Arabidopsis proline-rich protein important for development and abiotic stress tolerance is involved in microRNA biogenesis

Sequestration of DBR1 to stress granules promotes lariat intronic RNAs accumulation for heat-stress tolerance

Heat stress (HS) poses a significant challenge to plant survival, necessitating sophisticated molecular mechanisms to maintain cellular homeostasis. Here, we identify SICKLE (SIC) as a key modulator of HS responses in Arabidopsis (Arabidopsis thaliana). SIC is required for the sequestration of RNA DEBRANCHING ENZYME 1 (DBR1), a rate-limiting enzyme of lariat intronic RNA (lariRNA) decay, into stress granules (SGs). The sequestration of DBR1 by SIC enhances the accumulation of lariRNAs, branched circular RNAs derived from excised introns during pre-mRNA splicing, which in turn promote the transcription of their parental genes. Our findings further demonstrate that SIC-mediated DBR1 sequestration in SGs is crucial for plant HS tolerance, as deletion of the N-terminus of SIC (SIC1-244) impairs DBR1 sequestration and compromises plant response to HS. Overall, our study unveils a mechanism of transcriptional regulation in the HS response, where lariRNAs are enriched through DBR1 sequestration, ultimately promoting the transcription of heat stress tolerance genes.

Biomolecular condensates in plant RNA silencing: insights into formation, function, and stress responses

Biomolecular condensates are dynamic structures formed through diverse mechanisms, including liquid-liquid phase separation. These condensates have emerged as crucial regulators of cellular processes in eukaryotic cells, enabling the compartmentalization of specific biological reactions while allowing for dynamic exchange of molecules with the surrounding environment. RNA silencing, a conserved gene regulatory mechanism mediated by small RNAs (sRNAs), plays pivotal roles in various biological processes. Multiple types of biomolecular condensate, including dicing bodies, processing bodies, small interfering RNA bodies, and Cajal bodies, have been identified as key players in RNA silencing pathways. These biomolecular condensates provide spatial compartmentation for the biogenesis, loading, action, and turnover of small RNAs. Moreover, they actively respond to stresses, such as viral infections, and modulate RNA silencing activities during stress responses. This review summarizes recent advances in understanding of dicing bodies and other biomolecular condensates involved in RNA silencing. We explore their formation, roles in RNA silencing, and contributions to antiviral resistance responses. This comprehensive overview provides insights into the functional significance of biomolecular condensates in RNA silencing and expands our understanding of their roles in gene expression and stress responses in plants.

JANUS, a spliceosome-associated protein, promotes miRNA biogenesis in Arabidopsis

MicroRNAs (miRNAs) are important regulators of genes expression. Their levels are precisely controlled through modulating the activity of the microprocesser complex (MC). Here, we report that JANUS, a homology of the conserved U2 snRNP assembly factor in yeast and human, is required for miRNA accumulation. JANUS associates with MC components Dicer-like 1 (DCL1) and SERRATE (SE) and directly binds the stem-loop of pri-miRNAs. In a hypomorphic janus mutant, the activity of DCL1, the numbers of MC, and the interaction of primary miRNA transcript (pri-miRNAs) with MC are reduced. These data suggest that JANUS promotes the assembly and activity of MC through its interaction with MC and/or pri-miRNAs. In addition, JANUS modulates the transcription of some pri-miRNAs as it binds the promoter of pri-miRNAs and facilitates Pol II occupancy of at their promoters. Moreover, global splicing defects are detected in janus. Taken together, our study reveals a novel role of a conserved splicing factor in miRNA biogenesis.

Meta-QTL and ortho analysis unravels the genetic architecture and key candidate genes for cold tolerance at seedling stage in rice

Rice, a critical cereal crop, grapples with productivity challenges due to its inherent sensitivity to low temperatures, primarily during the seedling and booting stages. Recognizing the polygenic complexity of cold stress signaling in rice, a meta-analysis was undertaken, focusing on 20 physiological traits integral to cold tolerance. This initiative allowed the consolidation of genetic data from 242 QTLs into 58 meta-QTLs, thereby significantly constricting the genetic and physical intervals, with 84% of meta-QTLs (MQTLs) being reduced to less than 2 Mb. The list of 10,505 genes within these MQTLs, was further refined utilizing expression datasets to pinpoint 46 pivotal genes exhibiting noteworthy differential regulation during cold stress. The study underscored the presence of several TFs such as WRKY, NAC, CBF/DREB, MYB, and bHLH, known for their roles in cold stress response. Further, ortho-analysis involving maize, barley, and Arabidopsis identified OsWRKY71, among others, as a prospective candidate for enhancing cold tolerance in diverse crop plants. In conclusion, our study delineates the intricate genetic architecture underpinning cold tolerance in rice and propounds significant candidate genes, offering crucial insights for further research and breeding strategies focused on fortifying crops against cold stress, thereby bolstering global food resilience.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01412-1.

The DEAD-box helicase RCF1 plays roles in miRNA biogenesis and RNA splicing in Arabidopsis

RCF1 is a highly conserved DEAD-box RNA helicase found in yeast, plants, and mammals. Studies about the functions of RCF1 in plants are limited. Here, we uncovered the functions of RCF1 in Arabidopsis thaliana as a player in pri-miRNA processing and splicing, as well as in pre-mRNA splicing. A mutant with miRNA biogenesis defects was isolated, and the defect was traced to a recessive point mutation in RCF1 (rcf1-4). We show that RCF1 promotes D-body formation and facilitates the interaction between pri-miRNAs and HYL1. Finally, we show that intron-containing pri-miRNAs and pre-mRNAs exhibit a global splicing defect in rcf1-4. Together, this work uncovers roles for RCF1 in miRNA biogenesis and RNA splicing in Arabidopsis.

PEP444c encoded within the MIR444c gene regulates microRNA444c accumulation in barley

MicroRNAs are small, noncoding RNA molecules that regulate the expression of their target genes. The MIR444 gene family is present exclusively in monocotyledons, and microRNAs444 from this family have been shown to target certain MADS-box transcription factors in rice and barley. We identified three barley MIR444 (MIR444a/b/c) genes and comprehensively characterised their structure and the processing pattern of the primary transcripts (pri-miRNAs444). Pri-microRNAs444 undergo extensive alternative splicing, generating functional and nonfunctional pri-miRNA444 isoforms. We show that barley pri-miRNAs444 contain numerous open reading frames (ORFs) whose transcripts associate with ribosomes. Using specific antibodies, we provide evidence that selected ORFs encoding PEP444a within MIR444a and PEP444c within MIR444c are expressed in barley plants. Moreover, we demonstrate that CRISPR-associated endonuclease 9 (Cas9)-mediated mutagenesis of the PEP444c-encoding sequence results in a decreased level of PEP444 transcript in barley shoots and roots and a 5-fold reduced level of mature microRNA444c in roots. Our observations suggest that PEP444c encoded by the MIR444c gene is involved in microRNA444c biogenesis in barley.

microRNA biogenesis and stabilization in plants

MicroRNAs (miRNAs) are short endogenous non-coding RNAs that regulate gene expression at the post-transcriptional level in a broad range of eukaryotic species. In animals, it is estimated that more than 60% of mammalian genes are targets of miRNAs, with miRNAs regulating cellular processes such as differentiation and proliferation. In plants, miRNAs regulate gene expression and play essential roles in diverse biological processes, including growth, development, and stress responses. Arabidopsis mutants with defective miRNA biogenesis are embryo lethal, and abnormal expression of miRNAs can cause severe developmental phenotypes. It is therefore crucial that the homeostasis of miRNAs is tightly regulated. In this review, we summarize the key mechanisms of plant miRNA biogenesis and stabilization. We provide an update on nuclear proteins with functions in miRNA biogenesis and proteins linking miRNA biogenesis to environmental triggers.

Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants

Drought stress is one of the most serious threats to sustainable agriculture and is predicted to be further intensified in the coming decades. Therefore, understanding the mechanism of drought stress tolerance and the development of drought-resilient crops are the major goals at present. In recent years, noncoding microRNAs (miRNAs) have emerged as key regulators of gene expressions under drought stress conditions and are turning out to be the potential candidates that can be targeted to develop drought-resilient crops in the future. miRNAs are known to target and decrease the expression of various genes to govern the drought stress response in plants. In addition, emerging evidence also suggests a regulatory role of long non-coding RNAs (lncRNAs) in the regulation of miRNAs and the expression of their target genes by a process referred as miRNA sponging. In this review, we present the regulatory roles of miRNAs in the modulation of drought-responsive genes along with discussing their biosynthesis and action mechanisms. Additionally, the interactive roles of miRNAs with phytohormone signaling components have also been highlighted to present the global view of miRNA functioning under drought-stress conditions.

Understanding the evolution of miRNA biogenesis machinery in plants with special focus on rice

miRNA biogenesis process is an intricate and complex event consisting of many proteins working in a highly coordinated fashion. Most of these proteins have been studied in Arabidopsis; however, their orthologs and functions have not been explored in other plant species. In the present study, we have manually curated all the experimentally verified information present in the literature regarding these proteins and found a total of 98 genes involved in miRNA biogenesis in Arabidopsis. The conservation pattern of these proteins was identified in other plant species ranging from dicots to lower organisms, and we found that a major proportion of proteins involved in the pri-miRNA processing are conserved. However, nearly 20% of the genes, mostly involved in either transcription or functioning of the miRNAs, were absent in the lower organisms. Further, we manually curated a regulatory network of the core components of the biogenesis process and found that nearly half (46%) of the proteins interact with them, indicating that the processing step is perhaps the most under surveillance/regulation. We have subsequently attempted to characterize the orthologs identified in Oryza sativa, on the basis of transcriptome and epigenetic modifications under field drought conditions in order to assess the impact of drought on the process. We found several participating genes to be differentially expressed and/or epigenetically methylated under drought, although the core components like DCL1, SE, and HYL1 remain unaffected by the stress itself. The study enhances our present understanding of the biogenesis process and its regulation.

Variations in Circadian Clock Organization & Function: A Journey from Ancient to Recent

Circadian clock components exhibit structural variations in different plant systems, and functional variations during various abiotic stresses. These variations bear relevance for plant fitness and could be important evolutionarily. All organisms on earth have the innate ability to measure time as diurnal rhythms that occur due to the earth's rotations in a 24-h cycle. Circadian oscillations arising from the circadian clock abide by its fundamental properties of periodicity, entrainment, temperature compensation, and oscillator mechanism, which is central to its function. Despite the fact that a myriad of research in Arabidopsis thaliana illuminated many detailed aspects of the circadian clock, many more variations in clock components' organizations and functions remain to get deciphered. These variations are crucial for sustainability and adaptation in different plant systems in the varied environmental conditions in which they grow. Together with these variations, circadian clock functions differ drastically even during various abiotic and biotic stress conditions. The present review discusses variations in the organization of clock components and their role in different plant systems and abiotic stresses. We briefly introduce the clock components, entrainment, and rhythmicity, followed by the variants of the circadian clock in different plant types, starting from lower non-flowering plants, marine plants, dicots to the monocot crop plants. Furthermore, we discuss the interaction of the circadian clock with components of various abiotic stress pathways, such as temperature, light, water stress, salinity, and nutrient deficiency with implications for the reprogramming during these stresses. We also update on recent advances in clock regulations due to post-transcriptional, post-translation, non-coding, and micro-RNAs. Finally, we end this review by summarizing the points of applicability, a remark on the future perspectives, and the experiments that could clear major enigmas in this area of research.

Identification and analysis of proline-rich proteins and hybrid proline-rich proteins super family genes from Sorghum bicolor and their expression patterns to abiotic stress and zinc stimuli

Systematic genome-wide analysis of Sorghum bicolor revealed the identification of a total of 48 homologous genes comprising 21 proline-rich proteins (PRPs) and 27 hybrid proline-rich proteins (HyPRPs). Comprehensive scrutiny of these gene homologs was conducted for gene structure, phylogenetic investigations, chromosome mapping, and subcellular localization of proteins. Promoter analysis uncovered the regions rich with phosphorous- (BIHD), ammonium-, sulfur-responsive (SURE), and iron starvation-responsive (IRO2) along with biotic, abiotic, and development-specific cis-elements. Further, PRPs exhibit more methylation and acetylation sites in comparison with HyPRPs. miRNAs have been predicted which might play a role in cleavage and translation inhibition. Several of the SbPRP genes were stimulated in a tissue-specific manner under drought, salt, heat, and cold stresses. Additionally, exposure of plants to abscisic acid (ABA) and zinc (Zn) also triggered PRP genes in a tissue-dependent way. Among them, SbPRP17 has been found upregulated markedly in all tissues irrespective of the stress imposed. The expressions of SbHyPRPs, especially SbHyPRP2, SbHyPRP6, and SbHyPRP17 were activated under all stresses in all three tissues. On the other hand, SbHyPRP8 (root only) and SbHyPRP12 (all three tissues) were highly responsive to cold stress and ABA while SbHyPRP26 was induced by drought and Zn in the stem. Taken together, this study indicates the critical roles that SbPRPs and SbHyPRPs play during diverse abiotic stress conditions and notably the plausible roles that these genes play upon exposure to zinc, the crucial micronutrient in plants.

SICKLE represses photomorphogenic development of Arabidopsis seedlings via HY5- and PIF4-mediated signaling

Arabidopsis CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and PHYTOCHROME INTERACTING FACTORs (PIFs) are negative regulators, and ELONGATED HYPOCOTYL5 (HY5) is a positive regulator of seedling photomorphogenic development. Here, we report that SICKLE (SIC), a proline rich protein, acts as a novel negative regulator of photomorphogenesis. HY5 directly binds the SIC promoter and activates SIC expression in response to light. In turn, SIC physically interacts with HY5 and interferes with its transcriptional regulation of downstream target genes. Moreover, SIC interacts with PIF4 and promotes PIF4-activated transcription of itself. Interestingly, SIC is targeted by COP1 for 26S proteasome-mediated degradation in the dark. Collectively, our data demonstrate that light-induced SIC functions as a brake to prevent exaggerated light response via mediating HY5 and PIF4 signaling, and its degradation by COP1 in the dark avoid too strong inhibition on photomorphogenesis at the beginning of light exposure.

SICKLE modulates lateral root development by promoting degradation of lariat intronic RNA

Plant lateral roots (LRs) play vital roles in anchorage and uptake of water and nutrients. Here, we reveal that degradation of lariat intronic RNAs (lariRNAs) modulated by SICKLE (SIC) is required for LR development in Arabidopsis (Arabidopsis thaliana). Loss of SIC results in hyper-accumulation of lariRNAs and restricts the outgrowth of LR primordia, thereby reducing the number of emerged LRs. Decreasing accumulation of lariRNAs by over-expressing RNA debranching enzyme 1 (DBR1), a rate-limiting enzyme of lariRNA decay, restored LR defects in SIC-deficient plants. Mechanistically, SIC interacts with DBR1 and facilitates its nuclear accumulation, which is achieved through two functionally redundant regions (SIC1-244 and SIC252-319) for nuclear localization. Of the remaining amino acids in this region, six (SIC245-251) comprise a DBR1-interacting region while two (SICM246 and SICW251) are essential for DBR1-SIC interaction. Reducing lariRNAs restored microRNA (miRNA) levels and LR development in lariRNA hyper-accumulating plants, suggesting that these well-known regulators of LR development mainly function downstream of lariRNAs. Taken together, we propose that SIC acts as an enhancer of DBR1 nuclear accumulation by driving nuclear localization through direct interaction, thereby promoting lariRNA decay to fine-tune miRNA biogenesis and modulating LR development.

Dynamic modeling of ABA-dependent expression of the Arabidopsis RD29A gene

The abscisic acid (ABA) signaling pathway is the key defense mechanism against drought stress in plants. In the pathway, signal transduction among four core proteins, pyrabactin resistance (PYR), protein phosphatase 2C (PP2C), sucrose-non-fermenting-1-related protein kinase 2 (SnRK2), and ABRE binding factor (ABF) leads to altered gene expression kinetics that is driven by an ABA-responsive element (ABRE). A most recent and comprehensive study provided data suggesting that ABA alters the expression kinetics in over 6,500 genes through the ABF-ABRE associations in Arabidopsis. Of these genes, termed ABA gene regulatory network (GRN), over 50% contain a single ABRE within 4 kb of the gene body, despite previous findings suggesting that a single copy of ABRE is not sufficient to drive the gene expression. To understand the expression system of the ABA GRN by the single ABRE, a dynamic model of the gene expression for the desiccation 29A (RD29A) gene was constructed with ordinary differential equations. Parameter values of molecular-molecular interactions and enzymatic reactions in the model were implemented from the data obtained by previously conducted in vitro experiments. On the other hand, parameter values of gene expression and translation were determined by comparing the kinetics of gene expression in the model to the expression kinetics of RD29A in real plants. The optimized model recapitulated the trend of gene expression kinetics of RD29A in ABA dose-response that were previously investigated. Further analysis of the model suggested that a single ABRE controls the time scale and dynamic range of the ABA-dependent gene expression through the PP2C feedback regulation even though an additional cis-element is required to drive the expression. The model construed in this study underpins the importance of a single ABRE in the ABA GRN.

Cold adaptation strategies in plants—An emerging role of epigenetics and antifreeze proteins to engineer cold resilient plants

Cold stress adversely affects plant growth, development, and yield. Also, the spatial and geographical distribution of plant species is influenced by low temperatures. Cold stress includes chilling and/or freezing temperatures, which trigger entirely different plant responses. Freezing tolerance is acquired via the cold acclimation process, which involves prior exposure to non-lethal low temperatures followed by profound alterations in cell membrane rigidity, transcriptome, compatible solutes, pigments and cold-responsive proteins such as antifreeze proteins. Moreover, epigenetic mechanisms such as DNA methylation, histone modifications, chromatin dynamics and small non-coding RNAs play a crucial role in cold stress adaptation. Here, we provide a recent update on cold-induced signaling and regulatory mechanisms. Emphasis is given to the role of epigenetic mechanisms and antifreeze proteins in imparting cold stress tolerance in plants. Lastly, we discuss genetic manipulation strategies to improve cold tolerance and develop cold-resistant plants.

Du13 encodes a C2 H2 zinc-finger protein that regulates Wxb pre-mRNA splicing and microRNA biogenesis in rice endosperm

Amylose content is a crucial physicochemical property responsible for the eating and cooking quality of rice (Oryza sativa L.) grain and is mainly controlled by the Waxy (Wx) gene. Previous studies have identified several Dull genes that modulate the expression of the Wx^b allele in japonica rice by affecting the splicing efficiency of the Wx^b pre-mRNA. Here, we uncover dual roles for a novel Dull gene in pre-mRNA splicing and microRNA processing. We isolated the dull mutant, du13, with a dull endosperm and low amylose content. Map-based cloning showed that Du13 encodes a C₂ H₂ zinc-finger protein. Du13 coordinates with the nuclear cap-binding complex to regulate the splicing of Wx^b transcripts in rice endosperm. Moreover, Du13 also regulates alternative splicing of other protein-coding transcripts and affects the biogenesis of a subset of microRNAs. Our results reveal an evolutionarily conserved link between pre-mRNA splicing and microRNA biogenesis in rice endosperm. Our findings also provide new insights into the functions of Dull genes in rice and expand our knowledge of microRNA biogenesis in monocots.

Impact of the sickle mutant and temperature on the structure of transcripts and RNAs from Arabidopsis thaliana

Objectives

The objective of this data set was to identify how interaction between temperature and the sickle-3 (sic-3) mutant alters the global messenger RNA (mRNA) content of Arabidopsis thaliana seedlings. The motivation was discovery of atypical mRNA splice variants in sic-3 that differed with seedling growth temperature. The expected outcome was identification of mRNA splice variants altered by sic-3, temperature, or the combination of temperature and genotype.

Data description

The data set is RNAseq profiling of Arabidopsis (Col-0 ecotype) wild type and sic-3 seedlings under 16 °C or 28 °C. A comprehensive view of global mRNA sequences and their content was captured by deep sequencing of RNA pools made from sets of seedlings sampled every 4 h over 20 h. This data set contains sequences representing the spectrum of mRNA splice variants from individual genes, as well as from mRNA-related sequences like spliced introns. This data set enables detection of significant changes in gene-level expression and relative levels of mRNA splice variants caused by the different growth temperatures, the sic-3 mutation or both factors. This data set is useful to study production of mRNA splice variants and other mRNA-related RNAs in a range of plant species because Arabidopsis is a model plant.

Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading

MicroRNAs (miRNAs) play crucial roles in gene expression regulation through RNA cleavage or translation repression. Here, we report the identification of an evolutionarily conserved WD40 domain protein as a player in miRNA biogenesis in Arabidopsis thaliana. A mutation in the REDUCTION IN BLEACHED VEIN AREA (RBV) gene encoding a WD40 domain protein led to the suppression of leaf bleaching caused by an artificial miRNA; the mutation also led to a global reduction in the accumulation of endogenous miRNAs. The nuclear protein RBV promotes the transcription of MIR genes into pri-miRNAs by enhancing the occupancy of RNA polymerase II (Pol II) at MIR gene promoters. RBV also promotes the loading of miRNAs into AGO1. In addition, RNA-seq revealed a global splicing defect in the mutant. Thus, this evolutionarily conserved, nuclear WD40 domain protein acts in miRNA biogenesis and RNA splicing.

MicroRNAs regulate gene expression through RNA cleavage or translation repression. Here the authors show that RBV, an evolutionarily conserved WD40 domain protein, acts to promote MIR transcription, pri-miRNA processing and miRNA loading into AGO1.

Small RNAs Participate in Plant-Virus Interaction and Their Application in Plant Viral Defense

Small RNAs are significant regulators of gene expression, which play multiple roles in plant development, growth, reproductive and stress response. It is generally believed that the regulation of plants’ endogenous genes by small RNAs has evolved from a cellular defense mechanism for RNA viruses and transposons. Most small RNAs have well-established roles in the defense response, such as viral response. During viral infection, plant endogenous small RNAs can direct virus resistance by regulating the gene expression in the host defense pathway, while the small RNAs derived from viruses are the core of the conserved and effective RNAi resistance mechanism. As a counter strategy, viruses evolve suppressors of the RNAi pathway to disrupt host plant silencing against viruses. Currently, several studies have been published elucidating the mechanisms by which small RNAs regulate viral defense in different crops. This paper reviews the distinct pathways of small RNAs biogenesis and the molecular mechanisms of small RNAs mediating antiviral immunity in plants, as well as summarizes the coping strategies used by viruses to override this immune response. Finally, we discuss the current development state of the new applications in virus defense based on small RNA silencing.

Regulation of pri-MIRNA processing: mechanistic insights into the miRNA homeostasis in plant

miRNAs in plant plays crucial role in controlling proper growth, development and fitness by modulating the expression of their target genes. Therefore to modulate the expression of any stress/development related gene specifically, it is better to modulate expression of the miRNA that can target that gene. To modulate the expression level of miRNA, it is prerequisite to uncover the underlying molecular mechanism of its biogenesis. The biogenesis pathway consists of two major steps, transcription of MIR gene to pri-MIRNA and processing of pri-MIRNA into mature miRNA via sequential cleavage steps. Both of these pathways are tightly controlled by several different factors involving structural and functional molecules. This review is mainly focused on different aspects of pri-MIRNA processing mechanism to emphasize on the fact that to modulate the level of a miRNA in the cell only over-expression or knock-down of that MIR gene is not always sufficient rather it is also crucial to take processing regulation into consideration. The data collected from the recent and relevant literatures depicts that processing regulation is controlled by several aspects like structure and size of the pri-MIRNA, presence of introns in MIR gene and their location, interaction of processing factors with the core components of processing machinery etc. These detailed information can be utilized to figure out the particular point which can be utilized to modulate the expression of the miRNA which would ultimately be beneficial for the scientist and researcher working in this field to generate protocol for engineering plant with improved yield and stress tolerance.

Identification of putative key genes for thermal adaptation in the Japanese mantis shrimp (Oratosquilla oratoria) through population genomic analysis

Little is known about the mechanisms underlying the relationship between genetic variation and the adaptation of Oratosquilla oratoria populations to different habitat temperature. Here, the genome-wide genetic information of three O. oratoria populations were obtained by IIB restriction site-associated DNA (2b-RAD) sequencing and 2403 single-nucleotide polymorphisms (SNPs) were identified. Based on the 2403 SNPs, we found a remarkable genetic differentiation between the Yellow Sea and the East China Sea groups of O. oratoria. Furthermore, 63 SNPs are thought to be associated with different sea temperatures. Based on the 63 SNPs, it is hypothesised that the long-term temperature differences may contribute to the variation of genes associated with multiple biological functions, such as material metabolism, cytoskeleton, cellular processes, inflammatory response and hormonal regulation. This study provides new information for elucidating the molecular mechanisms underlying the relationship between genetic variation and the adaptation of Oratosquilla oratoria populations to different temperature.

Recent advances in the regulation of plant miRNA biogenesis

MicroRNAs (miRNAs) are essential non-coding riboregulators of gene expression in plants and animals. In plants, miRNAs guide their effector protein named ARGONAUTE (AGO) to find target RNAs for gene silencing through target RNA cleavage or translational inhibition. miRNAs are derived from primary miRNA transcripts (pri-miRNAs), most of which are transcribed by the DNA-dependent RNA polymerase II. In plants, an RNase III enzyme DICER-LIKE1-containing complex processes pri-miRNAs in the nucleus into miRNAs. To ensure proper function of miRNAs, plants use multiple mechanisms to control miRNA accumulation. On one hand, pri-miRNA levels are controlled through transcription and stability. On the other hand, the activities of the DCL1 complex are regulated by many protein factors at transcriptional, post-transcriptional and post-translational levels. Notably, recent studies reveal that pri-miRNA structure/sequence features and modifications also play important roles in miRNA biogenesis. In this review, we summarize recent progresses on the mechanisms regulating miRNA biogenesis.

OsTMF attenuates cold tolerance by affecting cell wall properties in rice

Plant cell wall composition and structure can be modified as plants adapt to environmental stresses; however, the underlying regulatory mechanisms remain elusive. Here, we report that OsTMF, a homologue of the human TATA modulatory factor (TMF) in rice (Oryza sativa) and highly conserved in plants, negatively regulates cold tolerance through modification of cell wall properties. Cold stress increased the expression of OsTMF and accumulation of OsTMF in the nucleus, where OsTMF acts as a transcription activator and modulates the expression of genes involved in pectin degradation (OsBURP16), cellulose biosynthesis (OsCesA4 and OsCesA9), and cell wall structural maintenance (genes encoding proline-rich proteins and peroxidases). OsTMF directly activated the expression of OsBURP16, OsCesA4, and OsCesA9 through binding to the TATA cis-elements in their promoters. Under cold stress conditions, OsTMF negatively regulated pectin content and peroxidase activity and positively regulated cellulose content, causing corresponding alterations to cell wall properties, all of which collectively contribute to the negative effect of OsTMF on cold tolerance. Our findings unravel a previously unreported molecular mechanism of a conserved plant TMF protein in the regulation of cell wall changes under cold stress.

Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour

miRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan. We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8, dlo-miR397a and DlLAC7, dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan.

Spliceosome disassembly factors ILP1 and NTR1 promote miRNA biogenesis in Arabidopsis thaliana

The intron-lariat spliceosome (ILS) complex is highly conserved among eukaryotes, and its disassembly marks the end of a canonical splicing cycle. In this study, we show that two conserved disassembly factors of the ILS complex, Increased Level of Polyploidy1-1D (ILP1) and NTC-Related protein 1 (NTR1), positively regulate microRNA (miRNA) biogenesis by facilitating transcriptional elongation of MIRNA (MIR) genes in Arabidopsis thaliana. ILP1 and NTR1 formed a stable complex and co-regulated alternative splicing of more than a hundred genes across the Arabidopsis genome, including some primary transcripts of miRNAs (pri-miRNAs). Intriguingly, pri-miRNAs, regardless of having introns or not, were globally down-regulated when the ILP1 or NTR1 function was compromised. ILP1 and NTR1 interacted with core miRNA processing proteins Dicer-like 1 and Serrate, and were required for proper RNA polymerase II occupancy at elongated regions of MIR chromatin, without affecting either MIR promoter activity or pri-miRNA decay. Our results provide further insights into the regulatory role of spliceosomal machineries in the biogenesis of miRNAs.

Abscisic Acid Receptors Modulate Metabolite Levels and Phenotype in Arabidopsis Under Normal Growing Conditions

Abscisic acid (ABA) is a vital phytohormone that accumulates in response to various biotic and abiotic stresses, as well as plant growth. In Arabidopsis thaliana, there are 14 members of the ABA receptor family, which are key positive regulators involved in ABA signaling. Besides reduced drought stress tolerance, the quadruple and sextuple mutants (pyr1pyl1pyl2pyl4 (1124) and pyr1pyl1pyl2pyl4pyl5pyl8 (112458) show abnormal growth phenotypes, such as decreases in yield and height, under non-stress conditions. However, it remains unknown whether ABA receptors mediate ABA signaling to regulate plant growth and development. Here, we showed the primary metabolite profiles of 1124, 112458 and wild-type (WT) plants grown under normal conditions. The metabolic changes were significantly different between ABA receptor mutants and WT. Guanosine, for the biosynthesis of cyclic guanosine 3′,5′-monophosphate (cGMP), is an important second messenger that acts to regulate the level of ABA. In addition, other amino acids were increased in the 112458 mutant, including proline. These results, together with phenotype analysis, indicated that ABA receptors are involved in ABA signaling to modulate metabolism and plant growth under normal conditions.

Chilli leaf curl virus infection downregulates the expression of the genes encoding chloroplast proteins and stress-related proteins

Virus infection alters the expression of several host genes involved in various cellular and biological processes in plants. Most of the studies performed till now have mainly focused on genes which are up-regulated and later projected them as probable stress tolerant/susceptible genes. Nevertheless, genes which are down-regulated during plant-virus interaction could also play a critical role on disease development as well as in combating the virus infection. Hence, to identify such down-regulated genes and pathway, we performed reverse suppression subtractive hybridization in Capsicum annuum var. Punjab Lal following Chilli leaf curl virus (ChiLCV) infection. The screening and further processing suggested that majority of the genes (approximately 35% ESTs) showed homology with the genes encoding chloroplast proteins and 16% genes involved in the biotic and abiotic stress response. Additionally, we identified several genes, functionally known to be involved in metabolic processes, protein synthesis and degradation, ribosomal proteins, energy production, DNA replication and transcription, and transporters. We also found 3% transcripts which did not show homology with any known genes. The redundancy analysis revealed the maximum percentage of chlorophyll a-b binding protein (15/96) and auxin-binding proteins (13/96). We developed a protein interactome network to characterise the relationships between proteins and pathway involved during the ChiLCV infection. We identified that the most of the interaction occurs either among the chloroplast proteins (Arabidopsis proteins interactive map) or biotic and abiotic stress responsive proteins (Solanum lycopersicum interactome). Taken together, our study provides the first transcriptome and protein interactome of the down-regulated genes during C. annuum-ChiLCV interaction. These resources could be exploited in deciphering the steps involved in the process of virus infection.

In-Cold Exposure to Z-3-Hexenal Provides Protection Against Ongoing Cold Stress in Zea mays

Green leaf volatiles (GLVs), which have mostly been described as providers of protection against insect herbivory and necrotrophic pathogen infections, were recently shown to provide significant fortification against cold stress damage. It was further demonstrated that cold-damaged maize seedlings released a significant amount of GLVs, in particular, Z-3-hexenal (Z-3-HAL). Here, we report that the in-cold treatment of maize seedlings with Z-3-HAL significantly improved cold stress resistance. The transcripts for cold-protective genes were also significantly increased in the Z-3-HAL treated maize seedlings over those found in only cold stressed plants. Consequently, the maize seedlings treated with HAL during cold showed a significantly increased structural integrity, significantly less damage, and increased growth after cold stress, relative to the non-HAL treated maize seedlings. Together, these results demonstrate the protective effect of in-cold treatment with HAL against cold damage, and suggest that the perception of these compounds during cold episodes significantly improves resistance against this abiotic stress.

Advances and challenges in uncovering cold tolerance regulatory mechanisms in plants

Contents Summary I. Introduction II. Cold stress and physiological responses in plants III. Sensing of cold signals in plants IV. Messenger molecules involved in cold signal transduction V. Cold signal transduction in plants VI. Conclusions and perspectives Acknowledgements References SUMMARY: Cold stress is a major environmental factor that seriously affects plant growth and development, and influences crop productivity. Plants have evolved a series of mechanisms that allow them to adapt to cold stress at both the physiological and molecular levels. Over the past two decades, much progress has been made in identifying crucial components involved in cold-stress tolerance and dissecting their regulatory mechanisms. In this review, we summarize recent major advances in our understanding of cold signalling and put forward open questions in the field of plant cold-stress responses. Answering these questions should help elucidate the molecular mechanisms underlying plant tolerance to cold stress.

MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions

MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced silencing complex (miRISC). By targeting complementary sequences, miRISC negatively regulates gene expression, thereby coordinating plant development and plant-environment interactions. In this review, we present and discuss recent updates on the mechanisms and regulation of miRNA biogenesis, miRISC assembly and actions as well as the regulatory roles of miRNAs in plant developmental plasticity, abiotic/biotic responses, and symbiotic/parasitic interactions. Finally, we suggest future directions for plant miRNA research.

Chromatin-based mechanisms of temperature memory in plants

For successful growth and development, plants constantly have to gauge their environment. Plants are capable to monitor their current environmental conditions, and they are also able to integrate environmental conditions over time and store the information induced by the cues. In a developmental context, such an environmental memory is used to align developmental transitions with favourable environmental conditions. One temperature-related example of this is the transition to flowering after experiencing winter conditions, that is, vernalization. In the context of adaptation to stress, such an environmental memory is used to improve stress adaptation even when the stress cues are intermittent. A somatic stress memory has now been described for various stresses, including extreme temperatures, drought, and pathogen infection. At the molecular level, such a memory of the environment is often mediated by epigenetic and chromatin modifications. Histone modifications in particular play an important role. In this review, we will discuss and compare different types of temperature memory and the histone modifications, as well as the reader, writer, and eraser proteins involved.

The PROTEIN PHOSPHATASE4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis

PROTEIN PHOSPHATASE4 (PP4) is a highly conserved Ser/Thr protein phosphatase found in yeast, plants, and animals. The composition and functions of PP4 in plants are poorly understood. Here, we uncovered the complexity of PP4 composition and function in Arabidopsis (Arabidopsis thaliana) and identified the composition of one form of PP4 containing the regulatory subunit PP4R3A. We show that PP4R3A, together with one of two redundant catalytic subunit genes, PROTEIN PHOSPHATASE X (PPX)1 and PPX2, promotes the biogenesis of microRNAs (miRNAs). PP4R3A is a chromatin-associated protein that interacts with RNA polymerase II and recruits it to the promoters of miRNA-encoding (MIR) genes to promote their transcription. PP4R3A likely also promotes the cotranscriptional processing of miRNA precursors, because it recruits the microprocessor component HYPONASTIC LEAVES1 to MIR genes and to nuclear dicing bodies. Finally, we show that hundreds of introns exhibit splicing defects in pp4r3a mutants. Together, this study reveals roles for Arabidopsis PP4 in transcription and nuclear RNA metabolism.

Thermal adaptation and plasticity of the plant circadian clock

Contents Summary 1215 I. Introduction 1215 II. Molecular organization of the plant circadian clock 1216 III. Temperature compensation 1219 IV. Temperature regulation of circadian behaviors 1220 V. Thermal adaptation of the clock: evolutionary considerations 1223 VI. Light and temperature information for the clock function - synergic or individual? 1224 VII. Concluding remarks and future prospects 1225 Acknowledgements 1225 References 1225 SUMMARY: Plant growth and development is widely affected by diverse temperature conditions. Although studies have been focused mainly on the effects of stressful temperature extremes in recent decades, nonstressful ambient temperatures also influence an array of plant growth and morphogenic aspects, a process termed thermomorphogenesis. Notably, accumulating evidence indicates that both stressful and nonstressful temperatures modulate the functional process of the circadian clock, a molecular timer of biological rhythms in higher eukaryotes and photosynthetic prokaryotes. The circadian clock can sustain robust and precise timing over a range of physiological temperatures. Genes and molecular mechanisms governing the temperature compensation process have been explored in different plant species. In addition, a ZEITLUPE/HSP90-mediated protein quality control mechanism helps plants maintain the thermal stability of the clock under heat stress. The thermal adaptation capability and plasticity of the clock are of particular interest in view of the growing concern about global climate changes. Considering these circumstances in the field, we believe that it is timely to provide a provoking discussion on the current knowledge of temperature regulation of the clock function. The review also will discuss stimulating ideas on this topic along with ecosystem management and future agricultural innovation.

The Plant microRNA Pathway: The Production and Action Stages

Plant microRNAs are an endogenous class of small regulatory RNA central to the posttranscriptional regulation of gene expression in plant development and environmental stress adaptation or in response to pathogen challenge. The plant microRNA pathway is readily separated into two distinct stages: (1) the production stage, which is localized to the plant cell nucleus and where the microRNA small RNA is processed from a double-stranded RNA precursor transcript, and (2) the action stage, which is localized to the plant cell cytoplasm and where the mature microRNA small RNA is loaded into an effector complex and is used by the complex as a sequence specificity guide to direct expression repression of target genes harboring highly complementary microRNA target sequences. Historical research indicated that the plant microRNA pathway was a highly structured, almost linear pathway requiring a small set of core machinery proteins. However, contemporary research has demonstrated that the plant microRNA pathway is highly dynamic, and to allow for this flexibility, a large and highly functionally diverse set of machinery proteins is now known to be required. For example, recent research has shown that plant microRNAs can regulate target gene expression via a translational repression mechanism of RNA silencing in addition to the standard messenger RNA cleavage-based mechanism of RNA silencing: a mode of RNA silencing originally assigned to all plant microRNAs. Using Arabidopsis thaliana as our model system, here we report on both the core and auxiliary sets of machinery proteins now known to be required for both microRNA production and microRNA action in plants.

DAWDLE Interacts with DICER-LIKE Proteins to Mediate Small RNA Biogenesis

DAWDLE (DDL) is a conserved forkhead-associated (FHA) domain-containing protein with essential roles in plant development and immunity. It acts in the biogenesis of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which regulate gene expression at the transcriptional and/or posttranscriptional levels. However, the functional mechanism of DDL and its impact on exogenous siRNAs remain elusive. Here, we report that DDL is required for the biogenesis of siRNAs derived from sense transgenes and inverted-repeat transgenes. Furthermore, we show that a mutation in the FHA domain of DDL disrupts the interaction of DDL with DICER-LIKE1 (DCL1), which is the enzyme that catalyzes miRNA maturation from primary miRNA transcripts (pri-miRNAs), resulting in impaired pri-miRNA processing. Moreover, we demonstrate that DDL interacts with DCL3, which is a DCL1 homolog responsible for siRNA production, and this interaction is crucial for optimal DCL3 activity. These results reveal that the interaction of DDL with DCLs is required for the biogenesis of miRNAs and siRNAs in Arabidopsis (Arabidopsis thaliana).

Green leaf volatiles protect maize (Zea mays) seedlings against damage from cold stress

Although considerable evidence has accumulated on the defensive activity of plant volatile organic compounds against pathogens and insect herbivores, less is known about the significance of volatile organic compounds emitted by plants under abiotic stress. Here, we report that green leaf volatiles (GLVs), which were previously shown to prime plant defences against insect herbivore attack, also protect plants against cold stress (4 °C). We show that the expression levels of several cold stress-related genes are significantly up-regulated in maize (Zea mays) seedlings treated with physiological concentrations of the GLV, (Z)-3-hexen-1-yl acetate (Z-3-HAC), and that seedlings primed with Z-3-HAC exhibit increased growth and reduced damage after cold stress relative to unprimed seedlings. Together, these data demonstrate the protective and priming effect of GLVs against cold stress and suggest an activity of GLVs beyond the activation of typical plant defence responses against herbivores and pathogens.

Loss of Drosha underlies dopaminergic neuron toxicity in models of Parkinson's disease

MiRNAs, a group of powerful modulator of gene expression, participate in multiple cellular processes under physiological and pathological conditions. Emerging evidence shows that Drosha, which controls the initial step in canonical miRNA biogenesis, is involved in modulating cell survival and death in models of several diseases. However, the role of Drosha in Parkinson’s disease (PD) has not been well established. Here, we show that the level of Drosha decreases in 6-OHDA-induced cellular and animal models of PD. 6-OHDA induced a p38 MAPK-dependent phosphorylation of Drosha. This triggered Drosha degradation. Enhancing the level of Drosha protected the dopaminergic (DA) neurons from 6-OHDA-induced toxicity in both in vitro and in vivo models of PD and alleviated the motor deficits of PD mice. These findings reveal that Drosha plays a critical role in the survival of DA neurons and suggest that stress-induced destabilization of Drosha may be part of the pathological process in PD.

A tomato proline-, lysine-, and glutamic-rich type gene SpPKE1 positively regulates drought stress tolerance

Plant abiotic resistance in cultivated species features limited variability. Using genes of wild species serves as a valid approach for improving abiotic resistance of cultivated plants. In this study, we uncovered a previously uncharacterized proline-, lysine-, and glutamic-rich protein gene (SpPKE1), which was isolated from drought-resistant wild tomato species Solanum pennellii (LA0716). When M82, which is a drought-sensitive tomato cultivar, was engineered to overexpress SpPKE1, its tolerance under drought stress was significantly improved by the accumulation of more chlorophyll, proline, and limited malondialdehyde compared with that in RNA interference (RNAi)-suppression lines, which were more sensitive than the wild-type plants. Several ion transporter genes, abiotic-related transcriptional factors, and reactive oxygen species-scavenging genes were upregulated in PKE1 overexpression (OE) lines but downregulated in RNAi plants. OE of SpPKE1 enhanced drought tolerance in tobacco. Screening results of yeast two-hybrid protein-protein interaction revealed that SpPKE1 can bind to an F-box protein that plays an important role in plant drought resistance. We posited that PKE1 enhanced drought tolerance by modulating the expressions of stress-responsive genes and interacting with the F-box protein.

MAC3A and MAC3B, Two Core Subunits of the MOS4-Associated Complex, Positively Influence miRNA Biogenesis

MAC3A and MAC3B are conserved U-box-containing proteins in eukaryotes. They are subunits of the MOS4-associated complex (MAC) that plays essential roles in plant immunity and development in Arabidopsis thaliana However, their functional mechanisms remain elusive. Here, we show that Arabidopsis MAC3A and MAC3B act redundantly in microRNA (miRNA) biogenesis. Lack of both MAC3A and MAC3B in the mac3b mac3b double mutant reduces the accumulation of miRNAs, causing elevated transcript levels of miRNA targets. mac3a mac3b also decreases the levels of primary miRNA transcripts (pri-miRNAs). However, MAC3A and MAC3B do not affect the promoter activity of genes encoding miRNAs (MIR genes), suggesting that they may not affect MIR transcription. This result, together with the fact that MAC3A associates with pri-miRNAs in vivo, indicates that MAC3A and MAC3B may stabilize pri-miRNAs. Furthermore, we find that MAC3A and MAC3B interact with the DCL1 complex that catalyzes miRNA maturation, promote DCL1 activity, and are required for the localization of HYL1, a component of the DCL1 complex. Besides MAC3A and MAC3B, two other MAC subunits, CDC5 and PRL1, also function in miRNA biogenesis. Based on these results, we propose that MAC functions as a complex to control miRNA levels through modulating pri-miRNA transcription, processing, and stability.

An Arabidopsis Nucleoporin NUP85 modulates plant responses to ABA and salt stress

Several nucleoporins in the nuclear pore complex (NPC) have been reported to be involved in abiotic stress responses in plants. However, the molecular mechanism of how NPC regulates abiotic stress responses, especially the expression of stress responsive genes remains poorly understood. From a forward genetics screen using an abiotic stress-responsive luciferase reporter (RD29A-LUC) in the sickle-1 (sic-1) mutant background, we identified a suppressor caused by a mutation in NUCLEOPORIN 85 (NUP85), which exhibited reduced expression of RD29A-LUC in response to ABA and salt stress. Consistently, the ABA and salinity induced expression of several stress responsive genes such as RD29A, COR15A and COR47 was significantly compromised in nup85 mutants and other nucleoporin mutants such as nup160 and hos1. Subsequently, Immunoprecipitation and mass spectrometry analysis revealed that NUP85 is potentially associated with HOS1 and other nucleoporins within the nup107-160 complex, along with several mediator subunits. We further showed that there is a direct physical interaction between MED18 and NUP85. Similar to NUP85 mutations, MED18 mutation was also found to attenuate expression of stress responsive genes. Taken together, we not only revealed the involvement of NUP85 and other nucleoporins in regulating ABA and salt stress responses, but also uncovered a potential relation between NPC and mediator complex in modulating the gene expression in plants.

Nuclear pore complex (NPC) mediates the traffic between nucleus and cytoplasm. This work identified NUCLEOPORIN 85 (NUP85) as an important factor for the expression of stress-responsive luciferase reporter gene RD29A-LUC in response to ABA and salt stress from a forward genetics screen. Mutation in NUP85 and other NPC components such as NUP160 and HOS1 resulted in decreased expression of several stress responsive genes such as RD29A, COR15A and COR47. Proteomics data uncovered a list of putative NUP85 associated proteins. Furthermore, NUP85 was demonstrated to interact with MED18, a master transcriptional regulator, to control the expression of stress responsive genes. The study has added a new layer of knowledge about the diverse functions of NPC in abiotic stress responses.

The 'how' and 'where' of plant microRNAs

Contents 1002 I. 1002 II. 1007 III. 1010 IV. 1013 1013 References 1013 SUMMARY: MicroRNAs (miRNAs) are small non-coding RNAs, of typically 20-24 nt, that regulate gene expression post-transcriptionally through sequence complementarity. Since the identification of the first miRNA, lin-4, in the nematode Caenorhabditis elegans in 1993, thousands of miRNAs have been discovered in animals and plants, and their regulatory roles in numerous biological processes have been uncovered. In plants, research efforts have established the major molecular framework of miRNA biogenesis and modes of action, and are beginning to elucidate the mechanisms of miRNA degradation. Studies have implicated restricted and surprising subcellular locations in which miRNA biogenesis or activity takes place. In this article, we summarize the current knowledge on how plant miRNAs are made and degraded, and how they repress target gene expression. We discuss not only the players involved in these processes, but also the subcellular sites in which these processes are known or implicated to take place. We hope to raise awareness that the cell biology of miRNAs holds the key to a full understanding of these enigmatic molecules.

Control of chrysanthemum flowering through integration with an aging pathway

Age, as a threshold of floral competence acquisition, prevents precocious flowering when there is insufficient biomass, and ensures flowering independent of environmental conditions; however, the underlying regulatory mechanisms are largely unknown. In this study, silencing the expression of a nuclear factor gene, CmNF-YB8, from the short day plant chrysanthemum (Chrysanthemum morifolium), results in precocious transition from juvenile to adult, as well as early flowering, regardless of day length conditions. The expression of SQUAMOSA PROMOTER BINDING-LIKE (SPL) family members, SPL3, SPL5, and SPL9, is upregulated in CmNF-YB8-RNAi plants, while expression of the microRNA, cmo-MIR156, is downregulated. In addition, CmNF-YB8 is shown to bind to the promoter of the cmo-MIR156 gene. Ectopic expression of cmo-miR156, using a virus-based microRNA expression system, restores the early flowering phenotype caused by CmNF-YB8 silencing. These results show that CmNF-YB8 influences flowering time through directly regulating the expression of cmo-MIR156 in the aging pathway.

The mechanisms by which plant age regulates flowering remain incompletely understood. Here the authors show that age dependent regulation of SPL transcription factors by miR156 influence flowering via control of NF-YB8 expression in Chrysanthemum.

The Arabidopsis MOS4-Associated Complex Promotes MicroRNA Biogenesis and Precursor Messenger RNA Splicing

In Arabidopsis thaliana, the MOS4-ASSOCIATED COMPLEX (MAC) is required for defense and development. The evolutionarily conserved, putative RNA helicase MAC7 is a component of the Arabidopsis MAC, and the human MAC7 homolog, Aquarius, is implicated in pre-mRNA splicing. Here, we show that mac7-1, a partial loss-of-function mutant in MAC7, and two other MAC subunit mutants, mac3a mac3b and prl1 prl2 (pleiotropic regulatory locus), exhibit reduced microRNA (miRNA) levels, indicating that MAC promotes miRNA biogenesis. The mac7-1 mutant shows reduced primary miRNA (pri-miRNA) levels without affecting miRNA gene (MIR) promoter activity or the half-life of pri-miRNA transcripts. As a nuclear protein, MAC7 is not concentrated in dicing bodies, but it affects the localization of HYPONASTIC LEAVES1 (HYL1), a key protein in pri-miRNA processing, to dicing bodies. Immunoprecipitation of HYL1 retrieved 11 known MAC subunits, including MAC7, indicating association between HYL1 and MAC. We propose that MAC7 links MIR transcription to pri-miRNA processing. RNA-seq analysis showed that downregulated genes in MAC subunit mutants are mostly involved in plant defense and stimulus responses, confirming a role of MAC in biotic and abiotic stress responses. We also discovered global intron retention defects in mutants in three subunits of MAC, thus linking MAC function to splicing in Arabidopsis.

The Protein Phosphatase 4 and SMEK1 Complex Dephosphorylates HYL1 to Promote miRNA Biogenesis by Antagonizing the MAPK Cascade in Arabidopsis

Phosphorylation plays an essential role in microRNA (miRNA) processing by regulating co-factors of the miRNA biogenesis machinery. HYL1 (Hyponastic Leaves 1), a core co-factor in plant miRNA biogenesis, is a short-lived phosphoprotein. However, the precise balance and regulatory mechanism of the stability and phosphorylation of HYL1 remain unclear. Here, we show that a highly conserved PP4 (Protein Phosphatase 4) and SMEK1 (Suppressor of MEK 1) complex dephosphorylates HYL1 to promote miRNA biogenesis, by antagonizing the MAPK cascade in Arabidopsis. The smek1 mutants exhibit defective miRNA biogenesis due to accelerated degradation of HYL1. SMEK1 stabilizes HYL1 in a dual manner: SMEK1, as a suppressor, inhibits MAPK activation to attenuate HYL1 phosphorylation; SMEK1 assembles a functional PP4 to target HYL1 for dephosphorylation. Moreover, the protein level of SMEK1 is increased in response to abscisic acid. Our results provide insights into the delicate balance between a protein kinase and a phosphatase during miRNA biogenesis.

The SnRK2 kinases modulate miRNA accumulation in Arabidopsis

MicroRNAs (miRNAs) regulate gene expression and play critical roles in growth and development as well as stress responses in eukaryotes. miRNA biogenesis in plants requires a processing complex that consists of the core components DICER-LIKE 1 (DCL1), SERRATE (SE) and HYPONASTIC LEAVES (HYL1). Here we show that inactivation of functionally redundant members of the SnRK2 kinases, which are the core components of abscisic acid (ABA) and osmotic stress signaling pathways, leads to reduction in miRNA accumulation under stress conditions. Further analysis revealed that the steady state level of HYL1 protein in plants under osmotic stress is dependent on the SnRK2 kinases. Additionally, our results suggest that the SnRK2 kinases physically associate with the miRNA processing components SE and HYL1 and can phosphorylate these proteins in vitro. These findings reveal an important role for the SnRK2 kinases in the regulation of miRNA accumulation and establish a mechanism by which ABA and osmotic stress signaling is linked to miRNA biogenesis.

Comparative Analysis of Expression Profiles of Panicle Development among Tolerant and Sensitive Rice in Response to Drought Stress

Water deficit caused a serious threat to crops, especially panicle development at reproductive growth phase. We investigated grain yield components and gene expression profiles of panicle among tolerant and sensitive rice in response to drought stress. Panicle morphologies exhibited that secondary branches per panicle were more severely affected as compared to primary branches per panicle. Moreover, grain weight per panicle showed significant decrease for both tolerant and sensitive varieties except for MILT1444. Expression profile analysis revealed that 783 differentially expressed genes (DEGs) were identified to be drought-induced from young panicles in 2 cm length. Hierarchical clustering indicated that 76.8% of DEGs were up-regulated for all six rice varieties, and the percentage of down-regulated genes was higher in sensitive group than tolerant group. Biological process category revealed that the shared Gene Ontology (GO) terms were involved in response to abiotic stimulus and stress, whereas the specific GO terms in tolerant group were identified as regulation of biological quality, homeostatic process, cell growth, anatomical structure morphogenesis and development, and the unique terms in sensitive varieties were identified as lipid metabolic process and secondary metabolic process. Furthermore, the gene-based association analysis narrowed down list of DEGs, and four genes common to all six varieties were selected as candidate for breeders. Together, we found several shared and distinct biological processes between tolerant and sensitive varieties, and candidate stress-responsive genes. These findings provided insight into functional mechanisms regulating drought stress response in panicle development and may also help to crop tolerant improvement.

Active 5' splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes

Arabidopsis, miR402 that is encoded within the first intron of a protein-coding gene At1g77230, is induced by heat stress. Its upregulation correlates with splicing inhibition and intronic proximal polyA site selection. It suggests that miR402 is not processed from an intron, but rather from a shorter transcript after selection of the proximal polyA site within this intron. Recently, introns and active 5΄ splice sites (5΄ss’) have been shown to stimulate the accumulation of miRNAs encoded within the first exons of intron-containing MIR genes. In contrast, we have observed the opposite effect of splicing inhibition on intronic miR402 production. Transient expression experiments performed in tobacco leaves revealed a significant accumulation of the intronic mature miR402 when the 5΄ss of the miR402-hosting intron was inactivated. In contrast, when the miR402 stem-loop structure was moved into the first exon, mutation of the first-intron 5΄ss resulted in a decrease in the miRNA level. Thus, the 5΄ss controls the efficiency of miRNA biogenesis. We also show that the SERRATE protein (a key component of the plant microprocessor) colocalizes and interacts with several U1 snRNP auxiliary proteins. We postulate that SERRATE-spliceosome connections have a direct effect on miRNA maturation.