compound. When a new antimicrobial compound is introduced from a research outcome, the main objective is to concentrate on its mode of action, which should be more specific to the target organisms as well as less hazardous to the environment. Wheat is the most demanding cereal crop globally. But due to present climate change scenario, some minor diseases are getting more importance and, on the other hand, major diseases are losing their virulence. Under these circumstances we need to know proper control measures against those diseases in time so that the farmers can be benefited. In this chapter, we mention in details the antimicrobial strategies adopted very recently, like fungicides, botanicals, bioantagonist, nanoformulations, etc., with their mode of actions against different diseases of wheat individually or in integrated manner. This chapter reviews recent literatures on conventional and non-conventional therapies with their potentiality to guide future research in the field of wheat protection.KeywordsAntimicrobialBotanicalsBiocontrol agentsDiseaseMode of actionFungicidesWheat
... Mapped traits in different Citrus germplasm * QTL: Quantitative Trait Locus; HLB: Citrus Huanglongbing; CTV: Citrus Tristeza VirusAdvances in biotechnology including genetic manipulation and genome editing have proven to be effective in the development of disease-resistant/tolerant crops(Goulin et al. 2019;Sun et al. 2019;Long et al. 2021). RNA interference (RNAi) and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)-based technologies have recently emerged as potential and promising approaches for improving citrus plants against different diseases like huanglongbing, citrus tristeza virus, canker, and many other fungal and viral diseases(Mann et al. 2008;Zhou et al. 2017;Goulin et al. 2019;Sun et al. 2019;Long et al. 2021). The effectiveness of RNAi for assessing gene functions has been reported in citrus defense mechanisms against pathogens, i.e., silencing of callose synthase 1 gene in C. limon by transient infiltration using Agrobacterium tumefaciens carrying dsRNAs encoding hairpin RNAs. ...
Citrus is an economically important fruit crop growing worldwide, with enormous health benefits. However, conventional citrus breeding has been hindered by a variety of genetic factors, thereby becoming obsolete and insufficient. Citrus research mostly focused on botanical, taxonomic, and cytogenetics issues. Nowadays the knowledge base has strengthened with the plausible outcomes of commercially successful varietal releases. Unfortunately; this has been gradual with only a few success stories among citrus rootstocks and even fewer among scion cultivars. Recent advancements in genetics, molecular biology, biotechnology, and omics (genomics, transcriptomics, proteomics, and metabolomics) have expedited citrus breeding and genetics research. Linkage mapping, genetic diversity, phylogenetic relationships, mutation breeding, mapping, and the international citrus genome sequencing initiatives along with functional analysis have been comprehensively summarized in this review. While providing information on future avenues, this review provides novel mechanistic compiled up-to-date information based on the past and recent progress, facilitating their broader applications to accelerate citrus breeding.
... Microbombardment also known as particle gun bombardment or biolistic process is based on bombarding siRNA, dsRNA, DNA that encodes hairpin constructs, or hpRNAs, as well as, sense or antisense RNA that stimulates the RNA resistantÀmediated pathway to control phytopathogens (Mann et al., 2008). Pooggin et al. (2003) reported that DNA construct of genes such as AC1 and AV2 bombarded in black gram (Vigna mungo) against Vigna mungo yellow mosaic virus (VMYMV) revealed complete recovery from VMYMV infection, recommending the efficacy of RNA silencing tactic by developing resistance to DNA viruses. ...
RNA interference (RNAi) in plant disease management is a novel gene silencing tool that uses several types of double-stranded RNAs (dsRNAs) to knock down the genes either at transcriptional or posttranscriptional level aimed at sequence-specific degradation of phytopathogen’s gene/s or gene/s that code for suppressor molecules to combat negative effects of plant pathogens in crop production. Transformative and nontransformative approaches viz. host-induced gene silencing, spray-induced gene silencing (SIGS), and virus-induced gene silencing have been exploited to elicit RNAi mechanism, and recent strategy SIGS uses exogenous applications of naked in vitro-synthesized or crude dsRNAs. Disease control via RNA silencing in plant disease management has broadly been studied for viral and fungal diseases, and very few investigations have been reported against bacterial diseases. This chapter summarizes the potential of RNAi technology in plant disease management to control major phytopathogens. It also critically and comprehensively examines various methods used for induction of RNAi mechanism and current applications of such strategies of RNAi in different crop systems against plant pathogens. Therefore it can be concluded that RNA silencing is a promising and effective tactic in managing phytopathogens without causing any deleterious effects on the environment.
... Two plant species whose complete genomes are already sequenced-Arabidopsis and poplar-have been selected as model plants for the VIGS system (Watson et al., 2005). Successful VIGS has been achieved in various plants such as soybean, Pisum sativum, tomato, the solanum family, etc. (Mann et al., 2008). ...
... This method can be used for gene silencing, detection of the mechanism of silencing, and protein purification. It is an easy, efficient, and versatile method (Mann et al., 2008). However, the short duration of silencing limits its use (Watson et al., 2005). ...
... The microparticles are coated with dsRNA, siRNA, or DNA encoding hairpin constructs to activate the RNAi pathway (Shabhir et al., 2010). The effect of silencing can be observed the next day after a bombardment, which continues for up to 3-4 days (Mann et al., 2008). Successful silencing induced via microbombardment was achieved in Nicotiana benthamiana (Klahre et al., 2002). ...
Plant diseases caused by microbial pathogens limit crop production and economic growth. Fungal pathogens cause a negative agronomic impact on agriculture-based industry; their mycotoxins affect both the yield and quality of the crop. Thus, the current need for environmentally friendly agronomic solutions has led to the development of RNA interference (RNAi) technology. RNAi has emerged as a promising approach in agricultural research for plant disease management. It is a gene-silencing technology induced by double-stranded RNA (dsRNA), which can be either injected in the pathogen exogenously or produced endogenously by transgenic plants. This dsRNA can cause the death of the pathogen or affect its viability. Thus, RNAi is likely to be the new approach underlying the next generation of resistant transgenic plants.
... Thus, new biotechnological approaches are needed in order to reduce the high production costs and support the citrus disease management. RNA interference (RNAi) and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-based technologies have emerged as potential and promising strategies for improving plant resistance to different pathogens (Mann et al., 2008). ...
... Besides the common strategies of achieving resistance such as applying toxic proteins, lectins, or inhibitors, plant mediated RNAi technology has emerged as a new possibility for combating insects, especially for addressing resistance development in targeted insect pests (Price and Gatehouse, 2008;Puyam et al., 2017). RNAi, initially characterized in Caenorhabditis elegans (Fire et al., 1998), has emerged as an efficient gene silencing approach in various organisms (Hannon, 2002;Mann et al., 2008;Sharma et al., 2013). The gene knockdown of different insects has been achieved via orally fed dsRNA, including insects from the Hymenoptera (Lynch and Desplan, 2006); Coleoptera (Tomoyasu et al., 2008); Diptera (Dzitoyeva et al., 2001); and Lepidoptera (Terenius et al., 2011). ...
Pests, diseases and weeds (biotic stresses) are significant limiting factors for crop yield and production. There is always need to have genotypes tolerant to different abiotic stresses. Conventional breeding approaches have been successful in developing plant genotypes tolerant to various pests and pathogens. However, the limitations associated with conventional breeding methods necessitated the development of alternative methods for developing new varieties with higher resistance to biotic stresses. The genetic engineering approach has been demonstrated to provide enormous options for the selection of resistance genes from different sources and introducing them into target plants for providing the desirable trait. The success of Bt-crops has proved the power of the genetic engineering approach in attaining the target of a pest resistant crop. The entomopathogenic bacteria are popularly used for control of insect pests and vector borne diseases in agricultural crops, among which, Bacillus thuringiensis (Bt) that produces insecticidal toxins is the most extensively utilized. Biopesticide formulations using Bt isolates have successfully controlled pest incidence in farmers' fields for decades. Development of insect tolerance transgenic harboring Bt toxin genes have also proved to be a successful technology in farmers' fields. Unfortunately, extensive use of Bt as a biopesticide or as a transgenic crop for pest control has led to problems such as low efficacy and development of resistance to Bt in various insects. Novel Bt toxin genes are being isolated and characterized in Bt isolates from unexplored environmental niches to overcome these problems. A better and in-depth understanding of host-pathogen interactions at the molecular level would be beneficial in this direction.
... Globally, pests are estimated to destroy about one-third of our crops and are an increasingly serious constraint to crop production, in spite of the advances in pest control technology over the last half century. It is estimated that insect pests cause a huge crop loss of 14% and plant pathogens cause an estimated loss up to 20-30% (Kashyap et al., 2017b;Mann et al., 2008;Pimentel, 2009). Nanomaterials are used efficiently for safe administration of pesticides at lower doses (Kashyap et al., 2015). ...
In recent years, microorganisms have been emanated as excellent ecofriendly and cost-effective nanofactories that have the ability to prevent the harmful toxic effects of chemicals and high energy demand for physiochemical synthesis. Over the past several years, microorganisms including bacteria, actinomycetes, fungi, archaea and viruses, have been studied extra- and intracellularly for the synthesis of metal nanoparticles. The nanoparticles are used in the synthesis of nanoformulation, nanoencapsulation and functionalized nanomaterials for next-generation fertilizers and pesticides that provide site-specific and controlled delivery of active ingredients to protect plants from abiotic and biotic stresses. Thus, the development of smart delivery system based on nanoparticles, usually in the form of nanofertilizers, nanopesticides and nanoherbicides has opened up a new mode of applications for sustainability of agri-sector in the arena of climate change. Briefly, in this article, advancements made in the area of microbial nanotechnology for climate resilient agriculture is reviewed and discussed.
... In the field of agriculture, weather and climate affect crop production and quality as well as the dynamics of pests, diseases and their regulation by natural enemies; a regulation that mostly goes unnoticed by humans (DeBach, 1964). Several reports indicate that plant pathogens cause significant economic crop yield losses every year (Sharma et al., 2017;Kashyap et al., 2017a;Mann et al., 2008). Oerke (2006) reported crop losses ranging from 25-50% depending on the crop. ...
Climate change has a direct effect on the occurrence and severity of diseases in crops, which will have a serious impact on global food security. The changing climate can affect plant-pathogen interactions by altering the pathogen life cycle, expression of host resistance, disease epidemiology and severity of disease epidemics, development of new races, virulence and overwintering or over summering of the pathogen, etc. Recent studies suggested that the predicting effects for unstudied pathosystems will be quite challenging. Therefore, disease management strategies should be reoriented in changing conditions with amalgamation of new strategies for sustainable food production. A summary of climate changes as well as direct effects of climate change on plant pathogens and suitable remedies for their effective management are provided in the chapter.
