Global Profiling of Dynamic Alternative Splicing Modulation in Arabidopsis Root upon Ralstonia solanacearum Infection

A Ralstonia solanacearum Effector Targets Splicing Factor SR34a to Reprogram Alternative Splicing and Regulate Plant Immunity

Alternative splicing is a critical post-transcriptional regulatory mechanism in eukaryotes. While infection with Ralstonia solanacearum GMI1000 significantly alters plant alternative splicing patterns, the underlying molecular mechanisms remain unclear. Herein, the effect of the GMI1000 Type III secretion system effectors on alternative splicing in the tomato cultivar Heinz 1706 was investigated. The RNA-seq analysis confirmed genome-wide alternative splicing changes induced by the Type III secretion system in tomato, including 1386 differential alternatively spliced events across 1023 genes, many of which are associated with plant defense. Seven nucleus-localized Type III effectors were transiently expressed in an RLPK splicing reporter system transgenic tobacco, identifying RipP2 as an effector that modulates alternative splicing levels. Sequence analysis, protein-protein interaction assays, and AlphaFold2 structural predictions revealed that RipP2 interacted with the tomato splicing factor SR34a. Furthermore, RipP2 acetylated a conserved lysine at position 132 within the SWQDLKD motif of SR34a, regulating its splicing pattern in defense-related genes and modulating plant immunity. This study elucidates how the "RipP2-SR34a module" influences plant immune responses by regulating the alternative splicing of immune-related genes, providing new insights into pathogen-plant interactions and splicing regulation.

Pathogen-responsive alternative splicing in plant immunity

Plant immunity involves a complex and finely tuned response to a wide variety of pathogens. Alternative splicing, a post-transcriptional mechanism that generates multiple transcripts from a single gene, enhances both the versatility and effectiveness of the plant immune system. Pathogen infection induces alternative splicing in numerous plant genes involved in the two primary layers of pathogen recognition: pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). However, the mechanisms underlying pathogen-responsive alternative splicing are just beginning to be understood. In this article, we review recent findings demonstrating that the interaction between pathogen elicitors and plant receptors modulates the phosphorylation status of splicing factors, altering their function, and that pathogen effectors target components of the host spliceosome, controlling the splicing of plant immunity-related genes.

Phytopathogens Reprogram Host Alternative mRNA Splicing

Alternative splicing (AS) is an evolutionarily conserved cellular process in eukaryotes in which multiple messenger RNA (mRNA) transcripts are produced from a single gene. The concept that AS adds to transcriptome complexity and proteome diversity introduces a new perspective for understanding how phytopathogen-induced alterations in host AS cause diseases. Recently, it has been recognized that AS represents an integral component of the plant immune system during parasitic, commensalistic, and symbiotic interactions. Here, I provide an overview of recent progress detailing the reprogramming of plant AS by phytopathogens and the functional implications on disease phenotypes. Additionally, I discuss the vital function of AS of immune receptors in regulating plant immunity and how phytopathogens use effector proteins to target key components of the splicing machinery and exploit alternatively spliced variants of immune regulators to negate defense responses. Finally, the functional association between AS and nonsense-mediated mRNA decay in the context of plant-pathogen interface is recapitulated.

Broad-spectrum nano-bactericide utilizing antimicrobial peptides and bimetallic Cu-Ag nanoparticles anchored onto multiwalled carbon nanotubes for sustained protection against persistent bacterial pathogens in crops

Worldwide crop yields are threatened by persistent pathogenic bacteria that cause significant damage and jeopardize global food security. Chemical pesticides have shown limited effectiveness in protecting crops from severe yield loss. To address this obstacle, there is a growing need to develop environmentally friendly bactericides with broad-spectrum and sustained protection against persistent crop pathogens. Here, we present a method for preparing a nanocomposite that combines antimicrobial peptides (AMPs) and bimetallic Cu-Ag nanoparticles anchored onto multiwalled carbon nanotubes (MWCNTs). The nanocomposite exhibited dual antibacterial activity by disrupting bacterial cell membranes and splicing nucleic acids. By functionalizing MWCNTs with small AMPs (sAMPs), we achieved enhanced stability and penetration of the nanocomposite, and improved loading capacity of the Cu-Ag nanoparticles. The synthesized MWCNTs&CuNCs@AgNPs@P nanocomposites demonstrated broad-spectrum lethality against both Gram-positive and Gram-negative bacterial pathogens. Glasshouse pot trials confirmed the efficacy of the nanocomposites in protecting rice crops against bacterial leaf blight and tomato crops against bacterial wilt. These findings highlight the excellent antibacterial properties of the MWCNTs&CuNCs@AgNPs@P nanocomposite and its potential to replace chemical pesticides, offering significant advantages for agricultural applications.

Molecular Insights into Plant-Microbe Interactions: A Comprehensive Review of Key Mechanisms

In most ecosystems, plants establish complex symbiotic relationships with organisms, such as bacteria and fungi, which significantly influence their health by promoting or inhibiting growth. These relationships involve biochemical exchanges at the cellular level that affect plant physiology and have evolutionary implications, such as species diversification, horizontal gene transfer, symbiosis and mutualism, environmental adaptation, and positive impacts on community structure and biodiversity. For these reasons, contemporary research, moving beyond observational studies, seeks to elucidate the molecular basis of these interactions; however, gaps in knowledge remain. This is particularly noticeable in understanding how plants distinguish between beneficial and antagonistic microorganisms. In light of the above, this literature review aims to address some of these gaps by exploring the key mechanisms in common interspecies relationships. Thus, our study presents novel insights into these evolutionary archetypes, focusing on the antibiosis process and microbial signaling, including chemotaxis and quorum sensing. Additionally, it examined the biochemical basis of endophytism, pre-mRNA splicing, and transcriptional plasticity, highlighting the roles of transcription factors and epigenetic regulation in the functions of the interacting organisms. These findings emphasize the importance of understanding these confluences in natural environments, which are crucial for future theoretical and practical applications, such as improving plant nutrition, protecting against pathogens, developing transgenic crops, sustainable agriculture, and researching disease mechanisms. It was concluded that because of the characteristics of the various biomolecules involved in these biological interactions, there are interconnected molecular networks in nature that give rise to different ecological scaffolds. These networks integrate a myriad of functionally organic units that belong to various kingdoms. This interweaving underscores the complexity and multidisciplinary integration required to understand plant-microbe interactions at the molecular level. Regarding the limitations inherent in this study, it is recognized that researchers face significant obstacles. These include technical difficulties in experimentation and fieldwork, as well as the arduous task of consolidating and summarizing findings for academic articles. Challenges range from understanding complex ecological and molecular dynamics to unbiased and objective interpretation of diverse and ever-changing literature.

Alternative Splicing, An Overlooked Defense Frontier of Plants with Respect to Bacterial Infection

Disease represents a major problem in sustainable agricultural development. Plants interact closely with various microorganisms during their development and in response to the prevailing environment. In particular, pathogenic microorganisms can cause plant diseases, affecting the fertility, yield, and longevity of plants. During the long coevolution of plants and their pathogens, plants have evolved both molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) signaling networks in order to regulate host cells in response to pathogen infestation. Additionally, in the postgenomic era, alternative splicing (AS) has become uncovered as one of the major drivers of proteome diversity, and abnormal RNA splicing is closely associated with bacterial infections. Currently, the complexity of host-bacteria interactions is a much studied area of research that has shown steady progress over the past decade. Although the development of high-throughput sequencing technologies and their application in transcriptomes have revolutionized our understanding of AS, many mechanisms related to host-bacteria interactions remain still unclear. To this end, this review summarizes the changes observed in AS during host-bacteria interactions and outlines potential therapeutics for bacterial diseases based on existing studies. In doing so, we hope to provide guidelines for plant disease management in agriculture.

Deciphering the role of alternative splicing as modulators of defense response in the MYMIV- Vigna mungo pathosystem

Alternative splicing (AS) is a crucial regulatory mechanism that impacts transcriptome and proteome complexity under stressful situations. Although its role in abiotic stresses is somewhat understood, our understanding of the mechanistic regulation of pre-mRNA splicing in plant-pathogen interaction is meagre. To comprehend this unexplored immune reprogramming mechanism, transcriptome profiles of Mungbean Yellow Mosaic India Virus (MYMIV)-resistant and susceptible Vigna mungo genotypes were analysed for AS genes that may underlie the resistance mechanism. Results revealed a repertoire of AS-isoforms accumulated during pathogenic infestation, with intron retention being the most common AS mechanism. Identification of 688 differential alternatively spliced (DAS) genes in the resistant host elucidates its robust antiviral response, whereas 322 DAS genes were identified in the susceptible host. Enrichment analyses confirmed DAS transcripts pertaining to stress, signalling, and immune system pathways have undergone maximal perturbations. Additionally, a strong regulation of the splicing factors has been observed both at transcriptional and post-transcriptional levels. qPCR validation of candidate DAS transcripts with induced expression upon MYMIV-infection demonstrated a competent immune response in the resistant background. The AS-impacted genes resulted either in partial/complete loss of functional domains or altered sensitivity to miRNA-mediated gene silencing. A complex regulatory module, miR7517-ATAF2, has been identified in an aberrantly spliced ATAF2 isoform that exposes an intronic miR7517 binding site, thereby suppressing the negative regulator to enhance defense reaction. The present study establishes AS as a non-canonical immune reprogramming mechanism that operates in parallel, thereby offering an alternative strategy for developing yellow mosaic-resistant V. mungo cultivars. This article is protected by copyright. All rights reserved.

Plant pathogens and symbionts target the plant nucleus

In plant-microbe interactions, symbionts and pathogens live within plants and attempt to avoid triggering plant defense responses. In order to do so, these microbes have evolved multiple mechanisms that target components of the plant cell nucleus. Rhizobia-induced symbiotic signaling requires the function of specific legume nucleoporins within the nuclear pore complex. Symbiont and pathogen effectors harbor nuclear localization sequences that facilitate movement across nuclear pores, allowing these proteins to target transcription factors that function in defense. Oomycete pathogens introduce proteins that interact with plant pre-mRNA splicing components in order to alter host splicing of defense-related transcripts. Together, these functions indicate that the nucleus is an active site of symbiotic and pathogenic functioning in plant-microbe interactions.

Comparative Analysis of Alternative Splicing in Two Contrasting Apple Cultivars Defense against Alternaria alternata Apple Pathotype Infection

Alternaria blotch disease, caused by the Alternaria alternata apple pathotype (A. alternata AP), is one of the most serious fungal diseases in apples. Alternative splicing (AS), one of the pivotal post-transcriptional regulatory mechanisms, plays essential roles in various disease resistance responses. Here, we performed RNA-Seq for two apple cultivars (resistant cultivar 'Jonathan' (J) and susceptible cultivar 'Starking Delicious' (SD)) infected by A. alternata AP to further investigate their AS divergence. In total, 1454, 1780, 1367 and 1698 specifically regulated differential alternative splicing (DAS) events were detected in J36, J72, SD36 and SD72 groups, respectively. Retained intron (RI) was the dominant AS pattern. Conformably, 642, 764, 585 and 742 uniquely regulated differentially spliced genes (DSGs) were found during A. alternata AP infection. Comparative analysis of AS genes in differential splicing and expression levels suggested that only a small proportion of DSGs overlapped with differentially expressed genes (DEGs). Gene ontology (GO) enrichment analysis demonstrated that the DSGs were significantly enriched at multiple levels of gene expression regulation. Briefly, the specific AS was triggered in apple defense against A. alternata AP. Therefore, this study facilitates our understanding on the roles of AS regulation in response to A. alternata AP infection in apples.

High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica

The Reference Transcriptomic Dataset (RTD) is an accurate and comprehensive collection of transcripts originating from a given organism. It holds the key to precise transcript quantification and downstream analysis of differential expressions and regulations. Currently, transcriptome annotations for most crop plants are far from complete. For example, Oryza sativa indica (O. sativa indica) is reported to have 40,759 transcripts in the Ensembl database without alternative transcript isoforms and alternative splicing (AS) events. To generate a high-quality RTD, we conducted RNA sequencing of rice leaf samples collected at various time points during Rhizoctonia solani infection. The obtained reads were analyzed by adopting the recently developed computational analysis pipeline to assemble the RTD with increased transcript and AS diversity for O. sativa indica (IndicaRTD). After stringent quality filtering, the newly constructed transcriptome annotation was comprised of 122,968 non-redundant transcripts from 53,695 genes. This study identified many novel transcripts compared to Ensembl deposited data that are important for regulating molecular and physiological processes in the plant system. Currently, the assembled IndicaRTD must allow fast quantification of transcript and gene expression with high precision.

Genome-Wide Profiling of Alternative Splicing and Gene Fusion during Rice Black-Streaked Dwarf Virus Stress in Maize (Zea mays L.)

Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease (MRDD), which is a viral disease that significantly affects maize yields worldwide. Plants tolerate stress through transcriptional reprogramming at the alternative splicing (AS), transcriptional, and fusion gene (FG) levels. However, it is unclear whether and how AS and FG interfere with transcriptional reprogramming in MRDD. In this study, we performed global profiling of AS and FG on maize response to RBSDV and compared it with transcriptional changes. There are approximately 1.43 to 2.25 AS events per gene in maize infected with RBSDV. GRMZM2G438622 was only detected in four AS modes (A3SS, A5SS, RI, and SE), whereas GRMZM2G059392 showed downregulated expression and four AS events. A total of 106 and 176 FGs were detected at two time points, respectively, including six differentially expressed genes and five differentially spliced genes. The gene GRMZM2G076798 was the only FG that occurred at two time points and was involved in two FG events. Among these, 104 GOs were enriched, indicating that nodulin-, disease resistance-, and chloroplastic-related genes respond to RBSDV stress in maize. These results provide new insights into the mechanisms underlying post-transcriptional and transcriptional regulation of maize response to RBSDV stress.