Proteomics and Metabolomics Studies on the Biotic Stress Responses of Rice: an Update

AbstractBiotic stresses represent a serious threat to rice production to meet global food demand and thus pose a major challenge for scientists, who need to understand the intricate defense mechanisms. Proteomics and metabolomics studies have found global changes in proteins and metabolites during defense responses of rice exposed to biotic stressors, and also reported the production of specific secondary metabolites (SMs) in some cultivars that may vary depending on the type of biotic stress and the time at which the stress is imposed. The most common changes were seen in photosynthesis which is modified differently by rice plants to conserve energy, disrupt food supply for biotic stress agent, and initiate defense mechanisms or by biotic stressors to facilitate invasion and acquire nutrients, depending on their feeding style. Studies also provide evidence for the correlation between reactive oxygen species (ROS) and photorespiration and photosynthesis which can broaden our understanding on the balance of ROS production and scavenging in rice-pathogen interaction. Variation in the generation of phytohormones is also a key response exploited by rice and pathogens for their own benefit. Proteomics and metabolomics studies in resistant and susceptible rice cultivars upon pathogen attack have helped to identify the proteins and metabolites related to specific defense mechanisms, where choosing of an appropriate method to identify characterized or novel proteins and metabolites is essential, considering the outcomes of host-pathogen interactions. Despites the limitation in identifying the whole repertoire of responsive metabolites, some studies have shed light on functions of resistant-specific SMs. Lastly, we illustrate the potent metabolites responsible for resistance to different biotic stressors to provide valuable targets for further investigation and application.

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A novel plant-fungal association reveals fundamental sRNA and gene expression reprogramming at the onset of symbiosis

BMC Biology ◽

10.1186/s12915-021-01104-2 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Ena Šečić ◽

Silvia Zanini ◽

Daniel Wibberg ◽

Lukas Jelonek ◽

Tobias Busche ◽

...

Keyword(s):

Gene Expression ◽

Nutrient Uptake ◽

Stress Responses ◽

Growth And Development ◽

De Novo ◽

Brachypodium Distachyon ◽

Defense Responses ◽

Grass Species ◽

Global Changes ◽

Plant Metabolites

Abstract Background Beneficial associations between plants and microbes are widespread in nature and have been studied extensively in the microbial-dominant environment of the rhizosphere. Such associations are highly advantageous for the organisms involved, benefiting soil microbes by providing them access to plant metabolites, while plant growth and development are enhanced through the promotion of nutrient uptake and/or protection against (a)biotic stresses. While the establishment and maintenance of mutualistic associations have been shown to require genetic and epigenetic reprogramming, as well as an exchange of effector molecules between microbes and plants, whether short RNAs are able to effect such changes is currently unknown. Here, we established an interaction between the model grass species Brachypodium distachyon (Bd, Pooideae) and the beneficial fungal root endophyte Serendipita indica (Si, syn. Piriformospora indica, Sebacinales) to elucidate RNA interference-based regulatory changes in gene expression and small (s)RNA profiles that occurred during establishment of a Sebacinalean symbiosis. Results Colonization of Bd roots with Si resulted in higher grain yield, confirming the mutualistic character of this interaction. Resequencing of the Si genome using the Oxford Nanopore technique, followed by de novo assembly yielded in 57 contigs and 9441 predicted genes, including putative members of several families involved in sRNA production. Transcriptome analysis at an early stage of the mutualistic interaction identified 2963 differentially expressed genes (DEG) in Si and 317 in Bd line 21-3. The fungal DEGs were largely associated with carbohydrate metabolism, cell wall degradation, and nutrient uptake, while plant DEGs indicated modulation of (a)biotic stress responses and defense pathways. Additionally, 10% of the upregulated fungal DEGs encode candidate protein effectors, including six DELD proteins typical for Sebacinales. Analysis of the global changes in the sRNA profiles of both associated organisms revealed several putative endogenous plant sRNAs expressed during colonization belonging to known micro (mi)RNA families involved in growth and developmental regulation. Among Bd- and Si-generated sRNAs with putative functions in the interacting organism, we identified transcripts for proteins involved in circadian clock and flowering regulation as well as immunity as potential targets of fungal sRNAs, reflecting the beneficial activity of Si. Conclusions We detected beneficial effects of Si colonization on Bd growth and development, and established a novel plant-mutualist interaction model between these organisms. Together, the changes in gene expression and identification of interaction-induced sRNAs in both organisms support sRNA-based regulation of defense responses and plant development in Bd, as well as nutrient acquisition and cell growth in Si. Our data suggests that a Sebacinalean symbiosis involves reciprocal sRNA targeting of genes during the interaction.

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Salt and Water Stress Responses in Plants

10.5772/intechopen.101072 ◽

2021 ◽

Author(s):

Mirela Irina Cordea ◽

Orsolya Borsai

Keyword(s):

Stress Responses ◽

Defense Mechanisms ◽

Crop Yields ◽

Stress Factors ◽

Abiotic Stress Factors ◽

Inorganic Molecules ◽

Ecological Disturbances ◽

Global Food ◽

Breeding Techniques ◽

Toxic Ions

Climate change-driven ecological disturbances have a great impact on freshwater availability which hampers agricultural production. Currently, drought and salinity are the two major abiotic stress factors responsible for the reduction of crop yields worldwide. Increasing soil salt concentration decreases plant water uptake leading to an apparent water limitation and later to the accumulation of toxic ions in various plant organs which negatively affect plant growth. Plants are autotrophic organisms that function with simple inorganic molecules, but the underlying pathways of defense mechanisms are much more complex and harder to unravel. However, the most promising strategy to achieve sustainable agriculture and to meet the future global food demand, is the enhancement of crop stress tolerance through traditional breeding techniques and genetic engineering. Therefore, it is very important to better understand the tolerance mechanisms of the plants, including signaling pathways, biochemical and physiological responses. Although, these mechanisms are based on a well-defined set of basic responses, they can vary among different plant species.

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Plant Defense Responses to Biotic Stress and Its Interplay With Fluctuating Dark/Light Conditions

Frontiers in Plant Science ◽

10.3389/fpls.2021.631810 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zahra Iqbal ◽

Mohammed Shariq Iqbal ◽

Abeer Hashem ◽

Elsayed Fathi Abd_Allah ◽

Mohammad Israil Ansari

Keyword(s):

Plant Defense ◽

Biotic Stress ◽

Defense Mechanisms ◽

Defense Mechanism ◽

Defense Responses ◽

Light Environment ◽

Microbial Pathogens ◽

Signaling Cascade ◽

Dark Light ◽

The Impact

Plants are subjected to a plethora of environmental cues that cause extreme losses to crop productivity. Due to fluctuating environmental conditions, plants encounter difficulties in attaining full genetic potential for growth and reproduction. One such environmental condition is the recurrent attack on plants by herbivores and microbial pathogens. To surmount such attacks, plants have developed a complex array of defense mechanisms. The defense mechanism can be either preformed, where toxic secondary metabolites are stored; or can be inducible, where defense is activated upon detection of an attack. Plants sense biotic stress conditions, activate the regulatory or transcriptional machinery, and eventually generate an appropriate response. Plant defense against pathogen attack is well understood, but the interplay and impact of different signals to generate defense responses against biotic stress still remain elusive. The impact of light and dark signals on biotic stress response is one such area to comprehend. Light and dark alterations not only regulate defense mechanisms impacting plant development and biochemistry but also bestow resistance against invading pathogens. The interaction between plant defense and dark/light environment activates a signaling cascade. This signaling cascade acts as a connecting link between perception of biotic stress, dark/light environment, and generation of an appropriate physiological or biochemical response. The present review highlights molecular responses arising from dark/light fluctuations vis-à-vis elicitation of defense mechanisms in plants.

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Differential Defense Responses of Upland and Lowland Switchgrass Cultivars to a Cereal Aphid Pest

International Journal of Molecular Sciences ◽

10.3390/ijms21217966 ◽

2020 ◽

Vol 21 (21) ◽

pp. 7966

Author(s):

Lise Pingault ◽

Nathan A. Palmer ◽

Kyle G. Koch ◽

Tiffany Heng-Moss ◽

Jeffrey D. Bradshaw ◽

...

Keyword(s):

Defense Mechanisms ◽

Panicum Virgatum ◽

Global Analysis ◽

Defense Responses ◽

Bioenergy Feedstock ◽

Cereal Aphid ◽

Aphid Infestation ◽

Biotic Stresses ◽

Panicum Virgatum L ◽

Sipha Flava

Yellow sugarcane aphid (YSA) (Sipha flava, Forbes) is a damaging pest on many grasses. Switchgrass (Panicum virgatum L.), a perennial C4 grass, has been selected as a bioenergy feedstock because of its perceived resilience to abiotic and biotic stresses. Aphid infestation on switchgrass has the potential to reduce the yields and biomass quantity. Here, the global defense response of switchgrass cultivars Summer and Kanlow to YSA feeding was analyzed by RNA-seq and metabolite analysis at 5, 10, and 15 days after infestation. Genes upregulated by infestation were more common in both cultivars compared to downregulated genes. In total, a higher number of differentially expressed genes (DEGs) were found in the YSA susceptible cultivar (Summer), and fewer DEGs were observed in the YSA resistant cultivar (Kanlow). Interestingly, no downregulated genes were found in common between each time point or between the two switchgrass cultivars. Gene co-expression analysis revealed upregulated genes in Kanlow were associated with functions such as flavonoid, oxidation-response to chemical, or wax composition. Downregulated genes for the cultivar Summer were found in co-expression modules with gene functions related to plant defense mechanisms or cell wall composition. Global analysis of defense networks of the two cultivars uncovered differential mechanisms associated with resistance or susceptibility of switchgrass in response to YSA infestation. Several gene co-expression modules and transcription factors correlated with these differential defense responses. Overall, the YSA-resistant Kanlow plants have an enhanced defense even under aphid uninfested conditions.

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Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement

Genes ◽

10.3390/genes10100771 ◽

2019 ◽

Vol 10 (10) ◽

pp. 771 ◽

Cited By ~ 31

Author(s):

Baillo ◽

Kimotho ◽

Zhang ◽

Keyword(s):

Transcription Factors ◽

Stress Tolerance ◽

Stress Responses ◽

Biotic Stress ◽

Crop Improvement ◽

Abiotic And Biotic Stress ◽

Crop Species ◽

Biotic Stresses ◽

Wide Range ◽

Tf Gene

In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses can have a marked effect on crop yield. The present and future effects of climate change necessitate the improvement of crop stress tolerance. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) that are master regulators of stress-responsive genes are excellent candidates for crop improvement. Related examples in recent studies include TF gene modulation and overexpression approaches in crop species to enhance stress tolerance. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families, only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. Moreover, although significant progress has been made in deciphering the roles of TFs in important cereal crops, fewer TF genes have been elucidated in sorghum. As a model drought-tolerant crop, sorghum research warrants further focus. This review summarizes recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement, particularly in sorghum. Other TF families and non-coding RNAs that regulate gene expression are discussed briefly. Despite the emphasis on sorghum, numerous examples from wheat, rice, maize, and barley are included. Collectively, the aim of this review is to illustrate the potential application of TF genes for stress tolerance improvement and the engineering of resistant crops, with an emphasis on sorghum.

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Regulatory Network Identification, Promoter and Expression Analysis of Arabidopsis thaliana NPR1 in Defense Responses against Stresses

Notulae Scientia Biologicae ◽

10.15835/nsb10310311 ◽

2018 ◽

Vol 10 (3) ◽

pp. 333-339

Author(s):

Amir G. SHAHRIARI ◽

Aminallah TAHMASEBI ◽

Sima SAZEGARI

Keyword(s):

Arabidopsis Thaliana ◽

Stress Responses ◽

Abiotic Stresses ◽

Defense Responses ◽

Wrky Transcription Factor ◽

Microarray Data Analysis ◽

Common Element ◽

Biotic And Abiotic Stresses ◽

Promoter Regions ◽

Biotic Stresses

Salicylic acid (SA) and jasmonic acid (JA) phytohormones have been known for their roles in plant defense behaviour against biotic and abiotic stresses. They regulate defense pathways by antagonistic interaction. NPR1 as a key regulatory factor in the cross-talk between SA and JA, signaling is essential for the inhibition of JA-responsive gene expression by SA. In silico promoter analysis of 1.5 kb promoter regions of NPR1 gene revealed that NPR1 contains 23 MYB and 20 WRKY transcription factor binding sites. Different cis-elements associated with various stress responses were identified in Arabidopsis thaliana NPR1. The most common element was allocated to the defense responses against biotic stresses. Based on gene network analysis, NPR1, TGA2 and TGA3 were predicted to have functional cooperation with each other. Affymetrix microarray data analysis of A. thaliana under SA treatment demonstrated that most genes involved in NPR1 network are up-regulated under SA treatment. Therefore, interaction and cooperation between these factors might serve to fine-tune regulation of defense and immune responses against biotic and abiotic stresses.

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Variation Between Three Eragrostis tef Accessions in Defense Responses to Rhopalosiphum padi Aphid Infestation

Frontiers in Plant Science ◽

10.3389/fpls.2020.598483 ◽

2020 ◽

Vol 11 ◽

Author(s):

Nathan M. Gyan ◽

Beery Yaakov ◽

Nati Weinblum ◽

Anuradha Singh ◽

Alon Cna’ani ◽

...

Keyword(s):

Stress Responses ◽

Defense Mechanisms ◽

Rhopalosiphum Padi ◽

Defense Responses ◽

The Other ◽

Eragrostis Tef ◽

Aphid Infestation ◽

Volatile Analysis ◽

Insect Order ◽

Physical Defense

Tef (Eragrostis tef), a staple crop that originated in the Horn of Africa, has been introduced to multiple countries over the last several decades. Crop cultivation in new geographic regions raises questions regarding the molecular basis for biotic stress responses. In this study, we aimed to classify the insect abundance on tef crop in Israel, and to elucidate its chemical and physical defense mechanisms in response to insect feeding. To discover the main pests of tef in the Mediterranean climate, we conducted an insect field survey on three selected accessions named RTC-144, RTC-405, and RTC-406, and discovered that the most abundant insect order is Hemiptera. We compared the differences in Rhopalosiphum padi (Hemiptera; Aphididae) aphid performance, preference, and feeding behavior between the three accessions. While the number of aphid progeny was lower on RTC-406 than on the other two, the aphid olfactory assay indicated that the aphids tended to be repelled from the RTC-144 accession. To highlight the variation in defense responses, we investigated the physical and chemical mechanisms. As a physical barrier, the density of non-granular trichomes was evaluated, in which a higher number of trichomes on the RTC-406 than on the other accessions was observed. This was negatively correlated with aphid performance. To determine chemical responses, the volatile and central metabolite profiles were measured upon aphid attack for 4 days. The volatile analysis exposed a rich and dynamic metabolic profile, and the central metabolism profile indicated that tef plants adjust their sugars and organic and amino acid levels. Overall, we found that the tef plants possess similar defense responses as other Poaceae family species, while the non-volatile deterrent compounds are yet to be characterized. A transcriptomic time-series analysis of a selected accession RTC-144 infested with aphids revealed a massive alteration of genes related to specialized metabolism that potentially synthesize non-volatile toxic compounds. This is the first report to reveal the variation in the defense mechanisms of tef plants. These findings can facilitate the discovery of insect-resistance genes leading to enhanced yield in tef and other cereal crops.

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Plant Responses to Biotic Stress: Old Memories Matter

Plants ◽

10.3390/plants11010084 ◽

2021 ◽

Vol 11 (1) ◽

pp. 84

Author(s):

Anirban Bhar ◽

Amrita Chakraborty ◽

Amit Roy

Keyword(s):

Immune Response ◽

Stress Responses ◽

Biotic Stress ◽

Current Knowledge ◽

Adaptive Immune Response ◽

General Concept ◽

Immune Memory ◽

Plant Responses ◽

Biotic Stresses ◽

Genomic Imprints

Plants are fascinating organisms present in most ecosystems and a model system for studying different facets of ecological interactions on Earth. In the environment, plants constantly encounter a multitude of abiotic and biotic stresses. The zero-avoidance phenomena make them more resilient to such environmental odds. Plants combat biotic stress or pathogenic ingression through a complex orchestration of intracellular signalling cascades. The plant–microbe interaction primarily relies on acquired immune response due to the absence of any specialised immunogenic cells for adaptive immune response. The generation of immune memory is mainly carried out by T cells as part of the humoral immune response in animals. Recently, prodigious advancements in our understanding of epigenetic regulations in plants invoke the “plant memory” theory afresh. Current innovations in cutting-edge genomic tools have revealed stress-associated genomic alterations and strengthened the idea of transgenerational memory in plants. In plants, stress signalling events are transferred as genomic imprints in successive generations, even without any stress. Such immunogenic priming of plants against biotic stresses is crucial for their eco-evolutionary success. However, there is limited literature capturing the current knowledge of the transgenerational memory of plants boosting biotic stress responses. In this context, the present review focuses on the general concept of memory in plants, recent advancements in this field and comprehensive implications in biotic stress tolerance with future perspectives.

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GLYI4 Plays A Role in Methylglyoxal Detoxification and Jasmonate-Mediated Stress Responses in Arabidopsis thaliana

Biomolecules ◽

10.3390/biom9100635 ◽

2019 ◽

Vol 9 (10) ◽

pp. 635 ◽

Cited By ~ 4

Author(s):

Silvia Proietti ◽

Gaia Salvatore Falconieri ◽

Laura Bertini ◽

Ivan Baccelli ◽

Elena Paccosi ◽

...

Keyword(s):

Stress Responses ◽

Genome Wide Association Study ◽

Pathogenic Fungus ◽

Stomatal Closure ◽

Defense Responses ◽

Primary Metabolism ◽

Lower Efficiency ◽

Biotic Stresses ◽

A Genome ◽

The Impact

Plant hormones play a central role in various physiological functions and in mediating defense responses against (a)biotic stresses. In response to primary metabolism alteration, plants can produce also small molecules such as methylglyoxal (MG), a cytotoxic aldehyde. MG is mostly detoxified by the combined actions of the enzymes glyoxalase I (GLYI) and glyoxalase II (GLYII) that make up the glyoxalase system. Recently, by a genome-wide association study performed in Arabidopsis, we identified GLYI4 as a novel player in the crosstalk between jasmonate (JA) and salicylic acid (SA) hormone pathways. Here, we investigated the impact of GLYI4 knock-down on MG scavenging and on JA pathway. In glyI4 mutant plants, we observed a general stress phenotype, characterized by compromised MG scavenging, accumulation of reactive oxygen species (ROS), stomatal closure, and reduced fitness. Accumulation of MG in glyI4 plants led to lower efficiency of the JA pathway, as highlighted by the increased susceptibility of the plants to the pathogenic fungus Plectospherella cucumerina. Moreover, MG accumulation brought about a localization of GLYI4 to the plasma membrane, while MeJA stimulus induced a translocation of the protein into the cytoplasmic compartment. Collectively, the results are consistent with the hypothesis that GLYI4 is a hub in the MG and JA pathways.

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Genome-Wide Transcriptomic Identification and Functional Insight of Lily WRKY Genes Responding to Botrytis Fungal Disease

Plants ◽

10.3390/plants10040776 ◽

2021 ◽

Vol 10 (4) ◽

pp. 776

Author(s):

Shipra Kumari ◽

Bashistha Kumar Kanth ◽

Ju young Ahn ◽

Jong Hwa Kim ◽

Geung-Joo Lee

Keyword(s):

Abiotic Stress ◽

Biotic Stress ◽

Developmental Stages ◽

Expression Patterns ◽

Lilium Longiflorum ◽

Biotic And Abiotic Stress ◽

Biotic Stresses ◽

Genome Wide

Genome-wide transcriptome analysis using RNA-Seq of Lilium longiflorum revealed valuable genes responding to biotic stresses. WRKY transcription factors are regulatory proteins playing essential roles in defense processes under environmental stresses, causing considerable losses in flower quality and production. Thirty-eight WRKY genes were identified from the transcriptomic profile from lily genotypes, exhibiting leaf blight caused by Botrytis elliptica. Lily WRKYs have a highly conserved motif, WRKYGQK, with a common variant, WRKYGKK. Phylogeny of LlWRKYs with homologous genes from other representative plant species classified them into three groups- I, II, and III consisting of seven, 22, and nine genes, respectively. Base on functional annotation, 22 LlWRKY genes were associated with biotic stress, nine with abiotic stress, and seven with others. Sixteen unique LlWRKY were studied to investigate responses to stress conditions using gene expression under biotic and abiotic stress treatments. Five genes—LlWRKY3, LlWRKY4, LlWRKY5, LlWRKY10, and LlWRKY12—were substantially upregulated, proving to be biotic stress-responsive genes in vivo and in vitro conditions. Moreover, the expression patterns of LlWRKY genes varied in response to drought, heat, cold, and different developmental stages or tissues. Overall, our study provides structural and molecular insights into LlWRKY genes for use in the genetic engineering in Lilium against Botrytis disease.

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