MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis

Evaluation of zma-miR408 and its target genes function on maize (Zea mays) leaf growth response to cold stress by VIGS-based STTM approach

miR408 is a conserved plant miRNA family that is known to regulate genes involved in copper metabolism. However, the function of miR408 in maize leaf growth regulation under cold stress isn't defined. In this study, endogenous maize miR408 was transiently silenced by using virus-induced gene silencing (VIGS) combined with short tandem target mimic (STTM) approaches. To this end, STTM-miR408a/b was designed, synthesized, and applied to maize seedlings. Subsequently, STTM-miR408a/b (STTM) and mock-treated (M) seedlings were subjected to cold stress (C) and the growth response of the seedlings was monitored. Finally, STTM-miR408a/b-treatment successfully downregulated the expression of endogenous mir408a/b and upregulated their putative targets Basic Blue Protein (BBP) and Blue Copper Protein (BCP) antagonistically in the STTM and STTM_C groups compared to M and M_C groups. On the other hand, their putative target Laccase (LAC22) gene was upregulated in the STTM group compared to the M group, but there were no significant expression differences between the M_C and STTM_C groups. The elongation rate of the STTM-miR408a/b-treated second and third leaves was reduced by 10% and 19% resulting in 19% and 11% shortening, respectively. Furthermore, the activity of catalase (CAT) and glutathione reductase (GR) was decreased by 57% in STTM, M_C, and STTM_C, and 29% and 28% in the M_C and STTM_C groups and ascorbate peroxidase (APX) was increased by 15% in M_C and STTM_C groups, respectively. These findings illuminated the maize leaf growth response to cold via regulation of expression of miR408 and its target genes and antioxidant system.

sly-miR408b Targets a Plastocyanin-Like Protein to Regulate Mycorrhizal Symbiosis in Tomato

Symbiosis between arbuscular mycorrhizal fungi and plants plays a crucial role in nutrient acquisition and stress resistance for terrestrial plants. microRNAs have been reported to participate in the regulation of mycorrhizal symbiosis by controlling the expression of their target genes. Herein, we found that sly-miR408b was significantly downregulated in response to mycorrhizal colonisation. Overexpression of sly-miR408b compromised mycorrhizal colonisation by Rhizophagus irregularis in tomato (Solanum lycopersicum) roots. A basic blue protein gene (SlBBP) was then identified as the new target gene of miR408b in tomato. The expression of membrane-located SlBBP was induced in a copper-dependent manner. Importantly, the loss function of SlBBP decreased the root mycorrhizal colonisation. Overexpression of SlBBP decreased SOD activity, which may interfere with the process of scavenging excessive reactive oxygen species (ROS). Mutation of RBOH1, which encodes ROS-producing enzymes NADPH oxidases, obviously reduced the arbuscule abundance in the mutant roots. Overall, our results provide evidence that sly-miR408b and its target gene SlBBP regulate mycorrhizal symbiosis in tomato through mediating ROS production.

The role of the Arabidopsis tandem zinc-finger C3H15 protein in metal homeostasis

Living organisms have developed finely regulated homeostatic networks to mitigate the effects of environmental fluctuations in transition metal micronutrients, including iron, zinc, and copper. In Saccharomyces cerevisiae, the tandem zinc-finger protein Cth2 post-transcriptionally regulates gene expression under conditions of iron deficiency by controlling the levels of mRNAs that code for non-essential ferroproteins. The molecular mechanism involves Cth2 binding to AU-rich elements present in the 3' untranslated region of target mRNAs, negatively affecting their stability and translation. Arabidopsis thaliana has two TZF proteins homologous to yeast Cth2, C3H14 and C3H15, which participate in cell wall remodelling. The present work examines the expression of representative metal homeostasis genes with putative AREs in plants with altered levels of C3H14 and C3H15 grown under varying metal availabilities. The results suggest that C3H15 may act as a post-transcriptional plant modulator of metal adequacy, as evidenced by the expression of SPL7, the main transcriptional regulator under copper deficiency, and PETE2, which encodes plastocyanin. In contrast to S. cerevisiae, the plant C3H15 affects copper and zinc homeostasis rather than iron. When grown under copper-deficient conditions, adult C3H15OE plants exhibit lower chlorophyll content and photosynthetic efficiency compared to control plants, suggesting accelerated senescence. Likewise, metal content in C3H15OE plants under copper deficiency shows altered mobilization of copper and zinc to seeds. These data suggest that the C3H15 protein plays a role in modulating both cell wall remodelling and metal homeostasis. The interaction between these processes may be the cause of altered metal translocation.

The microRNA408-plantacyanin module balances plant growth and drought resistance by regulating reactive oxygen species homeostasis in guard cells

The conserved microRNA (miRNA) miR408 enhances photosynthesis and compromises stress tolerance in multiple plants, but the cellular mechanism underlying its function remains largely unclear. Here, we show that in Arabidopsis (Arabidopsis thaliana), the transcript encoding the blue copper protein PLANTACYANIN (PCY) is the primary target for miR408 in vegetative tissues. PCY is preferentially expressed in the guard cells, and PCY is associated with the endomembrane surrounding individual chloroplasts. We found that the MIR408 promoter is suppressed by multiple abscisic acid (ABA)-responsive transcription factors, thus allowing PCY to accumulate under stress conditions. Genetic analysis revealed that PCY elevates reactive oxygen species (ROS) levels in the guard cells, promotes stomatal closure, reduces photosynthetic gas exchange, and enhances drought resistance. Moreover, the miR408-PCY module is sufficient to rescue the growth and drought tolerance phenotypes caused by gain- and loss-of-function of MYB44, an established positive regulator of ABA responses, indicating that the miR408-PCY module relays ABA signaling for regulating ROS homeostasis and drought resistance. These results demonstrate that miR408 regulates stomatal movement to balance growth and drought resistance, providing a mechanistic understanding of why miR408 is selected during land plant evolution and insights into the long-pursued quest of breeding drought-tolerant and high-yielding crops.

The transcription factor OsSPL9 endows rice with copper deficiency resilience

Copper (Cu) is a crucial micronutrient essential for the growth and development of plants. Rice exhibits remarkable resistance to Cu deficiency, but the underlying molecular mechanisms are not well understood. In this study, we reveal that the plant's ability to withstand Cu deficiency is orchestrated by a transcription factor known as OsSPL9. We have demonstrated that OsSPL9 functions as a central regulator of Cu homeostasis. Disrupting OsSPL9 through knockout significantly reduced the plant's tolerance to Cu deficiency. As a result, the spl9 mutants exhibited reduced Cu accumulation in their shoots when compared with wild-type plants. This reduction was linked to a disruption in the transport of Cu from older leaves to younger ones. Furthermore, we show that OsSPL9 directly bound to GTAC motifs in the promoters of key genes involved in Cu uptake and transport, as well as Cu-miRNAs, and enhanced their transcription under Cu-deficient conditions. Overall, our findings shed light on the molecular basis of rice resilience to Cu deficiency stress and place the transcription factor OsSPL9 as a master regulator of this response.

Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures

The orthotospovirus capsicum chlorosis virus (CaCV) is an important pathogen affecting capsicum plants. Elevated temperatures may affect disease progression and pose a potential challenge to capsicum production. To date, CaCV-resistant capsicum breeding lines have been established; however, the impact of an elevated temperature of 35 °C on this genetic resistance remains unexplored. Thus, this study aimed to investigate how high temperature (HT) influences the response of CaCV-resistant capsicum to the virus. Phenotypic analysis revealed a compromised resistance in capsicum plants grown at HT, with systemic necrotic spots appearing in 8 out of 14 CaCV-infected plants. Molecular analysis through next-generation sequencing identified 105 known and 83 novel microRNAs (miRNAs) in CaCV-resistant capsicum plants. Gene ontology revealed that phenylpropanoid and lignin metabolic processes, regulated by Can-miR408a and Can- miR397, are likely involved in elevated-temperature-mediated resistance-breaking responses. Additionally, real-time PCR validated an upregulation of Can-miR408a and Can-miR397 by CaCV infection at HT; however, only the Laccase 4 transcript, targeted by Can-miR397, showed a tendency of negative correlation with this miRNA. Overall, this study provides the first molecular insights into how elevated temperature affects CaCV resistance in capsicum plants and reveals the potential role of miRNA in temperature-sensitive tospovirus resistance.

Expression and Functional Identification of SPL6/7/9 Genes under Drought Stress in Sugarbeet Seedlings

Sugar beet is a significant sugar crop in China, primarily cultivated in arid regions of the north. However, drought often affects sugar beet cultivation, leading to reduced yield and quality. Therefore, understanding the impact of drought on sugar beets and studying their drought tolerance is crucial. Previous research has examined the role of SPL (SQUAMOSA promoter-binding protein-like) transcription factors in plant stress response; however, the precise contribution of SPLs to the drought stress response in sugar beets has yet to be elucidated. In this study, we identified and examined the BvSPL6, BvSPL7, and BvSPL9 genes in sugar beets, investigating their performance during the seedling stage under drought stress. We explored their drought resistance characteristics using bioinformatics, quantitative analysis, physiological experiments, and molecular biology experiments. Drought stress and rehydration treatments were applied to sugar beet seedlings, and the expression levels of BvSPL6, BvSPL7, and BvSPL9 genes in leaves were quantitatively analyzed at 11 different time points to evaluate sugar beets' response and tolerance to drought stress. Results indicated that the expression level of the BvSPL6/9 genes in leaves was upregulated during the mid-stage of drought stress and downregulated during the early and late stages. Additionally, the expression level of the BvSPL7 gene gradually increased with the duration of drought stress. Through analyzing changes in physiological indicators during different time periods of drought stress and rehydration treatment, we speculated that the regulation of BvSPL6/7/9 genes is associated with sugar beet drought resistance and their participation in drought stress response. Furthermore, we cloned the CDS sequences of BvSPL6, BvSPL7, and BvSPL9 genes from sugar beets and conducted sequence alignment with the database to validate the results. Subsequently, we constructed overexpression vectors, named 35S::BvSPL6, 35S::BvSPL7, and 35S::BvSPL9, and introduced them into sugar beets using Agrobacterium-mediated methods. Real-time fluorescence quantitative analysis revealed that the expression levels of BvSPL6/7/9 genes in transgenic sugar beets increased by 40% to 80%. The drought resistance of transgenic sugar beets was significantly enhanced compared with the control group.

Overlapping of copper-nanoparticles with microRNA reveals crippling of heat stress pathway in Solanum lycopersicum: Tomato case study

Despite the tangible benefits of copper nanoparticles (CuNPs) for plants, the increasing use of CuNPs poses a threat to plants and the environment. Although miRNAs have been shown to mediate heat shock and CuNPs by altering gene expression, no study has investigated how CuNPs in combination with heat shock (HS) affect the miRNA expression profile. Here, we exposed tomato plants to 0.01 CuONPs at 42 °C for 1 h after exposure. It was found that the expression levels of miR156a, miR159a and miR172a and their targets SPL3, MYB33 and AP2a were altered under CuNPs and HS + CuNPs. This alteration accelerated the change of vegetative phase and the process of leaf senescence. The overexpression of miR393 under CuNPs and HS + CuNPs could also be an indicator of the attenuation of leaf morphology. Interestingly, the down-regulation of Cu/ZnSOD1 and Cu/ZnSOD2 as target genes of miR398a, which showed strong abnormal expression, was replaced by FeSOD (FSD1), indicating the influence of CuNPs. In addition, CuNPs triggered the expression of some important genes of heat shock response, including HsFA2, HSP70-9 and HSP90-3, which showed lower expression compared to HS. Thus, CuNPs play an important role in altering the gene expression pathway during heat stress.

Molecular Mechanisms of Plant Responses to Copper: From Deficiency to Excess

Copper (Cu) is an essential nutrient for plant growth and development. This metal serves as a constituent element or enzyme cofactor that participates in many biochemical pathways and plays a key role in photosynthesis, respiration, ethylene sensing, and antioxidant systems. The physiological significance of Cu uptake and compartmentalization in plants has been underestimated, despite the importance of Cu in cellular metabolic processes. As a micronutrient, Cu has low cellular requirements in plants. However, its bioavailability may be significantly reduced in alkaline or organic matter-rich soils. Cu deficiency is a severe and widespread nutritional disorder that affects plants. In contrast, excessive levels of available Cu in soil can inhibit plant photosynthesis and induce cellular oxidative stress. This can affect plant productivity and potentially pose serious health risks to humans via bioaccumulation in the food chain. Plants have evolved mechanisms to strictly regulate Cu uptake, transport, and cellular homeostasis during long-term environmental adaptation. This review provides a comprehensive overview of the diverse functions of Cu chelators, chaperones, and transporters involved in Cu homeostasis and their regulatory mechanisms in plant responses to varying Cu availability conditions. Finally, we identified that future research needs to enhance our understanding of the mechanisms regulating Cu deficiency or stress in plants. This will pave the way for improving the Cu utilization efficiency and/or Cu tolerance of crops grown in alkaline or Cu-contaminated soils.

Linking the key physiological functions of essential micronutrients to their deficiency symptoms in plants

In this review, we untangle the physiological key functions of the essential micronutrients and link them to the deficiency responses in plants. Knowledge of these responses at the mechanistic level, and the resulting deficiency symptoms, have improved over the last decade and it appears timely to review recent insights for each of them. A proper understanding of the links between function and symptom is indispensable for an accurate and timely identification of nutritional disorders, thereby informing the design and development of sustainable fertilization strategies. Similarly, improved knowledge of the molecular and physiological functions of micronutrients will be important for breeding programmes aiming to develop new crop genotypes with improved nutrient-use efficiency and resilience in the face of changing soil and climate conditions.

ZmmiR398b negatively regulates maize resistance to sugarcane mosaic virus infection by targeting ZmCSD2/4/9

MicroRNAs (miRNAs) are widely involved in various biological processes of plants and contribute to plant resistance against various pathogens. In this study, upon sugarcane mosaic virus (SCMV) infection, the accumulation of maize (Zea mays) miR398b (ZmmiR398b) was significantly reduced in resistant inbred line Chang7-2, while it was increased in susceptible inbred line Mo17. Degradome sequencing analysis coupled with transient co-expression assays revealed that ZmmiR398b can target Cu/Zn-superoxidase dismutase2 (ZmCSD2), ZmCSD4, and ZmCSD9 in vivo, of which the expression levels were all upregulated by SCMV infection in Chang7-2 and Mo17. Moreover, overexpressing ZmmiR398b (OE398b) exhibited increased susceptibility to SCMV infection, probably by increasing reactive oxygen species (ROS) accumulation, which were consistent with ZmCSD2/4/9-silenced maize plants. By contrast, silencing ZmmiR398b (STTM398b) through short tandem target mimic (STTM) technology enhanced maize resistance to SCMV infection and decreased ROS levels. Interestingly, copper (Cu)-gradient hydroponic experiments demonstrated that Cu deficiency promoted SCMV infection while Cu sufficiency inhibited SCMV infection by regulating accumulations of ZmmiR398b and ZmCSD2/4/9 in maize. These results revealed that manipulating the ZmmiR398b-ZmCSD2/4/9-ROS module provides a prospective strategy for developing SCMV-tolerant maize varieties.

Evidence of microRNAs origination from chloroplast genome and their role in regulating Photosystem II protein N (psbN) mRNA

The microRNAs are endogenous, regulating gene expression either at the DNA or RNA level. Despite the availability of extensive studies on microRNA generation in plants, reports on their abundance, biogenesis, and consequent gene regulation in plant organelles remain naVve. Building on previous studies involving pre-miRNA sequencing in Abelmoschus esculentus, we demonstrated that three putative microRNAs were raised from the chloroplast genome. In the current study, we have characterized the genesis of these three microRNAs through a combination of bioinformatics and experimental approaches. The gene sequence for a miRNA, designated as AecpmiRNA1 (A. esculentus chloroplast miRNA), is potentially located in both the genomic DNA, i.e., nuclear and chloroplast genome. In contrast, the gene sequences for the other two miRNAs (AecpmiRNA2 and AecpmiRNA3) are exclusively present in the chloroplast genome. Target prediction revealed many potential mRNAs as targets for AecpmiRNAs. Further analysis using 5' RACE-PCR determined the AecpmiRNA3 binding and cleavage site at the photosystem II protein N (psbN). These results indicate that AecpmiRNAs are generated from the chloroplast genome, possessing the potential to regulate mRNAs arising from chloroplast gene(s). On the other side, the possibility of nuclear genome-derived mRNA regulation by AecpmiRNAs cannot be ruled out.

miR397b-LAC2 module regulates cadmium stress response by coordinating root lignification and copper homeostasis in Arabidopsis thaliana

Non-essential heavy metal cadmium (Cd) is toxic to plants and animals. Cadmium affects plant photosynthesis, respiration, and causes water imbalance and may lead to plant death. Cadmium induces toxicity by interfering with the essential metal copper (Cu) homeostasis, which affects plant nutrition. Though root lignin biosynthesis is positively regulated by Cd stress, the underlying mechanisms promoting lignin accumulation and controlling Cd-induced Cu limitation responses are unclear. Here, we elucidated the role of Cu-responsive microRNA (miR397b) in Arabidopsis thaliana plants for Cd stress by targeting the LACCASE2 (LAC2) gene. This study demonstrated the fundamental mechanism of miR397b-mediated Cd stress response by enhancing the lignin content in root tissues. We developed miR397b over-expressing plants, which showed considerable Cd stress tolerance. Plants with knockdown function of LAC2 also showed significant tolerance to Cd stress. miR397b overexpressing and lac2 mutant plants showed root reduction, higher biomass and chlorophyll content, and significantly lower Reactive Oxygen Species (ROS). This study demonstrated the miR397b-mediated Cd stress response in Arabidopsis by enhancing the lignin content in root tissues. We conclude that modulation in miR397b can be potentially used for improving plants for Cd tolerance and Cu homeostasis.

miR397-LACs mediated cadmium stress tolerance in Arabidopsis thaliana

Cadmium (Cd) is a non-essential heavy metal, assimilated in plant tissue with other nutrients, disturbing the ions' homeostasis in plants. The plant develops different mechanisms to tolerate the hazardous environmental effects of Cd. Recently studies found different miRNAs that are involved in Cd stress. In the current study, miR397 mutant lines were constructed to explore the molecular mechanisms of miR397 underlying Cd tolerance. Compared with the genetically modified line of overexpressed miR397 (artificial miR397, amiR397), the lines of downregulated miR397 (Short Tandem Target Mimic miR397, STTM miR397) showed more substantial Cd tolerance with higher chlorophyll a & b, carotenoid and lignin content. ICP-OES revealed higher cell wall Cd and low total Cd levels in STTM miR397 than in the wild-type and amiR397 plants.Further, the STTM plants produced fewer reactive oxygen species (ROS) and lower activity of antioxidants enzymes (e.g., catalase [CAT], malondialdehyde [MDA]) compared with amiR397 and wild-type plants after stress, indicating that silencing the expression of miR397 can reduce oxidative damage. In addition, the different family transporters' gene expression was much higher in the amiR397 plants than in the wild type and STTM miRNA397. Our results suggest that miR397 plays a role in Cd tolerance in Arabidopsis thaliana. Overexpression of miR397 could decrease Cd tolerance in plants by regulating the expression of LAC 2/4/17, changing the lignin content, which may play an important role in inducing different stress-tolerant mechanisms and protecting the cell from a hazardous condition. This study provides a basis to elucidate the functions of miR397 and the Cd stress tolerance mechanism in Arabidopsis thaliana.

MicroRNA397 regulates tolerance to drought and fungal infection by regulating lignin deposition in chickpea root

Plants deposit lignin in the secondary cell wall as a common response to drought and pathogen attacks. Cell wall localised multicopper oxidase family enzymes LACCASES (LACs) catalyse the formation of monolignol radicals and facilitate lignin formation. We show an upregulation of the expression of several LAC genes and a downregulation of microRNA397 (CamiR397) in response to natural drought in chickpea roots. CamiR397 was found to target LAC4 and LAC17L out of twenty annotated LACs in chickpea. CamiR397 and its target genes are expressed in the root. Overexpression of CamiR397 reduced expression of LAC4 and LAC17L and lignin deposition in chickpea root xylem causing reduction in xylem wall thickness. Downregulation of CamiR397 activity by expressing a short tandem target mimic (STTM397) construct increased root lignin deposition in chickpea. CamiR397-overexpressing and STTM397 chickpea lines showed sensitivity and tolerance, respectively, towards natural drought. Infection with a fungal pathogen Macrophomina phaseolina, responsible for dry root rot (DRR) disease in chickpea, induced local lignin deposition and LAC gene expression. CamiR397-overexpressing and STTM397 chickpea lines showed more sensitivity and tolerance, respectively, to DRR. Our results demonstrated the regulatory role of CamiR397 in root lignification during drought and DRR in an agriculturally important crop chickpea.

Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective

Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.

Beyond NPK: Mineral Nutrient-Mediated Modulation in Orchestrating Flowering Time

Flowering time in plants is a complex process regulated by environmental conditions such as photoperiod and temperature, as well as nutrient conditions. While the impact of major nutrients like nitrogen, phosphorus, and potassium on flowering time has been well recognized, the significance of micronutrient imbalances and their deficiencies should not be neglected because they affect the floral transition from the vegetative stage to the reproductive stage. The secondary major nutrients such as calcium, magnesium, and sulfur participate in various aspects of flowering. Micronutrients such as boron, zinc, iron, and copper play crucial roles in enzymatic reactions and hormone biosynthesis, affecting flower development and reproduction as well. The current review comprehensively explores the interplay between microelements and flowering time, and summarizes the underlying mechanism in plants. Consequently, a better understanding of the interplay between microelements and flowering time will provide clues to reveal the roles of microelements in regulating flowering time and to improve crop reproduction in plant industries.

Role of mi RNA in Phytoremediation of Heavy Metals and Metal Induced Stress Alleviation

Anthropogenic activities have contributed hugely in enhancing various types of environmental toxicity. One of these is higher accumulation of toxic heavy metals in soil and plant tissues. Although many heavy metals act as essential component for the growth and development of plants when present in low concentrations but at higher concentrations it becomes cytotoxic. Several innate mechanisms have evolved in plants to cope with it. In recent years the mechanism of using miRNA to combat metal induced toxicity has come to fore front. The miRNA or the microRNA regulates different physiological processes and induces a negative control in expressing the complementary target genes. The cleavage formation by post-transcriptional method and the inhibition of targeted translational mRNA are the two main procedures by which plant miRNAs function. The heavy and enhanced metal accumulation in plants has increased the production of different kinds of free radicals like reactive nitrogen and oxygen which damage the plants oxidatively. Several plant miRNA are capable of targeting and reducing the expression of those genes which are responsible for higher metal accumulation and storage. This can reduce the metal load and hence its negative impact on plant can also be reduced. This review depicts the biogenesis, the mode of action of miRNA, and the control mechanisms of miRNA in metal induced stress response in plant. A detailed review on the role of plant miRNA in alleviation of metal induced stress is discussed in this present study.

The miR408a-BBP-LAC3/CSD1 module regulates anthocyanin biosynthesis mediated by crosstalk between copper homeostasis and ROS homeostasis during light induction in Malus plants

INTRODUCTION

The expression of miR408 is affected by copper (Cu) conditions and positively regulates anthocyanin biosynthesis in Arabidopsis. However, the underlying mechanisms by which miR408 regulates anthocyanin biosynthesis mediated by Cu homeostasis and reactive oxygen species (ROS) homeostasis remain unclear in Malus plants.

OBJECTIVES

Our study aims to elucidate how miR408a and its target, basic blue protein (BBP) regulate Cu homeostasis and ROS homeostasis, and anthocyanin biosynthesis in Malus plants.

METHODS

The roles of miR408a and its target BBP in regulating anthocyanin biosynthesis, Cu homeostasis, and ROS homeostasis were mainly identified in Malus plants.

RESULTS

We found that the BBP protein interacted with the copper-binding proteins LAC3 (laccase) and CSD1 (Cu/Zn SOD superoxide dismutase), indicating a potential crosstalk between Cu homeostasis and ROS homeostasis might be mediated by miR408 to regulate the anthocyanin accumulation. Further studies showed that overexpressing miR408a or suppressing BBP transiently significantly increased the expression of genes related to Cu binding and Cu transport, leading to anthocyanin accumulation under light induction in apple fruit and Malus plantlets. Consistently, opposite results were obtained when repressing miR408a or overexpressing BBP. Moreover, light induction significantly increased the expression of miR408a, CSD1, and LAC3, but significantly reduced the BBP expression, resulting in increased Cu content and anthocyanin accumulation. Furthermore, excessive Cu significantly increased the anthocyanin accumulation, accompanied by reduced expression of miR408a and Cu transport genes, and upregulated expression of Cu binding proteins including BBP, LAC3, and CSD1 to maintain the Cu homeostasis and ROS homeostasis in Malus plantlets.

CONCLUSION

Our findings provide new insights into the mechanism by which the miR408a-BBP-LAC3/CSD1 module perceives light and Cu signals regulating Cu and ROS homeostasis, ultimately affecting anthocyanin biosynthesis in Malus plants.

The Small RNA Component of Arabidopsis thaliana Phloem Sap and Its Response to Iron Deficiency

In order to discover sRNA that might function during iron deficiency stress, RNA was prepared from phloem exudates of Arabidopsis thaliana, and used for RNA-seq. Bioanalyzer results indicate that abundant RNA from phloem is small in size-less than 200 nt. Moreover, typical rRNA bands were not observed. Sequencing of eight independent phloem RNA samples indicated that tRNA-derived fragments, specifically 5' tRFs and 5' tRNA halves, are highly abundant in phloem sap, comprising about 46% of all reads. In addition, a set of miRNAs that are present in phloem sap was defined, and several miRNAs and sRNAs were identified that are differentially expressed during iron deficiency.

Target Landscape of Conserved Plant MicroRNAs and the Complexities of Their Ancient MicroRNA-Binding Sites

In plants, microRNA (miRNA)-target interactions (MTIs) require high complementarity, a feature from which bioinformatic programs have predicted numerous and diverse targets for any given miRNA, promoting the idea of complex miRNA networks. Opposing this is a hypothesis of constrained miRNA specificity, in which functional MTIs are restricted to the few targets whose required expression output is compatible with the expression of the miRNA. To explore these opposing views, the bioinformatic pipeline Targets Ranked Using Experimental Evidence was applied to strongly conserved miRNAs to identity their high-evidence (HE) targets across species. For each miRNA family, HE targets predominantly consisted of homologs from one conserved target gene family (primary family). These primary families corresponded to the known canonical miRNA-target families, validating the approach. Very few additional HE target families were identified (secondary family), and if so, they were likely functionally related to the primary family. Many primary target families contained highly conserved nucleotide sequences flanking their miRNA-binding sites that were enriched in HE homologs across species. A number of these flanking sequences are predicted to form conserved RNA secondary structures that preferentially base pair with the miRNA-binding site, implying that these sites are highly structured. Our findings support a target landscape view that is dominated by the conserved primary target families, with a minority of either secondary target families or non-conserved targets. This is consistent with the constrained hypothesis of functional miRNA specificity, which potentially in part is being facilitated by features beyond complementarity.

microRNA408 and its encoded peptide regulate sulfur assimilation and arsenic stress response in Arabidopsis

MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in regulating various developmental and biological processes. The expression of miRNAs is differentially modulated in response to various biotic and abiotic stresses. Recent findings have shown that some pri-miRNAs encode small regulatory peptides known as microRNA-encoded peptides (miPEPs). miPEPs regulate the growth and development of plants by modulating corresponding miRNA expression; however, the role of these peptides under different stress conditions remains unexplored. Here, we report that pri-miR408 encodes a small peptide, miPEP408, that regulates the expression of miR408, its targets, and associated phenotype in Arabidopsis. We also report that miR408, apart from Plantacyanin (ARPN) and Laccase3 (LAC3), targets a glutathione S-transferase (GSTU25) that plays a role in sulfur assimilation and exhibits a range of detoxification activities with the environmental pollutant. Plants overexpressing miR408 showed severe sensitivity under low sulfur (LS), arsenite As(III), and LS + As(III) stress, while miR408 mutants developed using the CRISPR/Cas9 approach showed tolerance. Transgenic lines showed phenotypic alteration and modulation in the expression of genes involved in the sulfur reduction pathway and affect sulfate and glutathione accumulation. Similar to miR408 overexpressing lines, the exogenous application of synthetic miPEP408 and miPEP408OX lines led to sensitivity in plants under LS, As(III), and combined LS + As(III) stress compared to the control. This study suggests the involvement of miR408 and miPEP408 in heavy metal and nutrient deficiency responses through modulation of the sulfur assimilation pathway.

Delineating the tissue-mediated drought stress governed tuning of conserved miR408 and its targets in rice

Engineering drought tolerance in rice needs to focus on regulators that enhance tolerance while boosting plant growth and vigor. The present study delineated the concealed function and tissue-mediated interplay of the miR408/target module in imparting drought stress tolerance in rice. The plant miR408 family comprises three dominant mature forms (21 nt), including a distinct monocot variant (F-7 with 5' C) and is divided into six groups. miR408 majorly cleaves genes belonging to the blue copper protein in addition to several other species-specific targets in plants. Comparative sequence analysis in 4726 rice accessions identified 22 sequence variants (SNP and InDELs) in its promoter (15) and pre-miR408 region. Haplotype analysis of the sequence variants indicated eight haplotypes (three: Japonica-specific and five: Indica-specific) of the miR408 promoter. In drought-tolerant Nagina 22, miR408 follows flag leaf preferential expression. Under drought conditions, its levels are upregulated in flag leaf and roots which seems to be regulated by a differential fraction of methylated cytosines (mCs) in the precursor region. The active pool of miR408 regulated targets under control and drought conditions is impacted by the tissue type. Comparative expression analysis of the miR408/target module under different sets of conditions features 83 targets exhibiting antagonistic expression in rice, out of which 12 genes, including four PLANTACYANINS (OsUCL6, 7, 9 and 30), PIRIN, OsLPR1, OsCHUP1, OsDOF12, OsBGLU1, glycine-rich cell wall gene, OsDUT, and OsERF7, are among the high confidence targets. Further, overexpression of MIR408 in drought-sensitive rice cultivar (PB1) leads to the massive enhancement of vegetative growth in rice with improved ETR and Y(II) and enhanced dehydration stress tolerance. The above results suggest that miR408 is likely to act as a positive regulator of growth and vigor, as well as dehydration stress, making it a potential candidate for engineering drought tolerance in rice.

Information theory and machine learning illuminate large-scale metabolomic responses of Brachypodium distachyon to environmental change

Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from liquid chromatography tandem mass spectrometry (LC-MS/MS) can be identified, limiting our understanding of how metabolomes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS of leaves, roots, and other organs of Brachypodium distachyon (Poaceae) under 17 organ-condition combinations, including copper deficiency, heat stress, low phosphate, and arbuscular mycorrhizal symbiosis. We found that both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We found that 1 week of copper deficiency shielded the root, but not the leaf metabolome, from perturbation due to heat stress. Machine learning (ML)-based analysis annotated approximately 81% of the fragmented peaks versus approximately 6% using spectral matches alone. We performed one of the most extensive validations of ML-based peak annotations in plants using thousands of authentic standards, and analyzed approximately 37% of the annotated peaks based on these assessments. Analyzing responsiveness of each predicted metabolite class to environmental change revealed significant perturbations of glycerophospholipids, sphingolipids, and flavonoids. Co-accumulation analysis further identified condition-specific biomarkers. To make these results accessible, we developed a visualization platform on the Bio-Analytic Resource for Plant Biology website (https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi-bin/efpWeb.cgi), where perturbed metabolite classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and stress adaptation.

LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis

How the noncoding genome affects cellular functions is a key biological question. A particular challenge is to distinguish the effects of noncoding DNA elements from long noncoding RNAs (lncRNAs) that coincide at the same loci. Here, we identified the flowering-associated intergenic lncRNA (FLAIL) in Arabidopsis through early flowering flail mutants. Expression of FLAIL RNA from a different chromosomal location in combination with strand-specific RNA knockdown characterized FLAIL as a trans-acting RNA molecule. FLAIL directly binds to differentially expressed target genes that control flowering via RNA-DNA interactions through conserved sequence motifs. FLAIL interacts with protein and RNA components of the spliceosome to affect target mRNA expression through co-transcriptional alternative splicing (AS) and linked chromatin regulation. In the absence of FLAIL, splicing defects at the direct FLAIL target flowering gene LACCASE 8 (LAC8) correlated with reduced mRNA expression. Double mutant analyses support a model where FLAIL-mediated splicing of LAC8 promotes its mRNA expression and represses flowering. Our study suggests lncRNAs as accessory components of the spliceosome that regulate AS and gene expression to impact organismal development.

Genomic and transcriptomic analysis of sacred fig (Ficus religiosa)

BACKGROUND

Peepal/Bodhi tree (Ficus religiosa L.) is an important, long-lived keystone ecological species. Communities on the Indian subcontinent have extensively employed the plant in Ayurveda, traditional medicine, and spiritual practices. The Peepal tree is often thought to produce oxygen both during the day and at night by Indian folks. The goal of our research was to produce molecular resources using whole-genome and transcriptome sequencing techniques.

RESULTS

The complete genome of the Peepal tree was sequenced using two next-generation sequencers Illumina HiSeq1000 and MGISEQ-2000. We assembled the draft genome of 406 Mb, using a hybrid assembly workflow. The genome annotation resulted in 35,093 protein-coding genes; 53% of its genome consists of repetitive sequences. To understand the physiological pathways in leaf tissues, we analyzed photosynthetically distinct conditions: bright sunny days and nights. The RNA-seq analysis supported the expression of 26,479 unigenes. The leaf transcriptomic analysis of the diurnal and nocturnal periods revealed the expression of the significant number of genes involved in the carbon-fixation pathway.

CONCLUSIONS

This study presents a draft hybrid genome assembly for F. religiosa and its functional annotated genes. The genomic and transcriptomic data-derived pathways have been analyzed for future studies on the Peepal tree.

Characterization of plant laccase genes and their functions

Laccase is a copper-containing polyphenol oxidase found in different organisms. The multigene family that encodes laccases is widely distributed in plant genomes. Plant laccases oxidize monolignols to produce lignin which is important for plant growth and stress responses. Industrial applications of fungal and bacterial laccases are extensively explored and addressed. Recently many studies have focused on the significance of plant laccase, particularly in crop yield, and its functions in different environmental conditions. This review summarizes the transcriptional and posttranscriptional regulation of plant laccase genes and their functions in plant growth and development. It especially describes the responses of laccase genes to various stresses and their contributions to plant biotic and abiotic stress resistance. In-depth explanations and scientific advances will serve as foundations for research into plant laccase genes' function, mechanism, and possible applications.

Silicon in action: Between iron scarcity and excess copper

Essential micronutrients belonging to the transition metals, such as Fe and Cu, are indispensable for plant growth and stress tolerance; however, when present in excess, they can become potentially dangerous producers of reactive oxygen species. Therefore, their homeostases must be strictly regulated. Both microelement deficiencies and elevated concentrations of heavy metals in the soil are global problems that reduce the nutritional value of crops and seriously affect human health. Silicon, a beneficial element known for its protective properties, has been reported to alleviate the symptoms of Cu toxicity and Fe deficiency stress in plants; however, we are still far from a comprehensive understanding of the underlying molecular mechanisms. Although Si-mediated mitigation of these stresses has been clearly demonstrated for some species, the effects of Si vary depending on plant species, growing conditions and experimental design. In this review, the proposed mechanistic models explaining the effect of Si are summarized and discussed. Iron and copper compete for the common metal transporters and share the same transport routes, hence, inadequate concentration of one element leads to disturbances of another. Silicon is reported to beneficially influence not only the distribution of the element supplied below or above the optimal concentration, but also the distribution of other microelements, as well as their molar ratios. The influence of Si on Cu immobilization and retention in the root, as well as Si-induced Fe remobilization from the source to the sink organs are of vital importance. The changes in cellular Cu and Fe localization are considered to play a crucial role in restoring homeostasis of these microelements. Silicon has been shown to stimulate the accumulation of metal chelators involved in both the mobilization of deficient elements and scavenging excess heavy metals. Research into the mechanisms of the ameliorative effects of Si is valuable for reducing mineral stress in plants and improving the nutritional value of crops. This review aims to provide a thorough and critical overview of the current state of knowledge in this field and to discuss discrepancies in the observed effects of Si and different views on its mode of action.

Sly-miR398 Participates in Cadmium Stress Acclimation by Regulating Antioxidant System and Cadmium Transport in Tomato (Solanum lycopersicum)

Cadmium (Cd) pollution is one of the major threats in agricultural production, and can cause oxidative damage and growth limitation in plants. MicroRNA398 (miR398) is involved in plant resistance to different stresses, and the post-transcriptional regulation of miR398 on CSDs plays a key role. Here, we report that miR398 was down-regulated in tomato in response to Cd stress. Simultaneously, CSD1 and SOD were up-regulated, with CSD2 unchanged, suggesting CSD1 is involved in miR398-induced regulation under Cd stress. In addition, the role of miR398 in Cd tolerance in tomato was evaluated using a transgenic line overexpressing MIR398 (miR398#OE) in which the down-expression of miR398 was disrupted. The results showed that Cd stress induced more significant growth inhibition, oxidative damage, and antioxidant enzymes disorder in miR398#OE than that in wild type (WT). Moreover, higher Cd concentration in the shoot and xylem sap, and net Cd influx rate, were observed in miR398#OE, which could be due to the increased Cd uptake genes (IRT1, IRT2, and NRAMP2) and decreased Cd compartmentalization gene HMA3. Overall, our results indicate that down-regulated miR398 plays a protective role in tomato against Cd stress by modulating the activity of antioxidant enzymes and Cd uptake and translocation.

Recent Insights into Plant miRNA Biogenesis: Multiple Layers of miRNA Level Regulation

MicroRNAs are small RNAs, 20-22 nt long, the main role of which is to downregulate gene expression at the level of mRNAs. MiRNAs are fundamental regulators of plant growth and development in response to internal signals as well as in response to abiotic and biotic factors. Therefore, the deficiency or excess of individual miRNAs is detrimental to particular aspects of a plant's life. In consequence, the miRNA levels must be appropriately adjusted. To obtain proper expression of each miRNA, their biogenesis is controlled at multiple regulatory layers. Here, we addressed processes discovered to influence miRNA steady-state levels, such as MIR transcription, co-transcriptional pri-miRNA processing (including splicing, polyadenylation, microprocessor assembly and activity) and miRNA-encoded peptides synthesis. MiRNA stability, RISC formation and miRNA export out of the nucleus and out of the plant cell also define the levels of miRNAs in various plant tissues. Moreover, we show the evolutionary conservation of miRNA biogenesis core proteins across the plant kingdom.

Genome-wide analysis of the laccase gene family in wheat and relationship with arbuscular mycorrhizal colonization

We identified 156 laccase genes belonging to 11 subfamilies in the wheat genome, and the natural variation of laccase genes significantly affected the development of wheat-arbuscular mycorrhizal symbiosis. Laccases (LACs) have a variety of functions in plant lignification, cell elongation and stress responses. This study aimed to reveal the phylogeny, chromosomal spatial distribution, coexpression and evolution of LAC genes in the wheat genome and to investigate the possible roles of LAC genes during arbuscular mycorrhizal (AM) symbiosis. The genomic characteristics of LAC genes were analyzed by using bioinformatics analysis methods, and the polymorphisms of LAC genes were analyzed by using a diverse wheat panel composed of 289 wheat cultivars. We identified 156 LAC genes belonging to 11 subfamilies in the wheat genome, and segmental duplication dominated the amplification of the LAC gene family in the wheat genome. LACs are dominantly located in the R2 region of wheat chromosomes. Some LACs are collinear with the characterized LACs in Arabidopsis thaliana or rice. A number of genes encoding transcription factors, kinases, and phosphatases were coexpressed with LAC genes in wheat. TaLACs may be potential targets for some miRNAs. Most TaLACs are mainly expressed in the roots and stems of plants. The expression of TaLACs could be regulated by the inoculation of Fusarium graminearum or AM fungi. The polymorphisms of TaLACs mainly accumulate by random drift instead of by selection. Through candidate gene association analysis, we found that the natural variations in TaLACs significantly affected root colonization by AM fungi. The present study provides useful information for further study of the biological functions of LAC genes in wheat, especially the roles of LAC genes during the development of AM symbiosis.

Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation

Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.

Identification of microRNAs responsive to arbuscular mycorrhizal fungi in Panicum virgatum (switchgrass)

BACKGROUND

MicroRNAs (miRNAs) are important post-transcriptional regulators involved in the control of a range of processes, including symbiotic interactions in plants. MiRNA involvement in arbuscular mycorrhizae (AM) symbiosis has been mainly studied in model species, and our study is the first to analyze global miRNA expression in the roots of AM colonized switchgrass (Panicum virgatum), an emerging biofuel feedstock. AM symbiosis helps plants gain mineral nutrition from the soil and may enhance switchgrass biomass production on marginal lands. Our goals were to identify miRNAs and their corresponding target genes that are controlling AM symbiosis in switchgrass.

RESULTS

Through genome-wide analysis of next-generation miRNA sequencing reads generated from switchgrass roots, we identified 122 mature miRNAs, including 28 novel miRNAs. By comparing miRNA expression profiles of AM-inoculated and control switchgrass roots, we identified 15 AM-responsive miRNAs across lowland accession "Alamo", upland accession "Dacotah", and two upland/lowland F₁ hybrids. We used degradome sequencing to identify target genes of the AM-responsive miRNAs revealing targets of miRNAs residing on both K and N subgenomes. Notably, genes involved in copper ion binding were targeted by downregulated miRNAs, while upregulated miRNAs mainly targeted GRAS family transcription factors.

CONCLUSION

Through miRNA analysis and degradome sequencing, we revealed that both upland and lowland switchgrass genotypes as well as upland-lowland hybrids respond to AM by altering miRNA expression. We demonstrated complex GRAS transcription factor regulation by the miR171 family, with some miR171 family members being AM responsive while others remained static. Copper miRNA downregulation was common amongst the genotypes tested and we identified superoxide dismutases and laccases as targets, suggesting that these Cu-miRNAs are likely involved in ROS detoxification and lignin deposition, respectively. Other prominent targets of the Cu miRNAs were blue copper proteins. Overall, the potential effect of AM colonization on lignin deposition pathways in this biofuel crop highlights the importance of considering AM and miRNA in future biofuel crop development strategies.

Plant responses to metals stress: microRNAs in focus

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

Energy status-promoted growth and development of Arabidopsis require copper deficiency response transcriptional regulator SPL7

Copper (Cu) is a cofactor of around 300 Arabidopsis proteins, including photosynthetic and mitochondrial electron transfer chain enzymes critical for adenosine triphosphate (ATP) production and carbon fixation. Plant acclimation to Cu deficiency requires the transcription factor SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE7 (SPL7). We report that in the wild type (WT) and in the spl7-1 mutant, respiratory electron flux via Cu-dependent cytochrome c oxidase is unaffected under both normal and low-Cu cultivation conditions. Supplementing Cu-deficient medium with exogenous sugar stimulated growth of the WT, but not of spl7 mutants. Instead, these mutants accumulated carbohydrates, including the signaling sugar trehalose 6-phosphate, as well as ATP and NADH, even under normal Cu supply and without sugar supplementation. Delayed spl7-1 development was in agreement with its attenuated sugar responsiveness. Functional TARGET OF RAPAMYCIN and SNF1-RELATED KINASE1 signaling in spl7-1 argued against fundamental defects in these energy-signaling hubs. Sequencing of chromatin immunoprecipitates combined with transcriptome profiling identified direct targets of SPL7-mediated positive regulation, including Fe SUPEROXIDE DISMUTASE1 (FSD1), COPPER-DEFICIENCY-INDUCED TRANSCRIPTION FACTOR1 (CITF1), and the uncharacterized bHLH23 (CITF2), as well as an enriched upstream GTACTRC motif. In summary, transducing energy availability into growth and reproductive development requires the function of SPL7. Our results could help increase crop yields, especially on Cu-deficient soils.

MicroRNA398: A Master Regulator of Plant Development and Stress Responses

MicroRNAs (miRNAs) play crucial roles in plant development and stress responses, and a growing number of studies suggest that miRNAs are promising targets for crop improvement because they participate in the regulation of diverse, important agronomic traits. MicroRNA398 (miR398) is a conserved miRNA in plants and has been shown to control multiple stress responses and plant growth in a variety of species. There are many studies on the stress response and developmental regulation of miR398. To systematically understand its function, it is necessary to summarize the evolution and functional roles of miR398 and its target genes. In this review, we analyze the evolution of miR398 in plants and outline its involvement in abiotic and biotic stress responses, in growth and development and in model and non-model plants. We summarize recent functional analyses, highlighting the role of miR398 as a master regulator that coordinates growth and diverse responses to environmental factors. We also discuss the potential for fine-tuning miR398 to achieve the goal of simultaneously improving plant growth and stress tolerance.

Recovery after deficiency: systemic copper prioritization and partitioning in the leaves and stems of hybrid poplar

Copper (Cu) is important for many aspects of plant function including photosynthesis. It has been suggested that photosynthesis, especially in young leaves, is prioritized for Cu delivery after deficiency in hybrid poplar. To determine relative Cu delivery prioritization, we enriched hydroponic plant growth media of Cu-deficient poplar with 98% 65Cu and tracked Cu delivery after deficiency to young leaves, mature leaves and stems. Young leaves acquired ~58% more 65Cu on Day 1 and ~65% more 65Cu by Day 3 compared with mature leaves. Additionally, stomatal conductance (gs) was measured on leaves for 6 weeks and during a 3-day 65Cu pulse resupply period. During deficiency, mature leaves maintained a higher gs than younger leaves but 3 days after Cu resupply the younger leaves that had recovered showed the highest gs. In conclusion, these results provide a quantitative understanding of how Cu is systemically transported and distributed to photosynthetic and stem tissues.

Integrated breeding approaches to enhance the nutritional quality of food legumes

Global food security, both in terms of quantity and quality remains as a challenge with the increasing population. In parallel, micronutrient deficiency in the human diet leads to malnutrition and several health-related problems collectively known as "hidden hunger" more prominent in developing countries around the globe. Biofortification is a potential tool to fortify grain legumes with micronutrients to mitigate the food and nutritional security of the ever-increasing population. Anti-nutritional factors like phytates, raffinose (RFO's), oxalates, tannin, etc. have adverse effects on human health upon consumption. Reduction of the anti-nutritional factors or preventing their accumulation offers opportunity for enhancing the intake of legumes in diet besides increasing the bioavailability of micronutrients. Integrated breeding methods are routinely being used to exploit the available genetic variability for micronutrients through modern "omic" technologies such as genomics, transcriptomics, ionomics, and metabolomics for developing biofortified grain legumes. Molecular mechanism of Fe/Zn uptake, phytate, and raffinose family oligosaccharides (RFOs) biosynthesis pathways have been elucidated. Transgenic, microRNAs and genome editing tools hold great promise for designing nutrient-dense and anti-nutrient-free grain legumes. In this review, we present the recent efforts toward manipulation of genes/QTLs regulating biofortification and Anti-nutrient accumulation in legumes using genetics-, genomics-, microRNA-, and genome editing-based approaches. We also discuss the success stories in legumes enrichment and recent advances in development of low Anti-nutrient lines. We hope that these emerging tools and techniques will expedite the efforts to develop micronutrient dense legume crop varieties devoid of Anti-nutritional factors that will serve to address the challenges like malnutrition and hidden hunger.

S-Adenosyl-L-Methionine and Cu(II) Impact Green Plant Regeneration Efficiency

The biological improvement of triticale, a cereal of increasing importance in agriculture, may be accelerated via the production of doubled haploid lines using in vitro culture. Among the relevant factors affecting the culture efficiency are Cu(II) or Ag(I) acting, e.g., as cofactors of enzymes. The copper ions are known to positively affect green plant regeneration efficiency. However, the biochemical basis, mainly its role in the generation of in vitro-induced genetic and epigenetic variation and green plant regeneration efficiency, is not well understood. Here, we employed structural equation modeling to evaluate the relationship between de novo DNA methylation affecting the asymmetric context of CHH sequences, the methylation-sensitive Amplified Fragment Length Polymorphism related sequence variation, and the concentration of Cu(II) and Ag(I) ions in induction media, as well as their effect on S-adenosyl-L-methionine perturbations, observed using FTIR spectroscopy, and the green plant regeneration efficiency. Our results allowed the construction of a theory-based model reflecting the biological phenomena associated with green plant regeneration efficiency. Furthermore, it is shown that Cu(II) ions in induction media affect plant regeneration, and by manipulating their concentration, the regeneration efficiency can be altered. Additionally, S-adenosyl-L-methionine is involved in the efficiency of green plant regeneration through methylation of the asymmetric CHH sequence related to de novo methylation. This shows that the Yang cycle may impact the production of green regenerants.

The MicroRNA397a-LACCASE17 module regulates lignin biosynthesis in Medicago ruthenica (L.)

Mechanical strength is essential for the upright growth habit, which is one of the most important characteristics of terrestrial plants. Lignin, a phenylpropanoid-derived polymer mainly present in secondary cell walls plays critical role in providing mechanical support. Here, we report that the prostrate-stem cultivar of the legume forage Medicago ruthenica cultivar 'Mengnong No. 1' shows compromised mechanical strength compared with the erect-stem cultivar 'Zhilixing'. The erect-stem cultivar, 'Zhilixing' has significantly higher lignin content, leading to higher mechanical strength than the prostrate-stem cultivar. The low abundance of miRNA397a in the Zhiixing cultivar causes reduced cleavage of MrLAC17 transcript, which results in enhanced expression level of MrLAC17 compared to that in the prostrate-stem cultivar Mengnong No. 1. Complementation of the Arabidopsis lac4 lac17 double mutants with MrLAC17 restored the lignin content to wild-type levels, confirming that MrLAC17 perform an exchangeable role with Arabidopsis laccases. LAC17-mediated lignin polymerization is therefore increased in the 'Zhilixing', causing the erect stem phenotype. Our data reveal the importance of the miR397a in the lignin biosynthesis and suggest a strategy for molecular breeding targeting plant architecture in legume forage.

microRNAs: Key Players in Plant Response to Metal Toxicity

Environmental metal pollution is a common problem threatening sustainable and safe crop production. Heavy metals (HMs) cause toxicity by targeting key molecules and life processes in plant cells. Plants counteract excess metals in the environment by enhancing defense responses, such as metal chelation, isolation to vacuoles, regulating metal intake through transporters, and strengthening antioxidant mechanisms. In recent years, microRNAs (miRNAs), as a small non-coding RNA, have become the central regulator of a variety of abiotic stresses, including HMs. With the introduction of the latest technologies such as next-generation sequencing (NGS), more and more miRNAs have been widely recognized in several plants due to their diverse roles. Metal-regulated miRNAs and their target genes are part of a complex regulatory network. Known miRNAs coordinate plant responses to metal stress through antioxidant functions, root growth, hormone signals, transcription factors (TF), and metal transporters. This article reviews the research progress of miRNAs in the stress response of plants to the accumulation of HMs, such as Cu, Cd, Hg, Cr, and Al, and the toxicity of heavy metal ions.

An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism

The present review highlights the regulatory roles of microRNAs in plant secondary metabolism and focuses on different bioengineering strategies to modulate secondary metabolite content in plants. MicroRNAs (miRNAs) are the class of small endogenous, essential, non-coding RNAs that riboregulate the gene expression involved in various biological processes in most eukaryotes. MiRNAs has emerged as important regulators in plants that function by silencing target genes through cleavage or translational inhibition. These miRNAs plays an important role in a wide range of plant biological and metabolic processes, including plant development and various environmental response controls. Several important plant secondary metabolites like alkaloids, terpenoids, and phenolics are well studied for their function in plant defense against different types of pests and herbivores. Due to the presence of a wide range of biological and pharmaceutical properties of plant secondary metabolites, it is important to study the regulation of their biosynthetic pathways. The contribution of miRNAs in regulating plant secondary metabolism is not well explored. Recent advancements in molecular techniques have improved our knowledge in understanding the molecular function of genes, proteins, enzymes, and small RNAs involved in different steps of secondary metabolic pathways. In the present review, we have discussed the recent progress made on miRNA biogenesis, its regulation, and highlighted the current research developed in the field of identification, analysis, and characterizations of various miRNAs that regulate plant secondary metabolism. We have also discussed how different bioengineering strategies such as artificial miRNA (amiRNA), endogenous target mimicry, and CRISPR/Cas9 could be utilized to enhance the secondary metabolite production in plants.

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

Lignans, as secondary metabolites synthesized within a phenylpropanoid pathway, play various roles in plants, including their involvement in growth and plant defense processes. The health and nutritional benefits of lignans are unquestionable, and many studies have been devoted to these attributes. Although the regulatory role of miRNAs in the biosynthesis of secondary metabolites has been widely reported, there is no systematic review available on the miRNA-based regulatory mechanism of lignans biosynthesis. However, the genetic background of lignan biosynthesis in plants is well characterized. We attempted to put together a regulatory mosaic based on current knowledge describing miRNA-mediated regulation of genes, enzymes, or transcription factors involved in this biosynthesis process. At the same time, we would like to underline the fact that further research is necessary to improve our understanding of the miRNAs regulating plant lignan biosynthesis by exploitation of current approaches for functional identification of miRNAs.

CITF1 Functions Downstream of SPL7 to Specifically Regulate Cu Uptake in Arabidopsis

Copper (Cu) is one of the most indispensable micronutrients, and proper Cu homeostasis is required for plants to maintain essential cellular functions. Plants activate the Cu uptake system during Cu limitation. Although SPL7 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 7) and CITF1 (Cu-DEFICIENCY INDUCED TRANSCRIPTION FACTOR 1) are two transcription factors in Cu homeostasis, it remains unclear how SPL7 and CITF1 control the Cu uptake system. Here, we reveal that overexpression of CITF1 causes the enhanced tolerance to Cu deficiency and the elevated expression of Cu uptake genes COPT2, FRO4 and FRO5. Electrophoretic mobility shift assays (EMSA) and transient expression assays indicate that SPL7 directly binds to and activates the promoter of CITF1. The overexpression of CITF1 partially rescues the sensitivity of spl7-1 to Cu deficiency. Transcriptome data suggest that SPL7 and CITF1 coregulate the Cu-homeostasis-signaling network, and CITF1 has its own independent functions. Moreover, both SPL7 and CITF1 can directly bind to and activate the promoters of three Cu uptake genes COPT2, FRO4 and FRO5. This work shows the functions of CITF1 in the Cu-homeostasis-signaling network, providing insights into the complicated molecular mechanism underlying Cu homeostasis.

Explosive seed dispersal depends on SPL7 to ensure sufficient copper for localized lignin deposition via laccases

The sudden explosion of seed pods in popping cress (Cardamine hirsuta) takes less than 3 ms to accelerate seeds away from the plant. This explosive mechanism relies on polar deposition of the cell-wall polymer lignin. To investigate the genetic basis for polar lignin deposition, we conducted a mutant screen and identified SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 7 (SPL7)—a transcriptional regulator of copper homeostasis. We discovered three multicopper laccases, LAC4, 11, and 17, that precisely colocalize with, and are required for, the polar deposition of lignin in explosive seed pods. Activity of these three laccases depends on SPL7 to acclimate to copper deficiency. Our findings demonstrate how mineral nutrition is integrated with polar lignin deposition to facilitate dispersal.

Exploding seed pods evolved in the Arabidopsis relative Cardamine hirsuta via morphomechanical innovations that allow the storage and rapid release of elastic energy. Asymmetric lignin deposition within endocarpb cell walls is one such innovation that is required for explosive seed dispersal and evolved in association with the trait. However, the genetic control of this novel lignin pattern is unknown. Here, we identify three lignin-polymerizing laccases, LAC4, 11, and 17, that precisely colocalize with, and are redundantly required for, asymmetric lignification of endocarpb cells. By screening for C. hirsuta mutants with less lignified fruit valves, we found that loss of function of the transcription factor gene SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 7 (SPL7) caused a reduction in endocarpb cell-wall lignification and a consequent reduction in seed dispersal range. SPL7 is a conserved regulator of copper homeostasis and is both necessary and sufficient for copper to accumulate in the fruit. Laccases are copper-requiring enzymes. We discovered that laccase activity in endocarpb cell walls depends on the SPL7 pathway to acclimate to copper deficiency and provide sufficient copper for lignin polymerization. Hence, SPL7 links mineral nutrition to efficient dispersal of the next generation.

Insights into the Response of Perennial Ryegrass to Abiotic Stress: Underlying Survival Strategies and Adaptation Mechanisms

Perennial ryegrass (Lolium perenne L.) is an important turfgrass and gramineous forage widely grown in temperate regions around the world. However, its perennial nature leads to the inevitable exposure of perennial ryegrass to various environmental stresses on a seasonal basis and from year to year. Like other plants, perennial ryegrass has evolved sophisticated mechanisms to make appropriate adjustments in growth and development in order to adapt to the stress environment at both the physiological and molecular levels. A thorough understanding of the mechanisms of perennial ryegrass response to abiotic stresses is crucial for obtaining superior stress-tolerant varieties through molecular breeding. Over the past decades, studies of perennial ryegrass at the molecular and genetic levels have revealed a lot of useful information to understand the mechanisms of perennial ryegrass adaptation to an adverse environment. Unfortunately, molecular mechanisms by which perennial ryegrass adapts to abiotic stresses have not been reviewed thus far. In this review, we summarize the recent works on the genetic and molecular mechanisms of perennial ryegrass response to the major abiotic stresses (i.e., drought, salinity, and extreme temperatures) and discuss new directions for future studies. Such knowledge will provide valuable information for molecular breeding in perennial ryegrass to improve stress resistance and promote the sustainability of agriculture and the environment.

Genome-Wide Identification and Transcript Analysis Reveal Potential Roles of Oligopeptide Transporter Genes in Iron Deficiency Induced Cadmium Accumulation in Peanut

The oligopeptide transporter (OPT) family is a group of proton-coupled symporters that play diverse roles, including metal homeostasis. However, little is known about this family of peanuts. To reveal the potential roles of AhOPT genes in Fe/Cd interactions, peanut AhOPT genes were genome-widely identified, and the relationships between gene expression and Cd accumulation were detected in two contrasting peanut cultivars (Fenghua 1 and Silihong) under Fe-sufficient or Fe-deficient conditions. A total of 40 AhOPT genes were identified in peanuts, which were divided into two subfamilies (PT and YS). Most AhOPT genes underwent gene duplication events predominated by whole-genome duplication. Clustered members generally have similar protein structures. However, gene structural divergences occurred in most of the duplicated genes. Transcription analysis revealed that AhOPT3.2/3.4 and AhYSL3.1/3.2 might be responsible for Fe deficiency tolerance, while AhOPT3.1/3.4, AhOPT7.1/7.2, and AhYSL1.1 be involved in Fe/Cd interactions. These genes might be regulated by transcription factors, including ATHB-12, ATHB-6, DIVARICATA, MYB30, NAC02, DOF3.4, IDD7, and LUX. Reduced expressions of AhYSL3.1/3.2 and higher expressions of AhOPT3.4 might contribute to higher Fe-deficiency tolerance in Silihong. Higher expression of AhOPT7.3 and AhOPT6.1 might be responsible for low Cd accumulation in Fenghua 1. Our results confirmed that AhOPT3/6/7 and AhYSL1/3 might be involved in the transport of Fe and/or Cd in peanuts and provided new clues to understanding potential mechanisms of Fe/Cd interactions.

The molecular basis of zinc homeostasis in cereals

Plants require zinc (Zn) as an essential cofactor for diverse molecular, cellular and physiological functions. Zn is crucial for crop yield, but is one of the most limiting micronutrients in soils. Grasses like rice, wheat, maize and barley are crucial sources of food and nutrients for humans. Zn deficiency in these species therefore not only reduces annual yield but also directly results in Zn malnutrition of more than two billion people in the world. There has been good progress in understanding Zn homeostasis and Zn deficiency mechanisms in plants. However, our current knowledge of monocots, including grasses, remains insufficient. In this review, we provide a summary of our knowledge of molecular Zn homeostasis mechanisms in monocots, with a focus on important cereal crops. We additionally highlight divergences in Zn homeostasis of monocots and the dicot model Arabidopsis thaliana, as well as important gaps in our knowledge that need to be addressed in future research on Zn homeostasis in cereal monocots.

miR398 Attenuates Heat-Induced Leaf Cell Death via Its Target CSD1 in Chinese Cabbage

Previous research has shown that miR398 contributed to plant thermotolerance by silencing its target gene COPPER/ZINC SUPEROXIDE DISMUTASE1 (CSD1) in Arabidopsis thaliana. However, the phylogenesis of miR398 and CSD1 in Brassica crop and their role in regulating leaf cell death under heat stress remains unexplored. Here, we characterized the homologous genes of miR398a and CSD1 in Brassica rapa ssp. pekinensis (Chinese cabbage) and found miR398a abundance was accumulated under heat stress (38 °C and 46 °C for 1 h) in Chinese cabbage, while the expression level of its targets BraCSD1-1 and BraCSD2-1 were downregulated. To further explore their role in heat response, we constructed the transgenic plants overexpressing artificial miR398a (aBra-miR398a), Bra-miR398a target mimic (Bra-MIM398a), and BraCSD1-1 in Chinese cabbage for genetic study. Under high temperatures, p35S::aBra-miR398a lines reduced the areas of leaf cell death and delayed the leaf cell death. By contrast, p35S::Bra-MIM398a and p35S::BraCSD1-1 plants enlarged the areas of leaf cell death and displayed the earliness of leaf cell death. Finally, we found that the expression level of stress-responsive genes BraLEA76, BraCaM1, BraPLC, BraDREB2A, and BraP5CS increased in transgenic plants overexpressing aBra-miR398a, which may contribute to their resistance to heat-induced leaf cell death. Taken together, these results revealed the function of Bra-miR398a in attenuating leaf cell death to ensure plant thermotolerance, indicating that the miR398-CSD1 module could be potential candidates for heat-resistant crop breeding.