Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation

Screening of cancer-specific biomarkers for hepatitis B-related hepatocellular carcinoma based on a proteome microarray

Hepatocellular carcinoma (HCC) is associated with one of the highest mortality rates among cancers, rendering its early diagnosis clinically invaluable. Serum biomarkers, specifically alpha-fetoprotein (AFP), represent the most promising and widely used diagnostic biomarkers for HCC. However, its detection rate is low in the early stages of HCC progression, and distinguishing specific false positives for other liver-related diseases, such as cirrhosis and acute hepatitis, remains challenging. Therefore, this study was conducted to identify biomarkers for hepatitis B (HBV)-related liver diseases by screening differentially expressed autoantibodies against tumor-associated antigens (TAAbs). We designed a large-scale multistage investigation, encompassing initial screening, HCC-focused, and ELISA validation cohorts to identify potential TAAbs in HBV-related liver diseases, spanning from healthy control (HC) individuals to patients with chronic hepatitis B (CHB), hepatitis B-related cirrhosis (HBC), and HCC, using protein microarray technology. The differential biological characteristics of TAAbs were analyzed using bioinformatics analysis. Validation of tumor-specific biomarkers for HCC was performed using ELISA. In the screening cohort, 547 candidate TAAbs were identified in the HCC group compared to those in the HC group. In the HCC-focused cohort, 64, 61, and 65 candidate TAAbs were identified in the CHB, HBC, and HCC groups, respectively, compared to those in the HC group. Thirty-four proteins exhibited continuously elevated expression from HCs to patients with CHB, HBC, and HCC. Among these, nine were identified as cancer-specific proteins. In the validation cohort, UBE2Z, CNOT3, and EID3 were correlated with liver function indicators in patients with hepatitis B-related HCC. Overall, UBE2Z, CNOT3, and EID3 emerged as cancer-specific biomarkers for HBV-related liver disease, providing a scientific basis for clinical application.

Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes

Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2-8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3'-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3'-ends, overlapping the Lsm3 binding sites ∼250 bp downstream of their last intron-exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.

Arginine methylation of SM-LIKE PROTEIN 4 antagonistically affects alternative splicing during Arabidopsis stress responses

Arabidopsis (Arabidopsis thaliana) PROTEIN ARGININE METHYLTRANSFERASE5 (PRMT5) post-translationally modifies RNA-binding proteins by arginine (R) methylation. However, the impact of this modification on the regulation of RNA processing is largely unknown. We used the spliceosome component, SM-LIKE PROTEIN 4 (LSM4), as a paradigm to study the role of R-methylation in RNA processing. We found that LSM4 regulates alternative splicing (AS) of a suite of its in vivo targets identified here. The lsm4 and prmt5 mutants show a considerable overlap of genes with altered AS raising the possibility that splicing of those genes could be regulated by PRMT5-dependent LSM4 methylation. Indeed, LSM4 methylation impacts AS, particularly of genes linked with stress response. Wild-type LSM4 and an unmethylable version complement the lsm4-1 mutant, suggesting that methylation is not critical for growth in normal environments. However, LSM4 methylation increases with abscisic acid and is necessary for plants to grow under abiotic stress. Conversely, bacterial infection reduces LSM4 methylation, and plants that express unmethylable-LSM4 are more resistant to Pseudomonas than those expressing wild-type LSM4. This tolerance correlates with decreased intron retention of immune-response genes upon infection. Taken together, this provides direct evidence that R-methylation adjusts LSM4 function on pre-mRNA splicing in an antagonistic manner in response to biotic and abiotic stress.

PAT mRNA decapping factors are required for proper development in Arabidopsis

Evolutionarily conserved protein associated with topoisomerase II (PAT1) proteins activate mRNA decay through binding mRNA and recruiting decapping factors to optimize posttranscriptional reprogramming. Here, we generated multiple mutants of pat1, pat1 homolog 1 (path1), and pat1 homolog 2 (path2) and discovered that pat triple mutants exhibit extremely stunted growth and all mutants with pat1 exhibit leaf serration while mutants with pat1 and path1 display short petioles. All three PATs can be found localized to processing bodies and all PATs can target ASYMMETRIC LEAVES 2-LIKE 9 transcripts for decay to finely regulate apical hook and lateral root development. In conclusion, PATs exhibit both specific and redundant functions during different plant growth stages and our observations underpin the selective regulation of the mRNA decay machinery for proper development.

Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

Transposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts are poorly understood. By long-read direct RNA sequencing and a dedicated bioinformatics pipeline, ParasiTE, we investigated the transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. The epigenetic state of intragenic TEs affects RNAPII elongation and usage of alternative poly(A) signals within TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequences into gene transcripts impact regulation of RNA stability and environmental responses of some loci. Our study provides insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.

Arabidopsis mRNA decay landscape shaped by XRN 5'-3' exoribonucleases

5'-3' exoribonucleases (XRNs) play crucial roles in the control of RNA processing, quality, and quantity in eukaryotes. Although genome-wide profiling of RNA decay fragments is now feasible, how XRNs shape the plant mRNA degradome remains elusive. Here, we profiled and analyzed the RNA degradomes of Arabidopsis wild-type and mutant plants with defects in XRN activity. Deficiency of nuclear XRN3 or cytoplasmic XRN4 activity but not nuclear XRN2 activity greatly altered Arabidopsis mRNA decay profiles. Short excised linear introns and cleaved pre-mRNA fragments downstream of polyadenylation sites were polyadenylated and stabilized in the xrn3 mutant, demonstrating the unique function of XRN3 in the removal of cleavage remnants from pre-mRNA processing. Further analysis of stabilized XRN3 substrates confirmed that pre-mRNA 3' end cleavage frequently occurs after adenosine. The most abundant decay intermediates in wild-type plants include not only the primary substrates of XRN4 but also the products of XRN4-mediated cytoplasmic decay. An increase in decay intermediates with 5' ends upstream of a consensus motif in the xrn4 mutant suggests that there is an endonucleolytic cleavage mechanism targeting the 3' untranslated regions of many Arabidopsis mRNAs. However, analysis of decay fragments in the xrn4 mutant indicated that, except for microRNA-directed slicing, endonucleolytic cleavage events in the coding sequence rarely result in major decay intermediates. Together, these findings reveal the major substrates and products of nuclear and cytoplasmic XRNs along Arabidopsis transcripts and provide a basis for precise interpretation of RNA degradome data.

Identification of LSM family members as potential chemoresistance predictive and therapeutic biomarkers for gastric cancer

Introduction

The Like-Smith (LSM) family plays a critical role in the progression of several cancers. However, the function of LSMs in chemoresistance of gastric cancer (GC) is still elusive.

Methods

The Cancer Genome Atlas (TCGA) database, Gene Expression Omnibus (GEO) database and Tumor Immune Estimation Resource Analysis (TIMER) were utilized to analyze the expression, prognostic value and immune infiltration of LSMs in GC patients. Moreover, qPCR and immunohistochemistry (IHC) experiment were conducted with clinical samples.

Results

The expression of LSMs was upregulated in GC tissues and most of LSMs were negatively correlated with overall survival of GC patients with 5-fluorouracil (5-FU) treatment. We further revealed that LSM5, 7 and 8 were hub genes of GEO (GSE14210). Besides, the qPCR results demonstrated that a higher level of LSM5 and LSM8 was associated with 5-FU chemoresistance in GC. Moreover, both TIMER and IHC revealed that a lower expression of LSM5 and LSM8 was correlated with high infiltration of T cells, regulatory T cells, B cells, macrophages, and neutrophils.

Discussion

Our study systematically investigated the expression pattern and biological features of LSM family members in GC, and identified LSM5 and LSM8 as potential biomarkers in GC with 5-FU chemotherapy.

Two environmental signal-driven RNA metabolic processes: Alternative splicing and translation

Plants live in fixed locations and have evolved adaptation mechanisms that integrate multiple responses to various environmental signals. Among the different components of these response pathways, receptors/sensors represent nodes that recognise environmental signals. Additionally, RNA metabolism plays an essential role in the regulation of gene expression and protein synthesis. With the development of RNA biotechnology, recent advances have been made in determining the roles of RNA metabolism in response to different environmental signals-especially the roles of alternative splicing and translation. In this review, we discuss recent progress in research on how the environmental adaptation mechanisms in plants are affected at the posttranscriptional level. These findings improve our understanding of the mechanism through which plants adapt to environmental changes by regulating the posttranscriptional level and are conducive for breeding stress-tolerant plants to cope with dynamic and rapidly changing environments.

The Sm core protein SmEb regulates salt stress responses through maintaining proper splicing of RCD1 pre-mRNA in Arabidopsis

Salt stress adversely impacts crop production. Several spliceosome components have been implicated in regulating salt stress responses in plants, however, the underlying molecular basis is still unclear. Here we report that the spliceosomal core protein SmEb is essential to salt tolerance in Arabidopsis. Transcriptome analysis showed that SmEb modulates alternative splicing of hundreds of pre-mRNAs in plant response to salt stress. Further study revealed that SmEb is crucial in maintaining proper ratio of two RCD1 splicing variants (RCD1.1/RCD1.2) important for salt stress response. In addition, RCD1.1 but not RCD1.2 is able to interact with the stress regulators and attenuates salt-sensitivity by decreasing salt-induced cell death in smeb-1 mutant. Together, our findings uncovered the essential role of SmEb in the regulation of alternative pre-mRNA splicing in salt stress response.

The 5'-3' mRNA Decay Pathway Modulates the Plant Circadian Network in Arabidopsis

Circadian rhythms enable organisms to anticipate and adjust their physiology to periodic environmental changes. These rhythms are controlled by biological clocks that consist of a set of clock genes that regulate each other's expression. Circadian oscillations in messenger RNA (mRNA) levels require the regulation of mRNA production and degradation. While transcription factors controlling clock function have been well characterized from cyanobacteria to humans, the role of factors controlling mRNA decay is largely unknown. Here, we show that mutations in SM-LIKE PROTEIN 1 (LSM1) and exoribonucleases 4 (XRN4), components of the 5'-3' mRNA decay pathway, alter clock function in Arabidopsis. We found that lsm1 and xrn4 mutants display long-period phenotypes for clock gene expression. In xrn4, these circadian defects were associated with changes in circadian phases of expression, but not overall mRNA levels, of several core-clock genes. We then used noninvasive transcriptome-wide mRNA stability analysis to identify genes and pathways regulated by XRN4. Among genes affected in the xrn4 mutant at the transcriptional and posttranscriptional level, we found an enrichment in genes involved in auxin, ethylene and drought recovery. Large effects were not observed for canonical core-clock genes, although the mRNAs of several auxiliary clock genes that control the pace of the clock were stabilized in xrn4 mutants. Our results establish that the 5'-3' mRNA decay pathway constitutes a novel posttranscriptional regulatory layer of the circadian gene network, which probably acts through a combination of small effects on mRNA stability of several auxiliary and some core-clock genes.

Modulation of plant development and chilling stress responses by alternative splicing events under control of the spliceosome protein SmEb in Arabidopsis

Cold stress resulting from chilling and freezing temperatures substantially inhibits plant growth and reduces crop production worldwide. Tremendous research efforts have been focused on elucidating the molecular mechanisms of freezing tolerance in plants. However, little is known about the molecular nature of chilling stress responses in plants. Here we found that two allelic mutants in a spliceosome component gene SmEb (smeb-1 and smeb-2) are defective in development and responses to chilling stress. RNA-seq analysis revealed that SmEb controls the splicing of many pre-messenger RNAs (mRNAs) under chilling stress. Our results suggest that SmEb is important to maintain proper ratio of the two COP1 splicing variants (COP1a/COP1b) to fine tune the level of HY5. In addition, the transcription factor BES1 shows a dramatic defect in pre-mRNA splicing in the smeb mutants. Ectopic expression of the two BES1 splicing variants enhances the chilling sensitivity of the smeb-1 mutant. Furthermore, biochemical and genetic analysis showed that CBFs act as negative upstream regulators of SmEb by directly suppressing its transcription. Together, our results demonstrate that proper alternative splicing of pre-mRNAs controlled by the spliceosome component SmEb is critical for plant development and chilling stress responses.

The Rysto immune receptor recognises a broadly conserved feature of potyviral coat proteins

Knowledge of the immune mechanisms responsible for viral recognition is critical for understanding durable disease resistance and successful crop protection. We determined how potato virus Y (PVY) coat protein (CP) is recognised by Ry_sto , a TNL immune receptor. We applied structural modelling, site-directed mutagenesis, transient overexpression, co-immunoprecipitation, infection assays and physiological cell death marker measurements to investigate the mechanism of Ry_sto -CP interaction. Ry_sto associates directly with PVY CP in planta that is conditioned by the presence of a CP central 149 amino acids domain. Each deletion that affects the CP core region impairs the ability of Ry_sto to trigger defence. Point mutations in the amino acid residues Ser₁₂₅ , Arg₁₅₇ , and Asp₂₀₁ of the conserved RNA-binding pocket of potyviral CP reduce or abolish Ry_sto binding and Ry_sto -dependent responses, demonstrating that appropriate folding of the CP core is crucial for Ry_sto -mediated recognition. Ry_sto recognises the CPs of at least 10 crop-damaging viruses that share a similar core region. It confers immunity to plum pox virus and turnip mosaic virus in both Solanaceae and Brassicaceae systems, demonstrating potential utility in engineering virus resistance in various crops. Our findings shed new light on how R proteins detect different viruses by sensing conserved structural patterns.

Arabidopsis RNA processing body components LSM1 and DCP5 aid in the evasion of translational repression during Cauliflower mosaic virus infection

Viral infections impose extraordinary RNA stress, triggering cellular RNA surveillance pathways such as RNA decapping, nonsense-mediated decay, and RNA silencing. Viruses need to maneuver among these pathways to establish infection and succeed in producing high amounts of viral proteins. Processing bodies (PBs) are integral to RNA triage in eukaryotic cells, with several distinct RNA quality control pathways converging for selective RNA regulation. In this study, we investigated the role of Arabidopsis thaliana PBs during Cauliflower mosaic virus (CaMV) infection. We found that several PB components are co-opted into viral factories that support virus multiplication. This pro-viral role was not associated with RNA decay pathways but instead, we established that PB components are helpers in viral RNA translation. While CaMV is normally resilient to RNA silencing, dysfunctions in PB components expose the virus to this pathway, which is similar to previous observations for transgenes. Transgenes, however, undergo RNA quality control-dependent RNA degradation and transcriptional silencing, whereas CaMV RNA remains stable but becomes translationally repressed through decreased ribosome association, revealing a unique dependence among PBs, RNA silencing, and translational repression. Together, our study shows that PB components are co-opted by the virus to maintain efficient translation, a mechanism not associated with canonical PB functions.

Relevance and Regulation of Alternative Splicing in Plant Heat Stress Response: Current Understanding and Future Directions

Alternative splicing (AS) is a major mechanism for gene expression in eukaryotes, increasing proteome diversity but also regulating transcriptome abundance. High temperatures have a strong impact on the splicing profile of many genes and therefore AS is considered as an integral part of heat stress response. While many studies have established a detailed description of the diversity of the RNAome under heat stress in different plant species and stress regimes, little is known on the underlying mechanisms that control this temperature-sensitive process. AS is mainly regulated by the activity of splicing regulators. Changes in the abundance of these proteins through transcription and AS, post-translational modifications and interactions with exonic and intronic cis-elements and core elements of the spliceosomes modulate the outcome of pre-mRNA splicing. As a major part of pre-mRNAs are spliced co-transcriptionally, the chromatin environment along with the RNA polymerase II elongation play a major role in the regulation of pre-mRNA splicing under heat stress conditions. Despite its importance, our understanding on the regulation of heat stress sensitive AS in plants is scarce. In this review, we summarize the current status of knowledge on the regulation of AS in plants under heat stress conditions. We discuss possible implications of different pathways based on results from non-plant systems to provide a perspective for researchers who aim to elucidate the molecular basis of AS under high temperatures.

Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana

Defects in RNA maturation and RNA decay factors may generate substrates for the RNA interference machinery. This phenomenon was observed in plants where mutations in some RNA-related factors lead to the production of RNA-quality control small interfering RNAs and several mutants show enhanced silencing of reporter transgenes. To assess the potential of RNAi activation on endogenous transcripts, we sequenced small RNAs from a set of Arabidopsis thaliana mutants with defects in various RNA metabolism pathways. We observed a global production of siRNAs caused by inefficient pre-mRNA cleavage and polyadenylation leading to read-through transcription into downstream antisense genes. In addition, in the lsm1a lsm1b double mutant, we identified NIA1, SMXL5, and several miRNA-targeted mRNAs as producing siRNAs, a group of transcripts suggested being especially sensitive to deficiencies in RNA metabolism. However, in most cases, RNA metabolism perturbations do not lead to the widespread production of siRNA derived from mRNA molecules. This observation is contrary to multiple studies based on reporter transgenes and suggests that only a very high accumulation of defective mRNA species caused by specific mutations or substantial RNA processing defects trigger RNAi pathways.

Genome-Wide Identification and Characterization of Small Peptides in Maize

Small peptides (sPeptides), <100 amino acids (aa) long, are encoded by small open reading frames (sORFs) often found in the 5' and 3' untranslated regions (or other parts) of mRNAs, in long non-coding RNAs, or transcripts from introns and intergenic regions; various sPeptides play important roles in multiple biological processes. In this study, we conducted a comprehensive study of maize (Zea mays) sPeptides using mRNA sequencing, ribosome profiling (Ribo-seq), and mass spectrometry (MS) on six tissues (each with at least two replicates). To identify maize sORFs and sPeptides from these data, we set up a robust bioinformatics pipeline and performed a genome-wide scan. This scan uncovered 9,388 sORFs encoding peptides of 2-100 aa. These sORFs showed distinct genomic features, such as different Kozak region sequences, higher specificity of translation, and high translational efficiency, compared with the canonical protein-coding genes. Furthermore, the MS data verified 2,695 sPeptides. These sPeptides perfectly discriminated all the tissues and were highly associated with their parental genes. Interestingly, the parental genes of sPeptides were significantly enriched in multiple functional gene ontology terms related to abiotic stress and development, suggesting the potential roles of sPeptides in the regulation of their parental genes. Overall, this study lays out the guidelines for genome-wide scans of sORFs and sPeptides in plants by integrating Ribo-seq and MS data and provides a more comprehensive resource of functional sPeptides in maize and gives a new perspective on the complex biological systems of plants.

Proteome impact on maize silks under the priming state induced by Trichoderma root colonization

Trichoderma activates plant proteins to counteract Fusarium infection. Comparison between proteomic and transcriptomic data suggests differential response regulation. Proteins from the phenylpropanoid pathway are activated to quickly respond to pathogen attack. Trichoderma species can stimulate local and distant immune responses in colonized plant tissues to prevent future pathogenic attacks. Priming of plant defenses is characterized by changes in transcriptional, metabolic, and epigenetic states after stimulus perception. We have previously investigated transcriptional reprogramming in silk tissues from maize plants inoculated with Trichoderma atroviride and challenged with Fusarium verticillioides (Agostini et al., Mol Plant-Microbe In 32:95-106, 2019). To better understand the molecular changes induced by T. atroviride in maize, a proteomic approach was conducted in this instance. Several proteins belonging to different metabolic categories were detected as priming-involved proteins. However, we detected a very low correlation with those priming-modulated transcripts suggesting the importance of regulatory events a posteriori of the transcriptional process to accomplish the final goal of blocking pathogen entry. Specifically, we focused on the phenylpropanoid pathway, since we detected several proteins that are upregulated in the priming state and might explain cell wall reinforcement as well as the increase in flavonoid and lignin content in maize silks after activation of induced systemic resistance.

Data-independent acquisition proteomic analysis of biochemical factors in rice seedlings following treatment with chitosan oligosaccharides

Chitosan oligosaccharides (COS) can elicit plant immunity and defence responses in rice plants, but exactly how this promotes plant growth remains largely unknown. Herein, we explored the effects of 0.5 mg/L COS on plant growth promotion in rice seedlings by measuring root and stem length, investigating biochemical factors in whole plants via proteomic analysis, and confirming upregulated and downregulated genes by real-time quantitative PCR. Pathway enrichment results showed that COS promoted root and stem growth, and stimulated metabolic (biosynthetic and catabolic processes) and photosynthesis in rice plants during the seedling stage. Expression levels of genes related to chlorophyll a-b binding, RNA binding, catabolic processes and calcium ion binding were upregulated following COS treatment. Furthermore, comparative analysis indicated that numerous proteins involved in the biosynthesis, metabolic (catabolic) processes and photosynthesis pathways were upregulated. The findings indicate that COS may upregulate calcium ion binding, photosynthesis, RNA binding, and catabolism proteins associated with plant growth during the rice seedling stage.

Prefoldins contribute to maintaining the levels of the spliceosome LSM2-8 complex through Hsp90 in Arabidopsis

Although originally identified as the components of the complex aiding the cytosolic chaperonin CCT in the folding of actins and tubulins in the cytosol, prefoldins (PFDs) are emerging as novel regulators influencing gene expression in the nucleus. Work conducted mainly in yeast and animals showed that PFDs act as transcriptional regulators and participate in the nuclear proteostasis. To investigate new functions of PFDs, we performed a co-expression analysis in Arabidopsis thaliana. Results revealed co-expression between PFD and the Sm-like (LSM) genes, which encode the LSM2–8 spliceosome core complex, in this model organism. Here, we show that PFDs interact with and are required to maintain adequate levels of the LSM2–8 complex. Our data indicate that levels of the LSM8 protein, which defines and confers the functional specificity of the complex, are reduced in pfd mutants and in response to the Hsp90 inhibitor geldanamycin. We provide biochemical evidence showing that LSM8 is a client of Hsp90 and that PFD4 mediates the interaction between both proteins. Consistent with our results and with the role of the LSM2–8 complex in splicing through the stabilization of the U6 snRNA, pfd mutants showed reduced levels of this snRNA and altered pre-mRNA splicing patterns.

Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways

In animals, RNA polymerase II initiates transcription bidirectionally from gene promoters to produce pre-mRNAs on the forward strand and promoter upstream transcripts (PROMPTs) on the reverse strand. PROMPTs are degraded by the nuclear exosome. Previous studies based on nascent RNA approaches concluded that Arabidopsis (Arabidopsis thaliana) does not produce PROMPTs. Here, we used steady-state RNA sequencing in mutants defective in nuclear RNA decay including the exosome to reassess the existence of Arabidopsis PROMPTs. While they are rare, we identified ∼100 cases of exosome-sensitive PROMPTs in Arabidopsis. Such PROMPTs are sources of small interfering RNAs in exosome-deficient mutants, perhaps explaining why plants have evolved mechanisms to suppress PROMPTs. In addition, we found ∼200 long, unspliced and exosome-sensitive antisense RNAs that arise from transcription start sites within parts of the genome encoding 3'-untranslated regions on the sense strand. The previously characterized noncoding RNA that regulates expression of the key seed dormancy regulator, DELAY OF GERMINATION1, is a typical representative of this class of RNAs. Transcription factor genes are overrepresented among loci with exosome-sensitive antisense RNAs, suggesting a potential for widespread control of gene expression via this class of noncoding RNAs. Lastly, we assess the use of alternative promoters in Arabidopsis and compare the accuracy of existing TSS annotations.

Hijacking of host cellular components as proviral factors by plant-infecting viruses

Plant viruses are important pathogens that cause serious crop losses worldwide. They are obligate intracellular parasites that commandeer a wide array of proteins, as well as metabolic resources, from infected host cells. In the past two decades, our knowledge of plant-virus interactions at the molecular level has exploded, which provides insights into how plant-infecting viruses co-opt host cellular machineries to accomplish their infection. Here, we review recent advances in our understanding of how plant viruses divert cellular components from their original roles to proviral functions. One emerging theme is that plant viruses have versatile strategies that integrate a host factor that is normally engaged in plant defense against invading pathogens into a viral protein complex that facilitates viral infection. We also highlight viral manipulation of cellular key regulatory systems for successful virus infection: posttranslational protein modifications for fine control of viral and cellular protein dynamics; glycolysis and fermentation pathways to usurp host resources, and ion homeostasis to create a cellular environment that is beneficial for viral genome replication. A deeper understanding of viral-infection strategies will pave the way for the development of novel antiviral strategies.

A Nuclear RNA Degradation Pathway Helps Silence Polycomb/H3K27me3-Marked Loci in Caenorhabditis elegans

In fission yeast and plants, RNA-processing pathways contribute to heterochromatin silencing, complementing well-characterized pathways of transcriptional repression. However, it was unclear whether this additional level of regulation occurs in metazoans. In a genetic screen, we uncovered a pathway of silencing in Caenorhabditis elegans somatic cells, whereby the highly conserved, RNA-binding complex LSM2-8 contributes to the repression of heterochromatic reporters and endogenous genes bearing the Polycomb mark H3K27me3. Importantly, the LSM2-8 complex works cooperatively with a 5'-3' exoribonuclease, XRN-2, and disruption of the pathway leads to selective mRNA stabilization. LSM2-8 complex-mediated RNA degradation does not target nor depend on H3K9me2/me3, unlike previously described pathways of heterochromatic RNA degradation. Up-regulation of lsm-8-sensitive loci coincides with a localized drop in H3K27me3 levels in the lsm-8 mutant. Put into the context of epigenetic control of gene expression, it appears that targeted RNA degradation helps repress a subset of H3K27me3-marked genes, revealing an unappreciated layer of regulation for facultative heterochromatin in animals.

RALF1-FERONIA complex affects splicing dynamics to modulate stress responses and growth in plants

The environmentally responsive signaling pathways that link global transcriptomic changes through alternative splicing (AS) to plant fitness remain unclear. Here, we found that the interaction of the extracellular rapid alkalinization FACTOR 1 (RALF1) peptide with its receptor FERONIA (FER) triggered a rapid and massive RNA AS response by interacting with and phosphorylating glycine-rich RNA binding protein7 (GRP7) to elevate GRP7 nuclear accumulation in Arabidopsis thaliana. FER-dependent GRP7 phosphorylation enhanced its mRNA binding ability and its association with the spliceosome component U1-70K to enable splice site selection, modulating dynamic AS. Genetic reversal of a RALF1-FER-dependent splicing target partly rescued mutants deficient in GRP7. AS of GRP7 itself induced nonsense-mediated decay feedback to the RALF1-FER-GRP7 module, fine-tuning stress responses, and cell growth. The RALF1-FER-GRP7 module provides a paradigm for regulatory mechanisms of RNA splicing in response to external stimuli.

LSM2-8 and XRN-2 contribute to the silencing of H3K27me3-marked genes through targeted RNA decay

In fission yeast and plants, RNA-processing and degradation contribute to heterochromatin silencing, alongside conserved pathways of transcriptional repression. It was unknown if similar pathways exist in metazoans. Here we describe a pathway of silencing in C. elegans somatic cells, in which the highly conserved RNA binding complex LSM2-8 contributes selectively to the repression of heterochromatic reporters and endogenous genes bearing the Polycomb mark, histone H3K27me3. It acts by degrading selected transcripts through the XRN-2 exoribonuclease. Disruption of the LSM2-8 pathway leads to mRNA stabilization. Unlike previously described pathways of heterochromatic RNA degradation, LSM2-8-mediated RNA degradation does not require nor deposit H3K9 methylation. Rather, loss of this pathway coincides with a localized reduction in H3K27me3 at lsm-8-sensitive loci. Thus, we have uncovered a mechanism of RNA degradation that selectively contributes to the silencing of a subset of H3K27me3-marked genes, revealing a previously unrecognized layer of post-transcriptional control in metazoan heterochromatin.

RNA Helicases from the DEA(D/H)-Box Family Contribute to Plant NMD Efficiency

Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic RNA surveillance mechanism that degrades aberrant mRNAs comprising a premature translation termination codon. The adenosine triphosphate (ATP)-dependent RNA helicase up-frameshift 1 (UPF1) is a major NMD factor in all studied organisms; however, the complexity of this mechanism has not been fully characterized in plants. To identify plant NMD factors, we analyzed UPF1-interacting proteins using tandem affinity purification coupled to mass spectrometry. Canonical members of the NMD pathway were found along with numerous NMD candidate factors, including conserved DEA(D/H)-box RNA helicase homologs of human DDX3, DDX5 and DDX6, translation initiation factors, ribosomal proteins and transport factors. Our functional studies revealed that depletion of DDX3 helicases enhances the accumulation of NMD target reporter mRNAs but does not result in increased protein levels. In contrast, silencing of DDX6 group leads to decreased accumulation of the NMD substrate. The inhibitory effect of DDX6-like helicases on NMD was confirmed by transient overexpression of RH12 helicase. These results indicate that DDX3 and DDX6 helicases in plants have a direct and opposing contribution to NMD and act as functional NMD factors.

Transcriptional responses of LSm14A after infection of blue eggshell layers with Newcastle disease viruses

LSm14A is a key innate immunity component of processing body (P-body) that mediates interferon-β (IFN-β) signaling by viral RNA. This is the first study to report chicken LSm14A (cLSm14A) cloning from blue eggshell layer, high tibia and frizzle chickens. The cLSm14A gene, encoding 461 amino acids, is highly homologous in the three types of chickens. The cLSm14A was extensively expressed in several tissues. The transcriptional level of cLSm14A was significantly increased in various stages of Newcastle disease virus (NDV) infection. In HEK293 cells, full length cLSm14A from blue eggshell layer was localized in the cytoplasm as dots. The results of this study indicated that cLSm14A is an important sensor that mediates innate immunity in chicken against NDV infections.

A Bacterial Effector Mimics a Host HSP90 Client to Undermine Immunity

The molecular chaperone HSP90 facilitates the folding of several client proteins, including innate immune receptors and protein kinases. HSP90 is an essential component of plant and animal immunity, yet pathogenic strategies that directly target the chaperone have not been described. Here, we identify the HopBF1 family of bacterial effectors as eukaryotic-specific HSP90 protein kinases. HopBF1 adopts a minimal protein kinase fold that is recognized by HSP90 as a host client. As a result, HopBF1 phosphorylates HSP90 to completely inhibit the chaperone's ATPase activity. We demonstrate that phosphorylation of HSP90 prevents activation of immune receptors that trigger the hypersensitive response in plants. Consequently, HopBF1-dependent phosphorylation of HSP90 is sufficient to induce severe disease symptoms in plants infected with the bacterial pathogen, Pseudomonas syringae. Collectively, our results uncover a family of bacterial effector kinases with toxin-like properties and reveal a previously unrecognized betrayal mechanism by which bacterial pathogens modulate host immunity.

Biological Function of Changes in RNA Metabolism in Plant Adaptation to Abiotic Stress

Plant growth and productivity are greatly impacted by environmental stresses. Therefore, plants have evolved various sophisticated mechanisms for adaptation to nonoptimal environments. Recent studies using RNA metabolism-related mutants have revealed that RNA processing, RNA decay and RNA stability play an important role in regulating gene expression at a post-transcriptional level in response to abiotic stresses. Studies indicate that RNA metabolism is a unified network, and modification of stress adaptation-related transcripts at multiple steps of RNA metabolism is necessary to control abiotic stress-related gene expression. Recent studies have also demonstrated the important role of noncoding RNAs (ncRNAs) in regulating abiotic stress-related gene expression and revealed their involvement in various biological functions through their regulation of DNA methylation, DNA structural modifications, histone modifications and RNA-RNA interactions. ncRNAs regulate mRNA transcription and their synthesis is affected by mRNA processing and degradation. In the present review, recent findings pertaining to the role of the metabolic regulation of mRNAs and ncRNAs in abiotic stress adaptation are summarized and discussed.

Computational identification of protein-protein interactions in model plant proteomes

Protein-protein interactions (PPIs) play essential roles in many biological processes. A PPI network provides crucial information on how biological pathways are structured and coordinated from individual protein functions. In the past two decades, large-scale PPI networks of a handful of organisms were determined by experimental techniques. However, these experimental methods are time-consuming, expensive, and are not easy to perform on new target organisms. Large-scale PPI data is particularly sparse in plant organisms. Here, we developed a computational approach for detecting PPIs trained and tested on known PPIs of Arabidopsis thaliana and applied to three plants, Arabidopsis thaliana, Glycine max (soybean), and Zea mays (maize) to discover new PPIs on a genome-scale. Our method considers a variety of features including protein sequences, gene co-expression, functional association, and phylogenetic profiles. This is the first work where a PPI prediction method was developed for is the first PPI prediction method applied on benchmark datasets of Arabidopsis. The method showed a high prediction accuracy of over 90% and very high precision of close to 1.0. We predicted 50,220 PPIs in Arabidopsis thaliana, 13,175,414 PPIs in corn, and 13,527,834 PPIs in soybean. Newly predicted PPIs were classified into three confidence levels according to the availability of existing supporting evidence and discussed. Predicted PPIs in the three plant genomes are made available for future reference.

RNA-Targeted Antiviral Immunity: More Than Just RNA Silencing

RNA silencing is a fundamental, evolutionarily conserved mechanism that regulates gene expression in eukaryotes. It also functions as a primary immune defense in microbes, such as viruses in plants. In addition to RNA silencing, RNA decay and RNA quality-control pathways are also two ancestral forms of intrinsic antiviral immunity, and the three RNA-targeted pathways may operate cooperatively for their antiviral function. Plant viruses encode viral suppressors of RNA silencing (VSRs) to suppress RNA silencing and facilitate virus infection. In response, plants may activate a counter-counter-defense mechanism to cope with VSR-mediated RNA silencing suppression. In this review, we summarize current knowledge of RNA silencing, RNA decay, and RNA quality control in antiviral defense, and highlight the mechanisms by which viruses compromise RNA-targeted immunity for their infection and survival in plants.

PP2C phosphatase Pic1 negatively regulates the phosphorylation status of Pti1b kinase, a regulator of flagellin-triggered immunity in tomato

Plant immune responses, including the production of reactive oxygen species (ROS), are triggered when pattern recognition receptors (PRRs) become activated upon detection of microbe-associated molecular patterns (MAMPs). Receptor-like cytoplasmic kinases are key components of PRR-dependent signaling pathways. In tomato, two such kinases, Pti1a and Pti1b, are important positive regulators of the plant immune response. However, it is unknown how these kinases control plant immunity at the molecular level and how their activity is regulated. To investigate these issues, we used mass spectrometry to search for interactors of Pti1b in Nicotiana benthamiana leaves and identified a PP2C protein phosphatase, referred to as Pic1. An in vitro pull-down assay and in vivo split-luciferase complementation assay verified this interaction. Pti1b was found to autophosphorylate on threonine-233, and this phosphorylation was abolished in the presence of Pic1. An arginine-to-cysteine substitution at position 240 in the Arabidopsis MARIS kinase was previously reported to convert it into a constitutive-active form. The analogous substitution in Pti1b made it resistant to Pic1 phosphatase activity, although it still interacted with Pic1. Treatment of N. benthamiana leaves with the MAMP flg22 induced threonine phosphorylation of Pti1b. The expression of Pic1, but not a phosphatase-inactive variant of this protein, in N. benthamiana leaves greatly reduced ROS production in response to treatment with MAMPs flg22 or csp22. The results indicate that Pic1 acts as a negative regulator by dephosphorylating the Pti1b kinase, thereby interfering with its ability to activate plant immune responses.

Transposable elements drive rapid phenotypic variation in Capsella rubella

The mechanisms underlying rapid adaptation to changing environments in species with reduced genetic variation, referred to as the “genetic paradox of invasion,” are unknown. We report that transposable elements (TEs) are highly enriched in the gene promoter regions of Capsella rubella compared with its outcrossing sister species Capsella grandiflora. We also show that a number of polymorphic TEs in C. rubella are associated with changes in gene expression. Frequent TE insertions at FLOWERING LOCUS C of C. rubella affect flowering-time variation, an important life history trait correlated with fitness. These results indicate that TE insertions drive rapid phenotypic variation, which could potentially help adapting to novel environments in species with limited genetic variation.

Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown. Capsella rubella, an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question. Its distribution is wider than those of its congeneric species, despite an extreme genetic bottleneck event that severely diminished its genetic variation. Here, we demonstrate that transposable elements (TEs) are an important source of genetic variation that could account for its high phenotypic diversity. TEs are (i) highly enriched in C. rubella compared with its outcrossing sister species Capsella grandiflora, and (ii) 4.2% of polymorphic TEs in C. rubella are associated with variation in the expression levels of their adjacent genes. Furthermore, we show that frequent TE insertions at FLOWERING LOCUS C (FLC) in natural populations of C. rubella could explain 12.5% of the natural variation in flowering time, a key life history trait correlated with fitness and adaptation. In particular, we show that a recent TE insertion at the 3′ UTR of FLC affects mRNA stability, which results in reducing its steady-state expression levels, to promote the onset of flowering. Our results highlight that TE insertions can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation.

Emerging Roles of LSM Complexes in Posttranscriptional Regulation of Plant Response to Abiotic Stress

It has long been assumed that the wide reprogramming of gene expression that modulates plant response to unfavorable environmental conditions is mainly controlled at the transcriptional level. A growing body of evidence, however, indicates that posttranscriptional regulatory mechanisms also play a relevant role in this control. Thus, the LSMs, a family of proteins involved in mRNA metabolism highly conserved in eukaryotes, have emerged as prominent regulators of plant tolerance to abiotic stress. Arabidopsis contains two main LSM ring-shaped heteroheptameric complexes, LSM1-7 and LSM2-8, with different subcellular localization and function. The LSM1-7 ring is part of the cytoplasmic decapping complex that regulates mRNA stability. On the other hand, the LSM2-8 complex accumulates in the nucleus to ensure appropriate levels of U6 snRNA and, therefore, correct pre-mRNA splicing. Recent studies reported unexpected results that led to a fundamental change in the assumed consideration that LSM complexes are mere components of the mRNA decapping and splicing cellular machineries. Indeed, these data have demonstrated that LSM1-7 and LSM2-8 rings operate in Arabidopsis by selecting specific RNA targets, depending on the environmental conditions. This specificity allows them to actively imposing particular gene expression patterns that fine-tune plant responses to abiotic stresses. In this review, we will summarize current and past knowledge on the role of LSM rings in modulating plant physiology, with special focus on their function in abiotic stress responses.

Beyond transcription factors: roles of mRNA decay in regulating gene expression in plants

Gene expression is typically quantified as RNA abundance, which is influenced by both synthesis (transcription) and decay. Cytoplasmic decay typically initiates by deadenylation, after which decay can occur through any of three cytoplasmic decay pathways. Recent advances reveal several mechanisms by which RNA decay is regulated to control RNA abundance. mRNA can be post-transcriptionally modified, either indirectly through secondary structure or through direct modifications to the transcript itself, sometimes resulting in subsequent changes in mRNA decay rates. mRNA abundances can also be modified by tapping into pathways normally used for RNA quality control. Regulated mRNA decay can also come about through post-translational modification of decapping complex subunits. Likewise, mRNAs can undergo changes in subcellular localization (for example, the deposition of specific mRNAs into processing bodies, or P-bodies, where stabilization and destabilization occur in a transcript- and context-dependent manner). Additionally, specialized functions of mRNA decay pathways were implicated in a genome-wide mRNA decay analysis in Arabidopsis. Advances made using plants are emphasized in this review, but relevant studies from other model systems that highlight RNA decay mechanisms that may also be conserved in plants are discussed.

Parallel Evolution of Common Allelic Variants Confers Flowering Diversity in Capsella rubella

Flowering time is an adaptive life history trait. Capsella rubella, a close relative of Arabidopsis thaliana and a young species, displays extensive variation for flowering time but low standing genetic variation due to an extreme bottleneck event, providing an excellent opportunity to understand how phenotypic diversity can occur with a limited initial gene pool. Here, we demonstrate that common allelic variation and parallel evolution at the FLC locus confer variation in flowering time in C. rubella. We show that two overlapping deletions in the 5' untranslated region (UTR) of C. rubella FLC, which are associated with local changes in chromatin conformation and histone modifications, reduce its expression levels and promote flowering. We further show that these two pervasive variants originated independently in natural C. rubella populations after speciation and spread to an intermediate frequency, suggesting a role of this parallel cis-regulatory change in adaptive evolution. Our results provide an example of how parallel mutations in the same 5' UTR region can shape phenotypic evolution in plants.

A Genetic Screen Identifies PRP18a, a Putative Second Step Splicing Factor Important for Alternative Splicing and a Normal Phenotype in Arabidopsis thaliana

Splicing of pre-mRNA involves two consecutive trans-esterification steps that take place in the spliceosome, a large dynamic ribonucleoprotein complex situated in the nucleus. In addition to core spliceosomal proteins, each catalytic step requires step-specific factors. Although the Arabidopsis thaliana genome encodes around 430 predicted splicing factors, functional information about these proteins is limited. In a forward genetic screen based on an alternatively-spliced GFP reporter gene in Arabidopsis thaliana, we identified a mutant impaired in putative step II factor PRP18a, which has not yet been investigated for its role in pre-mRNA splicing in plants. Step II entails cleavage at the 3' splice site accompanied by ligation of the 5' and 3' exons and intron removal. In the prp18 mutant, splicing of a U2-type intron with non-canonical AT-AC splice sites in GFP pre-mRNA is reduced while splicing of a canonical GT-AG intron is enhanced, resulting in decreased levels of translatable GFP mRNA and GFP protein. These findings suggest that wild-type PRP18a may in some cases promote splicing at weak, non-canonical splice sites. Analysis of genome-wide changes in alternative splicing in the prp18a mutant identified numerous cases of intron retention and a preponderance of altered 3' splice sites, suggesting an influence of PRP18a on 3' splice site selection. The prp18a mutant featured short roots on synthetic medium and small siliques, illustrating that wild-type PRP18a function is needed for a normal phenotype. Our study expands knowledge of plant splicing factors and provides foundational information and resources for further functional studies of PRP18 proteins in plants.

Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes

Arabidopsis thaliana contains two nuclear XRN2/3 5'-3' exonucleases that are homologs of yeast and human Rat1/Xrn2 proteins involved in the processing and degradation of several classes of nuclear RNAs and in transcription termination of RNA polymerase II. Using strand-specific short read sequencing we show that knockdown of XRN3 leads to an altered expression of hundreds of genes and the accumulation of uncapped and polyadenylated read-through transcripts generated by inefficiently terminated Pol II. Our data support the notion that XRN3-mediated changes in the expression of a subset of genes are caused by upstream read-through transcription and these effects are enhanced by RNA-mRNA chimeras generated in xrn3 plants. In turn, read-through transcripts that are antisense to downstream genes may trigger production of siRNA. Our results highlight the importance of XRN3 exoribonuclease in Pol II transcription termination in plants and show that disturbance in this process may significantly alter gene expression.

Arabidopsis mRNA decay landscape arises from specialized RNA decay substrates, decapping-mediated feedback, and redundancy

The decay of mRNA plays a vital role in modulating mRNA abundance, which, in turn, influences cellular and organismal processes. In plants and metazoans, three distinct pathways carry out the decay of most cytoplasmic mRNAs: The mRNA decapping complex, which requires the scaffold protein VARICOSE (VCS), removes a protective 5' cap, allowing for 5' to 3' decay via EXORIBONUCLEASE4 (XRN4, XRN1 in metazoans and yeast), and both the exosome and SUPPRESSOR OF VCS (SOV)/DIS3L2 degrade RNAs in the 3' to 5' direction. However, the unique biological contributions of these three pathways, and whether they degrade specialized sets of transcripts, are unknown. In Arabidopsis, the participation of SOV in RNA homeostasis is also unclear, because Arabidopsis sov mutants have a normal phenotype. We carried out mRNA decay analyses in wild-type, sov, vcs, and vcs sov seedlings, and used a mathematical modeling approach to determine decay rates and quantify gene-specific contributions of VCS and SOV to decay. This analysis revealed that VCS (decapping) contributes to decay of 68% of the transcriptome, and, while it initiates degradation of mRNAs with a wide range of decay rates, it especially contributes to decay of short-lived RNAs. Only a few RNAs were clear SOV substrates in that they decayed more slowly in sov mutants. However, 4,506 RNAs showed VCS-dependent feedback in sov that modulated decay rates, and, by inference, transcription, to maintain RNA abundances, suggesting that these RNAs might also be SOV substrates. This feedback was shown to be independent of siRNA activity.

mRNA Decapping and 5'-3' Decay Contribute to the Regulation of ABA Signaling in Arabidopsis thaliana

Defects in RNA processing and degradation pathways often lead to developmental abnormalities, impaired hormonal signaling and altered resistance to abiotic and biotic stress. Here we report that components of the 5'-3' mRNA decay pathway, DCP5, LSM1-7 and XRN4, contribute to a proper response to a key plant hormone abscisc acid (ABA), albeit in a different manner. Plants lacking DCP5 are more sensitive to ABA during germination, whereas lsm1a lsm1b and xrn4-5 mutants are affected at the early stages of vegetative growth. In addition, we show that DCP5 and LSM1 regulate mRNA stability and act in translational repression of the main components of the early ABA signaling, PYR/PYL ABA receptors and SnRK2s protein kinases. mRNA decapping DCP and LSM1-7 complexes also appear to modulate ABA-dependent expression of stress related transcription factors from the AP2/ERF/DREB family that in turn affect the level of genes regulated by the PYL/PYR/RCAR-PP2C-SnRK2 pathway. These observations suggest that ABA signaling through PYL/PYR/RCAR receptors and SnRK2s kinases is regulated directly and indirectly by the cytoplasmic mRNA decay pathway.

Polysomes, Stress Granules, and Processing Bodies: A Dynamic Triumvirate Controlling Cytoplasmic mRNA Fate and Function

Discoveries illuminate highly regulated dynamics of mRNA translation, sequestration, and degradation within the cytoplasm of plants.

Environment-dependent regulation of spliceosome activity by the LSM2-8 complex in Arabidopsis

Spliceosome activity is tightly regulated to ensure adequate splicing in response to internal and external cues. It has been suggested that core components of the spliceosome, such as the snRNPs, would participate in the control of its activity. The experimental indications supporting this proposition, however, remain scarce, and the operating mechanisms poorly understood. Here, we present genetic and molecular evidence demonstrating that the LSM2–8 complex, the protein moiety of the U6 snRNP, regulates the spliceosome activity in Arabidopsis, and that this regulation is controlled by the environmental conditions. Our results show that the complex ensures the efficiency and accuracy of constitutive and alternative splicing of selected pre-mRNAs, depending on the conditions. Moreover, miss-splicing of most targeted pre-mRNAs leads to the generation of nonsense mediated decay signatures, indicating that the LSM2–8 complex also guarantees adequate levels of the corresponding functional transcripts. Interestingly, the selective role of the complex has relevant physiological implications since it is required for adequate plant adaptation to abiotic stresses. These findings unveil an unanticipated function for the LSM2–8 complex that represents a new layer of posttranscriptional regulation in response to external stimuli in eukaryotes.

Transcriptome Analysis of the Effects of Shell Removal and Exogenous Gibberellin on Germination of Zanthoxylum Seeds

The zanthoxylum seeds are oil-rich and have a very thick, dense and oily shell. In the natural conditions the seeds have a very low germination rate. Prior to treatment with GAs to promote germination, the seeds were usually soaked in sulfuric acid to remove shells easily. A high-throughput sequencing of mRNAs was performed to investigate the effects of the above treatments on the germination of zanthoxylum seeds. Seven libraries were assembled into 100,982 unigenes and 59,509 unigenes were annotated. We focused on the expression profiles of the key genes related to the oil metabolisms and hormone regulations during seed germination. Our data indicated the endogenous ABA of seeds was rich. The effects that the exogenous GAs promoted germination were apparent in the secong day of germination. Especially, for the first time our results indicated the exogenous GAs lowered the aerobic metabolism including the oil metabolisms during imbibition. We inferred that the exogenous GAs had inhibitory effects on the oil metabolisms to avoide oxidative damages to the imbibed seeds, and the seed shell played the role similiar to the exogenous GAs in the initial stage of germination in the natural conditions.

Interconnections between mRNA degradation and RDR-dependent siRNA production in mRNA turnover in plants

Accumulation of an mRNA species is determined by the balance between the synthesis and the degradation of the mRNA. Individual mRNA molecules are selectively and actively degraded through RNA degradation pathways, which include 5'-3' mRNA degradation pathway, 3'-5' mRNA degradation pathway, and RNA-dependent RNA polymerase-mediated mRNA degradation pathway. Recent studies have revealed that these RNA degradation pathways compete with each other in mRNA turnover in plants and that plants have a hidden layer of non-coding small-interfering RNA production from a set of mRNAs. In this review, we summarize the current information about plant mRNA degradation pathways in mRNA turnover and discuss the potential roles of a novel class of the endogenous siRNAs derived from plant mRNAs.

mRNA decay in plants: both quantity and quality matter

In eukaryotes, degradation of messenger RNAs (mRNAs) is required for both mRNA quantity and quality control. Fine-tuning of the abundance of mRNAs that are to be translated can be achieved through a deadenylation-mediated RNA decay pathway involving progressive removal of poly(A) tails, decapping and exoribonuclease digestion. While the classical view assumes that mRNAs are degraded only after their exit from protein translation, recent studies have revealed mRNA decay can occur during translation in plants. Those mRNAs that have structural or functional defects can be filtered by translation-dependent RNA quality control pathways and rapidly degraded, so that translation fidelity is preserved. In addition, aberrant transcripts can also be efficiently eliminated through bidirectional RNA decay pathways. In the absence of those pathways, accumulation of those aberrant transcripts evokes the activation of RNA silencing, with detrimental consequences.

Plant RNA Regulatory Network and RNA Granules in Virus Infection

Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and their individual components contribute to these processes. In this review we discuss the roles of cellular RNA regulatory mechanisms and RNA granules in plant virus infection in the light of current knowledge and compare the findings to those made in animal virus studies.

Epigenetics and RNA Processing: Connections to Drought, Salt, and ABA?

There have been great research advances in epigenetics, RNA splicing, and mRNA processing over recent years. In parallel, there have been many advances in abiotic stress and Abscisic Acid (ABA) signaling. Here we overview studies that have examined stress-induced changes in the epigenome and RNA processing as well as cases where disrupting these processes changes the plant response to abiotic stress. We also highlight some examples where specific connections of stress or ABA signaling to epigenetics or RNA processing have been found. By implication, this also points out cases where such mechanistic connections are likely to exist but are yet to be characterized. In the absence of such specific connections to stress signaling, it should be kept in mind that stress sensitivity phenotypes of some epigenetic or RNA processing mutants maybe the result of indirect, pleiotropic effects and thus may perhaps not indicate a direct function in stress acclimation.

Control of seed dormancy in Arabidopsis by a cis-acting noncoding antisense transcript

Seed dormancy is one of the most crucial process transitions in a plant's life cycle. Its timing is tightly controlled by the expression level of the Delay of Germination 1 gene (DOG1). DOG1 is the major quantitative trait locus for seed dormancy in Arabidopsis and has been shown to control dormancy in many other plant species. This is reflected by the evolutionary conservation of the functional short alternatively polyadenylated form of the DOG1 mRNA. Notably, the 3' region of DOG1, including the last exon that is not included in this transcript isoform, shows a high level of conservation at the DNA level, but the encoded polypeptide is poorly conserved. Here, we demonstrate that this region of DOG1 contains a promoter for the transcription of a noncoding antisense RNA, asDOG1, that is 5' capped, polyadenylated, and relatively stable. This promoter is autonomous and asDOG1 has an expression profile that is different from known DOG1 transcripts. Using several approaches we show that asDOG1 strongly suppresses DOG1 expression during seed maturation in cis, but is unable to do so in trans Therefore, the negative regulation of seed dormancy by asDOG1 in cis results in allele-specific suppression of DOG1 expression and promotes germination. Given the evolutionary conservation of the asDOG1 promoter, we propose that this cis-constrained noncoding RNA-mediated mechanism limiting the duration of seed dormancy functions across the Brassicaceae.

Regulation of mRNA decay in plant responses to salt and osmotic stress

Plant acclimation to environmental stresses requires fast signaling to initiate changes in developmental and metabolic responses. Regulation of gene expression by transcription factors and protein kinases acting upstream are important elements of responses to salt and drought. Gene expression can be also controlled at the post-transcriptional level. Recent analyses on mutants in mRNA metabolism factors suggest their contribution to stress signaling. Here we highlight the components of mRNA decay pathways that contribute to responses to osmotic and salt stress. We hypothesize that phosphorylation state of proteins involved in mRNA decapping affect their substrate specificity.

The Nuclear Ribonucleoprotein SmD1 Interplays with Splicing, RNA Quality Control, and Posttranscriptional Gene Silencing in Arabidopsis

RNA quality control (RQC) eliminates aberrant RNAs based on their atypical structure, whereas posttranscriptional gene silencing (PTGS) eliminates both aberrant and functional RNAs through the sequence-specific action of short interfering RNAs (siRNAs). The Arabidopsis thaliana mutant smd1b was identified in a genetic screen for PTGS deficiency, revealing the involvement of SmD1, a component of the Smith (Sm) complex, in PTGS. The smd1a and smd1b single mutants are viable, but the smd1a smd1b double mutant is embryo-lethal, indicating that SmD1 function is essential. SmD1b resides in nucleoli and nucleoplasmic speckles, colocalizing with the splicing-related factor SR34. Consistent with this, the smd1b mutant exhibits intron retention at certain endogenous mRNAs. SmD1 binds to RNAs transcribed from silenced transgenes but not nonsilenced ones, indicating a direct role in PTGS. Yet, mutations in the RQC factors UPFRAMESHIFT3, EXORIBONUCLEASE2 (XRN2), XRN3, and XRN4 restore PTGS in smd1b, indicating that SmD1 is not essential for but rather facilitates PTGS. Moreover, the smd1b mtr4 double mutant is embryo-lethal, suggesting that SmD1 is essential for mRNA TRANSPORT REGULATOR4-dependent RQC. These results indicate that SmD1 interplays with splicing, RQC, and PTGS. We propose that SmD1 facilitates PTGS by protecting transgene-derived aberrant RNAs from degradation by RQC in the nucleus, allowing sufficient amounts to enter cytoplasmic siRNA bodies to activate PTGS.

Seed Dormancy in Arabidopsis Is Controlled by Alternative Polyadenylation of DOG1

DOG1 (Delay of Germination 1) is a key regulator of seed dormancy in Arabidopsis (Arabidopsis thaliana) and other plants. Interestingly, the C terminus of DOG1 is either absent or not conserved in many plant species. Here, we show that in Arabidopsis, DOG1 transcript is subject to alternative polyadenylation. In line with this, mutants in RNA 3' processing complex display weakened seed dormancy in parallel with defects in DOG1 proximal polyadenylation site selection, suggesting that the short DOG1 transcript is functional. This is corroborated by the finding that the proximally polyadenylated short DOG1 mRNA is translated in vivo and complements the dog1 mutant. In summary, our findings indicate that the short DOG1 protein isoform produced from the proximally polyadenylated DOG1 mRNA is a key player in the establishment of seed dormancy in Arabidopsis and characterizes a set of mutants in RNA 3' processing complex required for production of proximally polyadenylated functional DOG1 transcript.