Plant defense against virus diseases; growth hormones in highlights

Genome-Wide Identification and Characterization of the Pirin Gene Family in Nicotiana benthamiana

Background: Pirins are nuclear cupin proteins, one of several gene families within the plant cupin superfamily. However, the identification and functional analysis of Pirin proteins in Nicotiana benthamiana have not been explored. Methods: In this study, genome-wide analysis identifying NbPirin genes in N. benthamiana was conducted, as was phylogenetic analysis of Pirin genes in four Solanaceae species (including Capsicum annuum, Solanum lycopersicum, Solanum tuberosum, and N. benthamiana). In addition, we also evaluated the expression pattern of NbPirins under abiotic stress (temperature and phytohormones) and biotic stress (TMV, TuMV, and PVX). Results: A total of six Nbpirin genes were identified, which can be divided into three clades, and NbPirins also embraced a variety of abiotic or biotic cis-acting elements. The results showed that the expression of NbPirin1-6 was influenced by temperature variations, of which NbPirin6 was significantly upregulated at high temperatures (42 °C) but downregulated at low temperatures (4 °C). Notably, the expression of NbPirin6 exhibited a consistent decrease under ABA and MeJA treatments. Moreover, the expression of NbPirin1-6 was also affected by TMV, TuMV, and PVX infection. NbPirin1, NbPirin2, NbPirin3, and NbPirin5 showed higher expression levels under different viral infections compared to non-infection. Interestingly, NbPirin3 showed the highest expression level during TuMV infection (approximately a 20-fold increase compared to non-infection). Conclusions: Our study proposes the potential role of NbPirin6 in plant responses to abiotic stress, and the role of NbPirin3 in plant antiviral defense, and further lays the groundwork for future research on the functions of NbPirin proteins in responses to various stressors.

Hormonal changes associated with arbuscular mycorrhizal fungi indicate defense-like alterations in virus-stressed grapevine

Grapevine is an economically important crop, affected by major production losses due to high virus prevalence. Arbuscular mycorrhizal fungi (AMF) can reduce the impact of plant biotic stresses. However, hormonal response to the simultaneous presence of viruses and AMF remains largely unknown. In this study, we explored the potential of AMF to modify the grapevine's defense response to compatible virus infections. We used GRSPaV, GLRaV-3, and GPGV as infectious viral agents, separately or in different combinations. Two AMF inoculums were tested for their bioprotective abilities, RHIZ (Rhizophagus irregularis) and MIX (R. irregularis, Funneliformis mosseae, F. caledonium). Generally, MIX induced stronger physiological responses than RHIZ inoculum, especially during the earlier phase of symbiosis. The main findings were connected to the hormonal profile of the grapevine infected by all three viruses and inoculated with MIX. In particular, salicylic acid (SA) and abscisic acid (ABA) concentrations were induced five and fifteen months post AMF inoculation, respectively. Expressions of VvNCED1 and VvBG1 were up-regulated in uninoculated grapevines, indicating slower induction of stress response mechanisms. Parameters related to plant vigour and growth were induced in grapevine at both time points, regardless of the virus combination. In conclusion, the defense-like response induced by AMF in grapevines infected with multiple viruses is characterized by the induction of ABA and SA, accompanied by a consistent enhancement of vigor parameters. This study confirms AMF symbiosis as a potentially promising additional tool for combating viral diseases in vineyards.

Toxicity of coumarins in plant defense against pathogens

Coumarins are a specific type of secondary metabolite that can be found in many plants. These compounds are predominantly produced through the phenylpropanoid pathway. Coumarins have been proven to possess a range of biological activities, including antimicrobial properties and antioxidant functions that aid in plant disease resistance response. The antimicrobial effect of coumarins is achieved through various mechanisms. They disrupt the cell membranes of pathogens, inhibit enzymatic activity, and hinder nucleic acid synthesis. Additionally, coumarins stimulate plant defense responses by triggering the production of reactive oxygen species (ROS) and activating the expression of immunity-related genes and signaling pathways such as the salicylic acid-dependent pathway. Due to their crucial role in defense mechanisms, coumarins can be effectively used in sustainable agriculture practices that emphasize environmentally friendly integrated pest management strategies. By providing a comprehensive overview of the biosynthetic pathways, mode of action, and application of coumarins in plant defense, this review aims to highlight the potential importance of coumarins in developing safe and sustainable crop protection strategies.

Heat Stress and Plant-Biotic Interactions: Advances and Perspectives

Climate change presents numerous challenges for agriculture, including frequent events of plant abiotic stresses such as elevated temperatures that lead to heat stress (HS). As the primary driving factor of climate change, HS threatens global food security and biodiversity. In recent years, HS events have negatively impacted plant physiology, reducing plant's ability to maintain disease resistance and resulting in lower crop yields. Plants must adapt their priorities toward defense mechanisms to tolerate stress in challenging environments. Furthermore, selective breeding and long-term domestication for higher yields have made crop varieties vulnerable to multiple stressors, making them more susceptible to frequent HS events. Studies on climate change predict that concurrent HS and biotic stresses will become more frequent and severe in the future, potentially occurring simultaneously or sequentially. While most studies have focused on singular stress effects on plant systems to examine how plants respond to specific stresses, the simultaneous occurrence of HS and biotic stresses pose a growing threat to agricultural productivity. Few studies have explored the interactions between HS and plant-biotic interactions. Here, we aim to shed light on the physiological and molecular effects of HS and biotic factor interactions (bacteria, fungi, oomycetes, nematodes, insect pests, pollinators, weedy species, and parasitic plants), as well as their combined impact on crop growth and yields. We also examine recent advances in designing and developing various strategies to address multi-stress scenarios related to HS and biotic factors.

CaIAA2-CaARF9 module mediates the trade-off between pepper growth and immunity

To challenge the invasion of various pathogens, plants re-direct their resources from plant growth to an innate immune defence system. However, the underlying mechanism that coordinates the induction of the host immune response and the suppression of plant growth remains unclear. Here we demonstrate that an auxin response factor, CaARF9, has dual roles in enhancing the immune resistance to Ralstonia solanacearum infection and in retarding plant growth by repressing the expression of its target genes as exemplified by Casmc4, CaLBD37, CaAPK1b and CaRROP1. The expression of these target genes not only stimulates plant growth but also negatively impacts pepper resistance to R. solanacearum. Under normal conditions, the expression of Casmc4, CaLBD37, CaAPK1b and CaRROP1 is active when promoter-bound CaARF9 is complexed with CaIAA2. Under R. solanacearum infection, however, degradation of CaIAA2 is triggered by SA and JA-mediated signalling defence by the ubiquitin-proteasome system, which enables CaARF9 in the absence of CaIAA2 to repress the expression of Casmc4, CaLBD37, CaAPK1b and CaRROP1 and, in turn, impeding plant growth while facilitating plant defence to R. solanacearum infection. Our findings uncover an exquisite mechanism underlying the trade-off between plant growth and immunity mediated by the transcriptional repressor CaARF9 and its deactivation when complexed with CaIAA2.

Piriformospora indica suppresses the symptoms produced by Banana bract mosaic virus by inhibiting its replication and manipulating chlorophyll and carotenoid biosynthesis and degradation in banana

Banana bract mosaic virus (BBrMV) infection results in characteristic reddish streaks on pseudostem and chlorotic spindle lesions on leaves leading to traveler's palm appearance and complete crop loss depending on the stage of infection in banana plants. Here, we discuss the influence of P. indica colonization (a beneficial fungal root endophyte) on BBrMV infection, specific viral component genes responsible for symptom development, chlorophyll and carotenoid biosynthesis, and degradation in BBrMV-infected banana plants. P. indica colonization significantly and substantially reduced the severity of Banana bract mosaic disease (BBrMD) in addition to increased growth, development and yield of banana plants. The percent disease incidence (PDI) of BBrMV ranges from 50 to 70 per cent in plants raised from suckers and from 58 to 92 per cent in TC plants under artificial inoculation. P. indica-colonized plants inoculated with BBrMV resulted in an enhanced plant height, root length, leaf width, and leaf length of 72, 88, 90, and 60 per cent, respectively, compared to BBrMV alone-infected banana plants along with the reduced disease severity. BBrMV infection showed a drastic decrease of chlorophyll a, chlorophyll b, and total chlorophyll contents by down-regulating chlorophyll biosynthesis (Chlorophyll synthase-CHLG) and upregulating chlorophyll degradation (Chlorophyllase-CLH1 and CLH2 and Pheophytin pheophorbide hydrolase-PPH) genes; and by up-regulating carotenoids biosynthesis (Phytoene synthases-PSY1 and PSY2) and down-regulating its degradation (Phytoene desaturase-PDS) genes compared to P. indica-colonized banana plants challenge inoculated with BBrMV. P. indica also inhibited the expression of the viral genes (P3 and HC-Pro) involved in symptom development. P. indica-colonized banana plants reduced the BBrMV symptoms severity by enhancing chlorophyll biosynthesis; and decreasing chlorophyll degradation and carotenoid biosynthesis and degradation; and inhibiting the viral genes responsible for symptom development in addition to enhanced growth and yield of banana plants.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-03983-y.

Silencing of a Nicotiana benthamiana ascorbate oxidase gene reveals its involvement in resistance against cucumber mosaic virus

MAIN CONCLUSION

Silencing of an ascorbate oxidase (AO) gene in N. benthamiana enhanced disease severity from cucumber mosaic virus (CMV), showing higher accumulation and expansion of the spreading area of CMV. A Nicotiana benthamiana ascorbate oxidase (NbAO) gene was found to be induced upon cucumber mosaic virus (CMV) infection. Virus-induced gene silencing (VIGS) was employed to elucidate the function of AO in N. benthamiana. The tobacco rattle virus (TRV)-mediated VIGS resulted in an efficient silencing of the NbAO gene, i.e., 97.5% and 78.8% in relative quantification as compared to the control groups (TRV::eGFP- and the mock-inoculated plants), respectively. In addition, AO enzymatic activity decreased in the TRV::NtAO-silenced plants as compared to control. TRV::NtAO-mediated NbAO silencing induced a greater reduction in plant height by 15.2% upon CMV infection. CMV titer at 3 dpi was increased in the systemic leaves of NbAO-silenced plants (a 35-fold change difference as compared to the TRV::eGFP-treated group). Interestingly, CMV and TRV titers vary in different parts of systemically infected N. benthamiana leaves. In TRV::eGFP-treated plants, CMV accumulated only at the top half of the leaf, whereas the bottom half of the leaf was "occupied" by TRV. In contrast, in the NbAO-silenced plants, CMV accumulated in both the top and the bottom half of the leaf, suggesting that the silencing of the NbAO gene resulted in the expansion of the spreading area of CMV. Our data suggest that the AO gene might function as a resistant factor against CMV infection in N. benthamiana.

Genome-Wide Identification and Analysis of the ABCF Gene Family in Triticum aestivum

The ATP-binding cassette (ABC) superfamily of proteins is a group of evolutionarily conserved proteins. The ABCF subfamily is involved in ribosomal synthesis, antibiotic resistance, and transcriptional regulation. However, few studies have investigated the role of ABCF in wheat (Triticum aestivum) immunity. Here, we identified 18 TaABCFs and classified them into four categories based on their domain characteristics. Functional similarity between Arabidopsis and wheat ABCF genes was predicted using phylogenetic analysis. A comprehensive genome-wide analysis of gene structure, protein motifs, chromosomal location, and cis-acting elements was also performed. Tissue-specific analysis and expression profiling under temperature, hormonal, and viral stresses were performed using real-time quantitative reverse transcription polymerase chain reaction after randomly selecting one gene from each group. The results revealed that all TaABCF genes had the highest expression at 25 °C and responded to methyl jasmonate induction. Notably, TaABCF2 was highly expressed in all tissues except the roots, and silencing it significantly increased the accumulation of Chinese wheat mosaic virus or wheat yellow mosaic virus in wheat leaves. These results indicated that TaABCF may function in response to viral infection, laying the foundation for further studies on the mechanisms of this protein family in plant defence.

Cajal bodies: Evolutionarily conserved nuclear biomolecular condensates with properties unique to plants

Proper orchestration of the thousands of biochemical processes that are essential to the life of every cell requires highly organized cellular compartmentalization of dedicated microenvironments. There are 2 ways to create this intracellular segregation to optimize cellular function. One way is to create specific organelles, enclosed spaces bounded by lipid membranes that regulate macromolecular flux in and out of the compartment. A second way is via membraneless biomolecular condensates that form due to to liquid-liquid phase separation. Although research on these membraneless condensates has historically been performed using animal and fungal systems, recent studies have explored basic principles governing the assembly, properties, and functions of membraneless compartments in plants. In this review, we discuss how phase separation is involved in a variety of key processes occurring in Cajal bodies (CBs), a type of biomolecular condensate found in nuclei. These processes include RNA metabolism, formation of ribonucleoproteins involved in transcription, RNA splicing, ribosome biogenesis, and telomere maintenance. Besides these primary roles of CBs, we discuss unique plant-specific functions of CBs in RNA-based regulatory pathways such as nonsense-mediated mRNA decay, mRNA retention, and RNA silencing. Finally, we summarize recent progress and discuss the functions of CBs in responses to pathogen attacks and abiotic stresses, responses that may be regulated via mechanisms governed by polyADP-ribosylation. Thus, plant CBs are emerging as highly complex and multifunctional biomolecular condensates that are involved in a surprisingly diverse range of molecular mechanisms that we are just beginning to appreciate.

Geminiviral betasatellites: critical viral ammunition to conquer plant immunity

Geminiviruses have mastered plant cell modulation and immune invasion to ensue prolific infection. Encoding a relatively small number of multifunctional proteins, geminiviruses rely on satellites to efficiently re-wire plant immunity, thereby fostering virulence. Among the known satellites, betasatellites have been the most extensively investigated. They contribute significantly to virulence, enhance virus accumulation, and induce disease symptoms. To date, only two betasatellite proteins, βC1, and βV1, have been shown to play a crucial role in virus infection. In this review, we offer an overview of plant responses to betasatellites and counter-defense strategies deployed by betasatellites to overcome those responses.

Plant protection from virus: a review of different approaches

This review analyzes methods for controlling plant viral infection. The high harmfulness of viral diseases and the peculiarities of viral pathogenesis impose special requirements regarding developing methods to prevent phytoviruses. The control of viral infection is complicated by the rapid evolution, variability of viruses, and the peculiarities of their pathogenesis. Viral infection in plants is a complex interdependent process. The creation of transgenic varieties has caused much hope in the fight against viral pathogens. The disadvantages of genetically engineered approaches include the fact that the resistance gained is often highly specific and short-lived, and there are bans in many countries on the use of transgenic varieties. Modern prevention methods, diagnosis, and recovery of planting material are at the forefront of the fight against viral infection. The main techniques used for the healing of virus-infected plants include the apical meristem method, which is combined with thermotherapy and chemotherapy. These methods represent a single biotechnological complex method of plant recovery from viruses in vitro culture. It widely uses this method for obtaining non-virus planting material for various crops. The disadvantages of the tissue culture-based method of health improvement include the possibility of self-clonal variations resulting from the long-term cultivation of plants under in vitro conditions. The possibilities of increasing plant resistance by stimulating their immune system have expanded, which results from the in-depth study of the molecular and genetic bases of plant resistance toward viruses and the investigation of the mechanisms of induction of protective reactions in the plant organism. The existing methods of phytovirus control are ambiguous and require additional research. Further study of the genetic, biochemical, and physiological features of viral pathogenesis and the development of a strategy to increase plant resistance to viruses will allow a new level of phytovirus infection control to be reached.

Genome-Wide Identification and Functional Analysis of NAP1 in Triticum aestivum

As a main molecular chaperone of histone H2A-H2B, nucleosome assembly protein 1 (NAP1) has been widely researched in many species. However, there is little research investigating the function of NAP1 in Triticum aestivum. To understand the capabilities of the family of NAP1 genes in wheat and the relationship between TaNAP1 genes and plant viruses, we performed comprehensive genome-wide analysis and quantitative real-time polymerase chain reaction (qRT-PCR) for testing expression profiling under hormonal and viral stresses. Our results showed that TaNAP1 was expressed at different levels in different tissues, with higher expression in tissues with high meristematic capacity, such as roots. Furthermore, the TaNAP1 family may participate in plant defense mechanisms. This study provides a systematic analysis of the NAP1 gene family in wheat and lays the foundation for further studies on the function of TaNAP1 in the response of wheat plants to viral infection.

Stress Management in Plants: Examining Provisional and Unique Dose-Dependent Responses

The purpose of this review is to critically evaluate the effects of different stress factors on higher plants, with particular attention given to the typical and unique dose-dependent responses that are essential for plant growth and development. Specifically, this review highlights the impact of stress on genome instability, including DNA damage and the molecular, physiological, and biochemical mechanisms that generate these effects. We provide an overview of the current understanding of predictable and unique dose-dependent trends in plant survival when exposed to low or high doses of stress. Understanding both the negative and positive impacts of stress responses, including genome instability, can provide insights into how plants react to different levels of stress, yielding more accurate predictions of their behavior in the natural environment. Applying the acquired knowledge can lead to improved crop productivity and potential development of more resilient plant varieties, ensuring a sustainable food source for the rapidly growing global population.

Cauliflower mosaic virus: Virus-host interactions and its uses in biotechnology and medicine

Cauliflower mosaic virus (CaMV) was the first discovered plant virus with genomic DNA that uses reverse transcriptase for replication. The CaMV 35S promoter is a constitutive promoter and thus, an attractive driver of gene expression in plant biotechnology. It is used in most transgenic crops to activate foreign genes which have been artificially inserted into the host plant. In the last century, producing food for the world's population while preserving the environment and human health is the main topic of agriculture. The damage caused by viral diseases has a significant negative economic impact on agriculture, and disease control is based on two strategies: immunization and prevention to contain virus spread, so correct identification of plant viruses is important for disease management. Here, we discuss CaMV from different aspects: taxonomy, structure and genome, host plants and symptoms, transmission and pathogenicity, prevention, control and application in biotechnology as well as in medicine. Also, we calculated the CAI index for three ORFs IV, V, and VI of the CaMV virus in host plants, the results of which can be used in the discussion of gene transfer or antibody production to identify the CaMV.

Plant responses to drought stress: microRNAs in action

Drought is common in most regions of the world, and it has a significant impact on plant growth and development. Plants, on the other hand, have evolved their own defense systems to deal with the extreme weather. The reprogramming of gene expression by microRNAs (miRNAs) is one of these defense mechanisms. miRNAs are short noncoding RNAs that have emerged as key post-transcriptional gene regulators in a variety of species. Drought stress modulates the expression of certain miRNAs that are functionally conserved across plant species. These characteristics imply that miRNA-based genetic changes might improve drought resistance in plants. This study highlights current knowledge of plant miRNA biogenesis, regulatory mechanisms and their role in drought stress responses. miRNAs functions and their adaptations by plants during drought stress has also been explained that can be exploited to promote drought-resistance among economically important crops.

A Review of Vector-Borne Rice Viruses

Rice (Oryza sativa L.) is one of the major staple foods for global consumption. A major roadblock to global rice production is persistent loss of crops caused by plant diseases, including rice blast, sheath blight, bacterial blight, and particularly various vector-borne rice viral diseases. Since the late 19th century, 19 species of rice viruses have been recorded in rice-producing areas worldwide and cause varying degrees of damage on the rice production. Among them, southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV) in Asia, rice yellow mottle virus (RYMV) in Africa, and rice stripe necrosis virus (RSNV) in America currently pose serious threats to rice yields. This review systematizes the emergence and damage of rice viral diseases, the symptomatology and transmission biology of rice viruses, the arm races between viruses and rice plants as well as their insect vectors, and the strategies for the prevention and control of rice viral diseases.

Negative Interactions Balance Growth and Defense in Plants Confronted with Herbivores or Pathogens

Plants have evolved a series of defensive mechanisms against pathogens and herbivores, but the defense response always leads to decreases in growth or reproduction, which has serious implications for agricultural production. Growth and defense are negatively regulated not only through metabolic consumption but also through the antagonism of different phytohormones, such as jasmonic acid (JA) and salicylic acid (SA). Meanwhile, plants can limit the expression of defensive metabolites to reduce the costs of defense by producing constitutive defenses such as glandular trichomes or latex and accumulating specific metabolites, determining the activation of plant defense or the maintenance of plant growth. Interestingly, plant defense pathways might be prepared in advance which may be transmitted to descendants. Plants can also use external organisms to protect themselves, thus minimizing the costs of defense. In addition, plant relatives exhibit cooperation to deal with pathogens and herbivores, which is also a way to regulate growth and defense.

Plant responses to metals stress: microRNAs in focus

Metal toxicity can largely affect the growth and yield of numerous plant species. Plants have developed specific mechanisms to withstand the varying amounts of metals. One approach involves utilization of microRNAs (miRNAs) that are known for cleaving transcripts or inhibiting translation to mediate post-transcriptional control. Use of transcription factors (TFs) or gene regulation in metal detoxification largely depends on metal-responsive miRNAs. Moreover, systemic signals and physiological processes for plants response to metal toxicities are likewise controlled by miRNAs. Therefore, it is necessary to understand miRNAs and their regulatory networks in relation to metal stress. The miRNA-based approach can be important to produce metal-tolerant plant species. Here, we have reviewed the importance of plant miRNAs and their role in mitigating metal toxicities. The current review also discusses the specific advances that have occurred as a result of the identification and validation of several metal stress-responsive miRNAs.

Manufactured Nano-Objects Confer Viral Protection against Cucurbit Chlorotic Yellows Virus (CCYV) Infecting Nicotiana benthamiana

Nanotechnology has emerged as a new tool to combat phytopathogens in agricultural crops. Cucurbit chlorotic yellows virus (CCYV) mainly infects Solanaceae crops and causes significant crop losses. Nanomaterials (NMs) may have efficacy against plant viruses, but the mechanisms underlying complex nanomaterials-plant-virus interactions remain elusive. We challenged Nicotiana benthamiana plants with GFP-tagged CCYV and observed morphological, physiological, and molecular changes in response to 21-d foliar exposure to nanoscale Fe and Zn and C₆₀ fullerenes at 100 mg/L concentration for 21 days. We observed that in response to C₆₀ (100 mg/L) treatment, plants displayed a normal phenotype while the viral infection was not seen until 5 days post-inoculation. On the contrary, Fe and Zn were unable to suppress viral progression. The mRNA transcriptional analysis for GFP and viral coat protein revealed that the transcripts of both genes were 5-fold reduced in response to C₆₀ treatment. Evaluation of the chloroplast ultrastructure showed that NMs treatment maintained the normal chloroplast structure in the plants as compared to untreated plants. C₆₀ upregulated the defense-related phytohormones (abscisic acid and salicylic acid) by 42–43%. Our results demonstrate the protective function of carbon-based NMs, with suppression of CCYV symptoms via inhibition of viral replication and systemic movement.

Characterization of Virus-Inducible Orchid Argonaute 5b Promoter and Its Functional Characterization in Nicotiana benthamiana during Virus Infection

Plant ARGONAUTES (AGOs) play a significant role in the defense against viral infection. Previously, we have demonstrated that AGO5s encoded in Phalaenopsis aphrodite subsp. formosana (PaAGO5s) took an indispensable part in defense against major viruses. To understand the underlying defense mechanism, we cloned PaAGO5s promoters (pPaAGO5s) and analyzed their activity in transgenic Nicotiana benthamiana using β-glucuronidase (GUS) as a reporter gene. GUS activity analyses revealed that during Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV) infections, pPaAGO5b activity was significantly increased compared to pPaAGO5a and pPaAGO5c. Analysis of pPaAGO5b 5′-deletion revealed that pPaAGO5b_941 has higher activity during virus infection. Further, yeast one-hybrid analysis showed that the transcription factor NbMYB30 physically interacted with pPaAGO5b_941 to enhance its activity. Overexpression and silencing of NbMYB30 resulted in up- and downregulation of GUS expression, respectively. Exogenous application and endogenous measurement of phytohormones have shown that methyl jasmonate and salicylic acid respond to viral infections. NbMYB30 overexpression and its closest related protein, PaMYB30, in P. aphrodite subsp. formosana reduced CymMV accumulation in P. aphrodite subsp. formosana. Based on these discoveries, this study uncovers the interaction between virus-responsive promoter and the corresponding transcription factor in plants.

SAMDC3 enhances resistance to Barley stripe mosaic virus by promoting the ubiquitination and proteasomal degradation of viral γb protein

Posttranslational modifications (PTMs) play important roles in virus-host interplay. We previously demonstrated that Barley stripe mosaic virus (BSMV) γb protein is phosphorylated by different host kinases to support or impede viral infection. However, whether and how other types of PTMs participate in BSMV infection remains to be explored. Here, we report that S-adenosylmethionine decarboxylase 3 (SAMDC3) from Nicotiana benthamiana or wheat (Triticum aestivum) interacts with γb. BSMV infection induced SAMDC3 expression. Overexpression of SAMDC3 led to the destabilization of γb and reduction in viral infectivity, whereas knocking out NbSAMDC3 increased susceptibility to BSMV. NbSAMDC3 positively regulated the 26S proteasome-mediated degradation of γb via its PEST domain. Further mechanistic studies revealed that γb can be ubiquitinated in planta and that NbSAMDC3 promotes the proteasomal degradation of γb by increasing γb ubiquitination. We also found evidence that ubiquitination occurs at nonlysine residues (Ser-133 and Cys-144) within γb. Together, our results provide a function for SAMDC3 in defence against BSMV infection through targeting of γb abundance, which contributes to our understanding of how a plant host deploys the ubiquitin-proteasome system to mount defences against viral infections.

The interplay of plant hormonal pathways and geminiviral proteins: partners in disease development

Viruses belonging to the family Geminiviridae infect plants and are responsible for a number of diseases of crops in the tropical and sub-tropical regions of the World. The innate immune response of the plant assists in its defense against such viral pathogens by the recognition of pathogen/microbe-associated molecular patterns through pattern-recognition receptors. Phytohormone signalling pathways play a vital role in plant defense responses against these devastating viruses. Geminiviruses, however, have developed counter-defense strategies that prevail over the above defense pathways. The proteins encoded by geminiviruses act as suppressors of plant immunity by interacting with the signalling components of several hormones. In this review we focus on the molecular interplay of phytohormone pathways and geminiviral infection and try to find interesting parallels with similar mechanisms known in other plant-infecting viruses and strengthen the argument that this interplay is necessary for disease development.

Acibenzolar-S-methyl-mediated restriction of loading of plantago asiatica mosaic virus into vascular tissues of Nicotiana benthamiana

Long-distance movement via vascular tissues is an essential step for systemic infection by plant viruses. We previously reported that pre-treatment of Nicotiana benthamiana with acibenzolar-S-methyl (ASM) both suppressed the accumulation of plantago asiatica mosaic virus (PlAMV) in inoculated leaves and delayed the long-distance movement to uninoculated upper leaves. These two effects occurred independently of each other. However, it remained unclear where and when the viral long-distance movement is inhibited upon ASM treatment. In this study, we found that ASM treatment restricted the loading of GFP-expressing PlAMV (PlAMV-GFP) into vascular tissues in the inoculated leaves. This led to delays in viral translocation to the petiole and the main stem, and to untreated upper leaves. We used cryohistological fluorescence imaging to show that ASM treatment affected the viral localization and reduced its accumulation in the phloem, xylem, and mesophyll tissues. A stem girdling experiment, which blocked viral movement downward through phloem tissues, demonstrated that ASM treatment could inhibit viral systemic infection to upper leaves, which occurred even with viral downward movement restricted. Taken together, our results showed that ASM treatment affects the loading of PlAMV-GFP into the vascular system in the inoculated leaf, and that this plays a key role in the ASM-mediated delay of viral long-distance movement.

Manipulation of auxin signalling by plant viruses

Compatible plant-virus interactions result in dramatic changes of the plant transcriptome and morphogenesis, and are often associated with rapid alterations in plant hormone homeostasis and signalling. Auxin controls many aspects of plant organogenesis, development, and growth; therefore, plants can rapidly perceive and respond to changes in the cellular auxin levels. Auxin signalling is a tightly controlled process and, hence, is highly vulnerable to changes in the mRNA and protein levels of its components. There are several core nuclear components of auxin signalling. In the nucleus, the interaction of auxin response factors (ARFs) and auxin/indole acetic acid (Aux/IAA) proteins is essential for the control of auxin-regulated pathways. Aux/IAA proteins are negative regulators, whereas ARFs are positive regulators of the auxin response. The interplay between both is essential for the transcriptional regulation of auxin-responsive genes, which primarily regulate developmental processes but also modulate the plant immune system. Recent studies suggest that plant viruses belonging to different families have developed various strategies to disrupt auxin signalling, namely by (a) changing the subcellular localization of Aux/IAAs, (b) preventing degradation of Aux/IAAs by stabilization, or (c) inhibiting the transcriptional activity of ARFs. These interactions perturb auxin signalling and experimental evidence from various studies highlights their importance for virus replication, systemic movement, interaction with vectors for efficient transmission, and symptom development. In this microreview, we summarize and discuss the current knowledge on the interaction of plant viruses with auxin signalling components of their hosts.

Auxin Plays Multiple Roles during Plant-Pathogen Interactions

The plant hormone auxin governs many aspects of normal plant growth and development. Auxin also plays an important role in plant-microbe interactions, including interactions between plant hosts and pathogenic microorganisms that cause disease. It is now well established that indole-3-acetic acid (IAA), the most well-studied form of auxin, promotes disease in many plant-pathogen interactions. Recent studies have shown that IAA can act both as a plant hormone that modulates host signaling and physiology to increase host susceptibility and as a microbial signal that directly impacts the pathogen to promote virulence, but large gaps in our understanding remain. In this article, we review recent studies on the roles that auxin plays during plant-pathogen interactions and discuss the virulence mechanisms that many plant pathogens have evolved to manipulate host auxin signaling and promote pathogenesis.

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

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.

Transcriptome analysis of yellow passion fruit in response to cucumber mosaic virus infection

The cultivation and production of passion fruit (Passiflora edulis) are severely affected by viral disease. Yet there have been few studies of the molecular response of passion fruit to virus attack. In the present study, RNA-based transcriptional profiling (RNA-seq) was used to identify the gene expression profiles in yellow passion fruit (Passiflora edulis f. flavicarpa) leaves following inoculation with cucumber mosaic virus (CMV). Six RNA-seq libraries were constructed comprising a total of 42.23 Gb clean data. 1,545 differentially expressed genes (DEGs) were obtained (701 upregulated and 884 downregulated). Gene annotation analyses revealed that genes associated with plant hormone signal transduction, transcription factors, protein ubiquitination, detoxification, phenylpropanoid biosynthesis, photosynthesis and chlorophyll metabolism were significantly affected by CMV infection. The represented genes activated by CMV infection corresponded to transcription factors WRKY family, NAC family, protein ubiquitination and peroxidase. Several DEGs encoding protein TIFY, pathogenesis-related proteins, and RNA-dependent RNA polymerases also were upregualted by CMV infection. Overall, the information obtained in this study enriched the resources available for research into the molecular-genetic mechanisms of the passion fruit/CMV interaction, and might provide a theoretical basis for the prevention and management of passion fruit viral disease in the field.

Carbon-based nanomaterials suppress tobacco mosaic virus (TMV) infection and induce resistance in Nicotiana benthamiana

Although nanomaterials (NMs) may inhibit viral pathogens, the mechanisms governing plant-virus-nanomaterial interactions remain unknown. Nicotiana benthamiana plants were treated with nanoscale titanium dioxide (TiO2) and silver (Ag), C60 fullerenes, and carbon nanotubes (CNTs) at 100, 200 and 500 mg L-1 for a 21-day foliar exposure before inoculation with GFP-tagged tobacco mosaic virus (TMV). Plants treated with CNTs and C60 (200 mg L-1) exhibited normal phenotype and viral symptomology was not evident at 5 days post-infection. TiO2 and Ag failed to suppress viral infection. RT-qPCR analysis revealed that viral coat protein transcript abundance and GFP mRNA expression were reduced 74-81% upon CNTs and C60 treatment. TEM revealed that the chloroplast ultrastructure in carbon NM-treated plants was unaffected by TMV infection. Fluorescence measurement of CNTs and C60 (200 mg L-1) treated plants indicated photosynthesis equivalent to healthy controls. CNTs and C60 induced upregulation of the defense-related phytohormones abscisic acid and salicylic acid by 33-52%; the transcription of genes responsible for phytohormone biosynthesis was elevated by 94-104% in treated plants. Our findings demonstrate the protective role of carbon-based NMs, with suppression of TMV symptoms via hindered physical movement and viral replication. Given the lack of viral phytopathogen treatment options, this work represents a novel area of nano-enabled agriculture.

Arms race between rice and viruses: a review of viral and host factors

Much is known about the molecular interactions between positive-strand RNA viruses and dicotyledon plants. However, many important viral pathogens of the monocotyledon rice crop contain negative-strand or double-strand RNA genomes. Recent studies have shown that virus-derived small-interfering RNAs (siRNAs), host microRNAs and phytohormones regulate antiviral responses in rice plants and that rice-infecting RNA viruses encode a diverse repertoire of multifunctional proteins with counter-defensive activities. Moreover, the interactions between viral virulence proteins and host susceptibility factors also shape the virus-rice arms race. This review will focus on these recent advances and discuss strategies and challenges in the translation of discoveries made on molecular virus-rice interactions into practical virus control measures.

Influence of graphene on the multiple metabolic pathways of Zea mays roots based on transcriptome analysis

Graphene reportedly exerts positive effects on plant root growth and development, although the corresponding molecular response mechanism remains to be elucidated. Maize seeds were randomly divided into a control and experimental group, and the roots of Zea mays L. seedlings were watered with different concentrations (0-100 mg/L) of graphene to explore the effects and molecular mechanism of graphene on the growth and development of Z. mays L. Upon evaluating root growth indices, 50 mg/L graphene remarkably increased total root length, root volume, and the number of root tips and forks of maize seedlings compared to those of the control group. We observed that the contents of nitrogen and potassium in rhizosphere soil increased following the 50 mg/L graphene treatment. Thereafter, we compared the transcriptome changes in Z. mays roots in response to the 50 mg/L graphene treatment. Transcriptional factor regulation, plant hormone signal transduction, nitrogen and potassium metabolism, as well as secondary metabolism in maize roots subjected to graphene treatment, exhibited significantly upregulated expression, all of which could be related to mechanisms underlying the response to graphene. Based on qPCR validations, we proposed several candidate genes that might have been affected with the graphene treatment of maize roots. The transcriptional profiles presented here provide a foundation for deciphering the mechanism underlying graphene and maize root interaction.

Molecular and Cellular Mechanisms Involved in Host-Specific Resistance to Cyst Nematodes in Crops

Cyst nematodes are able to infect a wide range of crop species and are regarded as a major threat in crop production. In response to invasion of cyst nematodes, plants activate their innate immune system to defend themselves by conferring basal and host-specific defense responses depending on the plant genotype. Basal defense is dependent on the detection of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs), while host-specific defense mainly relies on the activation of canonical and non-canonical resistance (R) genes or quantitative trait loci (QTL). Currently, application of R genes and QTLs in crop species is a major approach to control cyst nematode in crop cultivation. However, emerging virulent cyst nematode field populations are threatening crop production due to host genetic selection by the application of a limited set of resistance genes in current crop cultivars. To counteract this problem, increased knowledge about the mechanisms involved in host-specific resistance mediated by R genes and QTLs to cyst nematodes is indispensable to improve their efficient and sustainable use in field crops. Despite the identification of an increasing number of resistance traits to cyst nematodes in various crops, the underlying genes and defense mechanisms are often unknown. In the last decade, indebt studies on the functioning of a number of cyst nematode R genes and QTLs have revealed novel insights in how plants respond to cyst nematode infection by the activation of host-specific defense responses. This review presents current knowledge of molecular and cellular mechanisms involved in the recognition of cyst nematodes, the activation of defense signaling and resistance response types mediated by R genes or QTLs. Finally, future directions for research are proposed to develop management strategies to better control cyst nematodes in crop cultivation.

Effect of virus infection on the secondary metabolite production and phytohormone biosynthesis in plants

Plants have evolved according to their environmental conditions and continuously interact with different biological entities. These interactions induce many positive and negative effects on plant metabolism. Many viruses also associate with various plant species and alter their metabolism. Further, virus-plant interaction also alters the expression of many plant hormones. To overcome the biotic stress imposed by the virus's infestation, plants produce different kinds of secondary metabolites that play a significant role in plant defense against the viral infection. In this review, we briefly highlight the mechanism of virus infection, their influence on the plant secondary metabolites and phytohormone biosynthesis in response to the virus-plant interactions.

What does it take to be antiviral? An Argonaute-centered perspective on plant antiviral defense

RNA silencing is a major mechanism of constitutive antiviral defense in plants, mediated by a number of proteins, including the Dicer-like (DCL) and Argonaute (AGO) endoribonucleases. Both DCL and AGO protein families comprise multiple members. In particular, the AGO protein family has expanded considerably in different plant lineages, with different family members having specialized functions. Although the general mode of action of AGO proteins is well established, the properties that make different AGO proteins more or less efficient at targeting viruses are less well understood. In this report, we review methodologies used to study AGO antiviral activity and current knowledge about which AGO family members are involved in antiviral defense. In addition, we discuss what is known about the different properties of AGO proteins thought to be associated with this function.

Silicon-mediated plant defense against pathogens and insect pests

Plant diseases and insect pests are one of the major limiting factors that reduce crop production worldwide. Silicon (Si) is one of the most abundant elements in the lithosphere and has a positive impact on plant health by effectively mitigating biotic and abiotic stresses. It also enhances plant resistance against insect pests and fungal, bacterial, and viral diseases. Therefore, this review critically converges its focus upon Si-mediated physical, biochemical, and molecular mechanisms in plant defense against pathogens and insect pests. It further explains Si-modulated interactive phytohormone signaling and enzymatic production and their involvement in inducing resistance against biotic stresses. Furthermore, this review highlights the recent research accomplishments which have successfully revealed the active role of Si in protecting plants against insect herbivory and various viral, bacterial, and fungal diseases. The article explores the potential in enhancing Si-mediated plant resistance against various economically important diseases and insect pests, further shedding light upon future issues regarding the role of Si in defense against pathogens and insect pests.

Seasonal dynamics and starvation impact on the gut microbiome of urochordate ascidian Halocynthia roretzi

Background

Gut microbiota plays important roles in host animal metabolism, homeostasis and environmental adaptation. However, the interplay between the gut microbiome and urochordate ascidian, the most closet relative of vertebrate, remains less explored. In this study, we characterized the gut microbial communities of urochordate ascidian (Halocynthia roretzi) across the changes of season and starvation stress using a comprehensive set of omic approaches including 16S rRNA gene amplicon sequencing, shotgun metagenomics, metabolomic profiling, and transcriptome sequencing.

Results

The 16S rRNA gene amplicon profiling revealed that ascidians harbor indigenous gut microbiota distinctly different to the marine microbial community and significant variations in composition and abundance of gut bacteria, with predominant bacterial orders representing each season. Depressed alpha-diversities of gut microbiota were observed across starvation stress when compared to the communities in aquafarm condition. Synechococcales involving photosynthesis and its related biosynthesis was reduced in abundance while the enrichments of Xanthomonadales and Legionellales may facilitate bile acid biosynthesis during starvation. Metabolomics analysis found that long chain fatty acids, linolenic acid, cyanoamino acid, and pigments derived from gut bacteria were upregulated, suggesting a beneficial contribution of the gut microbiome to the ascidian under starvation stress.

Conclusions

Our findings revealed seasonal variation of ascidian gut microbiota. Defense and energy-associated metabolites derived from gut microbiome may provide an adaptive interplay between gut microbiome and ascidian host that maintains a beneficial metabolic system across season and starvation stress. The diversity-generating metabolisms from both microbiota and host might lead to the co-evolution and environmental adaptation.

Graphical Abstract

Viral Hacks of the Plant Vasculature: The Role of Phloem Alterations in Systemic Virus Infection

For plant viruses, the ability to load into the vascular phloem and spread systemically within a host is an essential step in establishing a successful infection. However, access to the vascular phloem is highly regulated, representing a significant obstacle to virus loading, movement, and subsequent unloading into distal uninfected tissues. Recent studies indicate that during virus infection, phloem tissues are a source of significant transcriptional and translational alterations, with the number of virus-induced differentially expressed genes being four- to sixfold greater in phloem tissues than in surrounding nonphloem tissues. In addition, viruses target phloem-specific components as a means to promote their own systemic movement and disrupt host defense processes. Combined, these studies provide evidence that the vascular phloem plays a significant role in the mediation and control of host responses during infection and as such is a site of considerable modulation by the infecting virus. This review outlines the phloem responses and directed reprograming mechanisms that viruses employ to promote their movement through the vasculature.

Characterization, Expression Profiling, and Functional Analysis of PtDef, a Defensin-Encoding Gene From Populus trichocarpa

PtDef cloned from Populus trichocarpa contained eight cysteine domains specific to defensins. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis showed that PtDef was expressed in all tissues tested, with lower expression in leaves and higher expression in petioles, stems, and roots. Purified fused PtDef inhibited Aspergillus niger, Alternaria Nees, Mucor corymbifer, Marssonina populi, Rhizopus sp., and Neurospora crassa. PtDef also inhibited the growth of Escherichia coli by triggering autolysis. PtDef overexpression in Nanlin895 poplar (Populus × euramericana cv. Nanlin895) enhanced the level of resistance to Septotinia populiperda. qRT-PCR analysis also showed that the expression of 13 genes related to salicylic acid (SA) and jasmonic acid (JA) signal transduction differed between transgenic and wild-type (WT) poplars before and after inoculation, and that PR1-1 (12–72 h), NPR1-2, TGA1, and MYC2-1 expression was higher in transgenic poplars than in WT. During the hypersensitivity response (HR), large amounts of H₂O₂ were produced by the poplar lines, particularly 12–24 h after inoculation; the rate and magnitude of the H₂O₂ concentration increase were greater in transgenic lines than in WT. Overall, our findings suggest that PtDef, a defensin-encoding gene of P. trichocarpa, could be used for genetic engineering of woody plants for enhanced disease resistance.