Heavy metal-associated isoprenylated plant protein (HIPP): characterization of a family of proteins exclusive to plants

Copper excess transcriptional responses in roots of grapevine (Vitis sp.) rootstocks

Copper (Cu) is an essential element for plants, participating in photosynthesis, oxidative metabolism and cell wall synthesis. However, excessive Cu may become toxic, as Cu participates in Fenton chemistry and cause oxidative stress. Grapevine (Vitis sp.) is an important perennial crop, used for in natura consumption as well as for wine and juice. Vineyards are susceptible to fungal diseases that are commonly controlled by using Cu-based fungicides, which can lead to Cu accumulation in the soil. Since grape production is based on grafting scions of consumed-friendly varieties onto rootstocks that can withstand soil-borne diseases and stresses, it is important to identify rootstock genotypes that are tolerant to Cu excess. In this work, we compared physiological and molecular responses of four Vitis sp. rootstock genotypes to Cu excess, namely IAC, IBCA, Paulsen and Isabel. While IAC, IBCA, Paulsen were similarly tolerant, Isabel was the most sensitive to Cu excess. IAC and IBCA showed higher Cu accumulation in shoots, suggesting distinct partitioning strategy. We identified core Cu excess-responsive genes in grapevine roots of all four genotypes, including a putative HMA vacuolar Cu transporter and Cu-binding proteins. Genes related to the homeostasis of other elements are altered, such as iron (Fe) and phosphorus (P), suggesting that Cu excess alters the ionome balance. IAC and IBCA had extensive changes in their laccase gene repertoire, suggesting that could be related to the distinct Cu partitioning. Moreover, genes associated specifically with Isabel could be related to the genotype Cu excess sensitivity. Our work provides a valuable dataset for understanding variation in Cu tolerance how roots respond transcriptionally to Cu stress, and provide candidate genes for engineering Cu tolerance in grapevines.

Foliar application of zinc and selenium regulates cell wall fixation, physiological and gene expression to reduce cadmium accumulation in rice grains

Zinc (Zn) and selenium (Se) are beneficial elements for crops, enhancing crop quality and alleviating heavy metal toxicity. However, there is limited research on the role of foliar Zn and Se in the mechanism of reducing cadmium (Cd) uptake in crops. A field experiment was conducted to investigate the effect on subcellular distribution, leaf antioxidant enzyme activities, and the transcriptional regulation in the process of Cd accumulation of rice grains after foliar applications of Zn, Se, and their mixed solutions (ZnSe). The results show that Zn and ZnSe reduced Cd content in the grains of three different rice (13.9 %-21.8 %/11.9 %-29.5 %) by enhancing the fixation capacity of Cd in the flag leaf by improving the binding efficiency between pectin and Cd in the cell wall. Increased flag leaf antioxidant enzyme activities further mitigated the toxic effects of Cd on rice, while Zn and ZnSe treatments upregulated genes related to metal-binding proteins and antioxidant enzymes and downregulated metal transport genes. This study systematically elucidates the mechanisms by which foliar application of ZnSe alleviates Cd toxicity through the regulation of gene expression and physiological functions, providing a theoretical basis for reducing Cd accumulation in rice and ensuring the safe production of food.

The blast pathogen effector AVR-Pik binds and stabilizes rice heavy metal-associated (HMA) proteins to co-opt their function in immunity

Intracellular nucleotide-binding domain and leucine-rich repeat-containing (NLR) receptors play crucial roles in immunity across multiple domains of life. In plants, a subset of NLRs contain noncanonical integrated domains that are thought to have evolved from host targets of pathogen effectors to serve as pathogen baits. However, the functions of host proteins with similarity to NLR integrated domains and the extent to which they are targeted by pathogen effectors remain largely unknown. Here, we show that the blast fungus effector AVR-Pik binds a subset of related rice proteins containing a heavy metal-associated (HMA) domain, one of the domains that has repeatedly integrated into plant NLR immune receptors. We find that AVR-Pik binding stabilizes the rice small HMA (sHMA) proteins OsHIPP19 and OsHIPP20. Knockout of OsHIPP20 causes enhanced disease resistance towards the blast pathogen, indicating that OsHIPP20 is a susceptibility gene (S-gene). We propose that AVR-Pik has evolved to bind HMA domain proteins and co-opt their function to suppress immunity. Yet this binding carries a trade-off, it triggers immunity in plants carrying NLR receptors with integrated HMA domains.

Molecular identification and expression patterns of sweet cherry HIPPs and functional analysis of PavHIPP16 in cold stress

MAIN CONCLUSION

The HIPP proteins are involved in low-temperature stress, the growth of sweet cherry, and may be potential targets for genetic improvement. PavHIPP16 improved cold resistance in Arabidopsis. In response to abiotic stressors, the heavy metal-associated isoprenylated plant protein (HIPP) proteins play a crucial regulatory role. Although the function of HIPP has been identified in some plants, there have been fewer systematic studies conducted on sweet cherry (Prunus avium L.). Therefore, we performed a comprehensive analysis and expression profiling of PavHIPPs using bioinformatics, RT-PCR, and qRT-PCR techniques. Our findings revealed that 28 PavHIPP genes were unevenly distributed across eight chromosomes. We predicted nine motifs in PavHIPP proteins and observed similar gene structures among highly homologous proteins. The promoter sequences of PavHIPPs contained numerous regulatory elements associated with an adversity of stress. The expression levels of some members showed varying degrees of change under low-temperature treatment. These genes were differentially expressed during flower and fruit development. Arabidopsis overexpressing the PavHIPP16 (OE) gene showed significantly lower relative conductivity and malondialdehyde (MDA) content compared with the wild-type (WT) plants under cold environment. Conversely, peroxidase (POD) activity, superoxide dismutase (SOD) activity, and proline content were significantly higher in OE Arabidopsis than in WT plants. Overall, our results suggest that PavHIPP16 OE Arabidopsis thaliana exhibited enhanced adaptability compared to WT plants under cold conditions. This study provides a foundation for future investigations of the pathways regulating sweet cherry growth and development mediated by the HIPP genes.

Genome-wide identification of HIPP and mechanism of SlHIPP4/7/9/21/26/32 mediated phytohormones response to Cd, osmotic, and salt stresses in tomato

Heavy-metal-associated isoprenylated plant proteins (HIPPs) contributed to abiotic tolerance in vascular plants. Up to now, the HIPP gene family of tomato (Solanum lycopersicum L.) had not been thoroughly understood. In the present study, 34 SlHIPP genes were identified from the tomato genome using the Hidden Markov Model (HMM). The phylogenetic analysis revealed that the evolution of SlHIPPs was highly conserved. The cis-acting element analysis indicated that SlHIPP genes might be involved in phytohormones and abiotic stresses. We constructed venn diagram with 17 genes containing stress-related motifs as well as 15 genes and 19 genes expressing in leaves and roots in RNA-seq data, suggesting that SlHIPP4/7/9/21/26/32 were selected as candidate genes for study. The quantitative real-time PCR (qRT-PCR) analysis showed that 6 candidate genes were indicated to be involved in osmotic and salt stress tolerance and SlHIPP7/21/26/32 responded to cadmium (Cd) tolerance. The virus-induced silencing of 6 candidate genes caused growth inhibition in stress conditions, further illustrating that 6 candidate genes played a positive role in abiotic conditions. Importantly, the phytohormone analysis implied that 6 candidate genes mediated abscisic acid (ABA), salicylic acid (SA), gibberellin (GA3), auxin (IAA), or methyl jasmonate (MeJA) response to Cd, osmotic, or salt stress tolerance. These findings indicated that SlHIPP4/7/9/21/26/32 were key regulators of abiotic stress responses in tomato seedlings, functioning through multiple phytohormone pathways.

Ellagic acid alleviates aluminum and/or drought stress through morpho-physiochemical adjustments and stress-related gene expression in Zea mays L

This study investigates the potential of ellagic acid (EA) to mitigate the effects of drought and aluminum (Al3+) stresses in maize by examining various morpho-physiochemical parameters and gene expressions. Maize (Zea mays L.) serves as a crucial global food source, but its growth and productivity are significantly hindered by drought and aluminum (Al3+) stresses, which lead to impaired root development, elevated levels of reactive oxygen species (ROS), diminished photosynthetic efficiency, and reduced water and mineral absorption. Recently, ellagic acid (EA), a polyphenolic compound with potent antioxidant properties, has been identified for its role in regulating plant growth and enhancing stress tolerance mechanisms. However, the specific mechanisms through which EA contributes to Al3+ and/or drought tolerance in plants remain largely unknown. The present study was conducted to examine the defensive role of EA (100 μg/mL) in some morpho-physiochemical parameters and the expression profiles of some stress-related genes (ZmCPK22, ZmXTH1, ZmHIPP4, ZmSGR, ZmpsbA, ZmAPX1, and ZmGST1) in drought (polyethylene glycol-6000 (PEG-6000), - 0.6 MPa) and aluminum chloride (AlCl3, 60 μM) stressed Zea mays Ada 523 grown in nutrient solution. Our results indicated that drought and aluminum chloride stresses affected root length, shoot height, H2O2 content, chlorophyll content (SPAD), electrolyte leakage (EL), and relative water content (RWC) of maize with several significant (P < 0.05) shifts up and down. Conversely, EA (100 μg/mL) treatment had a mitigating effect on these parameters. Moreover, EA also mitigated the antioxidant enzyme activities (superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX)), and regulated the expressions of aforementioned genes. These findings determined that EA treatment could efficiently improve the gene expressions and morpho-physiochemical parameters under drought and/or Al3+ stresses, thereby increasing the seedlings' adaptability to these stresses.

Transcriptomic and physiological responses of Quercus acutissima and Quercus palustris to drought stress and rewatering

Establishment of oak seedlings, which is an important factor in forest restoration, is affected by drought that hampers the survival, growth, and development of seedlings. Therefore, it is necessary to understand how seedlings respond to and recover from water-shortage stress. We subjected seedlings of two oak species, Quercus acutissima and Quercus palustris, to drought stress for one month and then rewatered them for six days to observe physiological and genetic expression changes. Phenotypically, the growth of Q. acutissima was reduced and severe wilting and recovery failure were observed in Q. palustris after an increase in plant temperature. The two species differed in several physiological parameters during drought stress and recovery. Although the photosynthesis-related indicators did not change in Q. acutissima, they were decreased in Q. palustris. Moreover, during drought, content of soluble sugars was significantly increased in both species, but it recovered to original levels only in Q. acutissima. Malondialdehyde content increased in both the species during drought, but it did not recover in Q. palustris after rewatering. Among the antioxidant enzymes, only superoxide dismutase activity increased in Q. acutissima during drought, whereas activities of ascorbate peroxidase, catalase, and glutathione reductase increased in Q. palustris. Abscisic acid levels were increased and then maintained in Q. acutissima, but recovered to previous levels after rewatering in Q. palustris. RNA samples from the control, drought, recovery day 1, and recovery day 6 treatment groups were compared using transcriptome analysis. Q. acutissima exhibited 832 and 1076 differentially expressed genes (DEGs) related to drought response and recovery, respectively, whereas Q. palustris exhibited 3947 and 1587 DEGs, respectively under these conditions. Gene ontology enrichment of DEGs revealed "response to water," "apoplast," and "Protein self-association" to be common to both the species. However, in the heatmap analysis of genes related to sucrose and starch synthesis, glycolysis, antioxidants, and hormones, the two species exhibited very different transcriptome responses. Nevertheless, the levels of most DEGs returned to their pre-drought levels after rewatering. These results provide a basic foundation for understanding the physiological and genetic expression responses of oak seedlings to drought stress and recovery.

Effects of N, N-bis (carboxymethyl)-L-glutamic acid and polyaspartic acid on the phytoremediation of cadmium in contaminated soil at the presence of pyrene: Biochemical properties and transcriptome analysis

Chelator-assisted phytoremediation is an efficacious method for promoting the removal efficiency of heavy metals (HMs). The effects of N, N-bis(carboxymethyl)-L-glutamic acid (GLDA) and polyaspartic acid (PASP) on Cd uptake and pyrene removal by Solanum nigrum L. (S. nigrum) were compared in this study. Using GLDA or PASP, the removal efficiency of pyrene was over 98%. And PASP observably raised the accumulation and transport of Cd by S. nigrum compared with GLDA. Meanwhile, both GLDA and PASP markedly increased soil dehydrogenase activities (DHA) and microbial activities. DHA and microbial activities in the PASP treatment group were 1.05 and 1.06 folds of those in the GLDA treatment group, respectively. Transcriptome analysis revealed that 1206 and 1684 differentially expressed genes (DEGs) were recognized in the GLDA treatment group and PASP treatment group, respectively. Most of the DEGs found in the PASP treatment group were involved in the metabolism of carbohydrates, the biosynthesis of brassinosteroid and flavonoid, and they were up-regulated. The DEGs related to Cd transport were screened, and ABCG3, ABCC4, ABCG9 and Nramp5 were found to be relevant with the reduction of Cd stress in S. nigrum by PASP. Furthermore, with PASP treated, transcription factors (TFs) related to HMs such as WRKY, bHLH, AP2/ERF, MYB were down-regulated, while more MYB and bZIP TFs were up-regulated. These TFs associated with plant stress resistance would work together to induce oxidative stress. The above results indicated that PASP was more conducive for phytoremediation of Cd-pyrene co-contaminated soil than GLDA.

Zinc Treatment of Tea Plants Improves the Synthesis of Trihydroxylated Catechins via Regulation of the Zinc-Sensitive Protein CsHIPP3

The tea plant (Camellia sinensis [L.] O. Kussntze) is a global economic crop. Zinc treatment of tea plants can enhance catechin biosynthesis. However, the underlying molecular mechanism behind catechin formation through zinc regulation remains unclear. This study identified a zinc-responsive protein, C. sinensis heavy metal-associated isoprenylated plant protein 3 (CsHIPP3), from zinc-treated tea seedlings. CsHIPP3 expression was positively correlated with trihydroxylated catechin (TRIC) content. CsF3'5'H1 is a crucial regulator of the TRIC synthesis pathway. The interaction between CsHIPP3 and CsF3'5'H1 was assessed using bimolecular fluorescence complementation, firefly luciferase complementation imaging, and pulldown experiments. CsHIPP3 knockdown using virus-induced gene silencing technology decreased the content of each component of TRICs. Compared with the control, the relative catechin content was reduced by 40.12-55.39%. Co-overexpression of CsHIPP3 and CsF3'5'H1 significantly elevated the TRIC content in tea leaves and calli. Moreover, the TRIC content in transient co-overexpression leaves was 1.44-fold higher than that of the control group, and tea callus was 50.83% higher in transient co-overexpression than in the wild type. Thus, zinc-regulated TRIC synthesis in a zinc-rich environment was mediated by binding CsHIPP3 with CsF3'5'H1 to promote TRIC synthesis and accumulation.

The soybean plasma membrane GmDR1 protein conferring broad-spectrum disease and pest resistance regulates several receptor kinases and NLR proteins

Overexpression of Glycine max disease resistant 1 (GmDR1) exhibits broad-spectrum resistance against Fusarium virguliforme, Heterodera glycines (soybean cyst nematode), Tetranychus urticae (Koch) (spider mites), and Aphis glycines Matsumura (soybean aphids) in soybean. To understand the mechanisms of broad-spectrum immunity mediated by GmDR1, the transcriptomes of a strong and a weak GmDR1-overexpressor following treatment with chitin, a pathogen- and pest-associated molecular pattern (PAMP) common to these organisms, were investigated. The strong and weak GmDR1-overexpressors exhibited altered expression of 6098 and 992 genes, respectively, as compared to the nontransgenic control following chitin treatment. However, only 192 chitin- and 115 buffer-responsive genes exhibited over two-fold changes in expression levels in both strong and weak GmDR1-overexpressors as compared to the control. MapMan analysis of the 192 chitin-responsive genes revealed 64 biotic stress-related genes, of which 53 were induced and 11 repressed as compared to the control. The 53 chitin-induced genes include nine genes that encode receptor kinases, 13 encode nucleotide-binding leucine-rich repeat (NLR) receptor proteins, seven encode WRKY transcription factors, four ethylene response factors, and three MYB-like transcription factors. Investigation of a subset of these genes revealed three receptor protein kinases, seven NLR proteins, and one WRKY transcription factor genes that are induced following F. virguliforme and H. glycines infection. The integral plasma membrane GmDR1 protein most likely recognizes PAMPs including chitin and activates transcription of genes encoding receptor kinases, NLR proteins and defense-related genes. GmDR1 could be a pattern recognition receptor that regulates the expression of several NLRs for expression of PAMP-triggered immunity and/or priming the effector triggered immunity.

Single-molecule long-read methylation profiling reveals regional DNA methylation regulated by Elongator Complex Subunit 2 in Arabidopsis roots experiencing spaceflight

BACKGROUND

The Advanced Plant Experiment-04 - Epigenetic Expression (APEX-04-EpEx) experiment onboard the International Space Station examined the spaceflight-altered cytosine methylation in two genetic lines of Arabidopsis thaliana, wild-type Col-0 and the mutant elp2-5, which is deficient in an epigenetic regulator Elongator Complex Subunit 2 (ELP2). Whole-genome bisulfite sequencing (WGBS) revealed distinct spaceflight associated methylation differences, presenting the need to explore specific space-altered methylation at single-molecule resolution to associate specific changes over large regions of spaceflight related genes. To date, tools of multiplexed targeted DNA methylation sequencing remain limited for plant genomes.

RESULTS

To provide methylation data at single-molecule resolution, Flap-enabled next-generation capture (FENGC), a novel targeted multiplexed DNA capture and enrichment technique allowing cleavage at any specified sites, was applied to survey spaceflight-altered DNA methylation in genic regions of interest. The FENGC capture panel contained 108 targets ranging from 509 to 704 nt within the promoter or gene body regions of gene targets derived from spaceflight whole-genome data sets. In addition to genes with significant changes in expression and average methylation levels between spaceflight and ground control, targets with space-altered distributions of the proportion of methylated cytosines per molecule were identified. Moreover, trends of co-methylation of different cytosine contexts were exhibited in the same DNA molecules. We further identified significant DNA methylation changes in three previously biological process-unknown genes, and loss-of-function mutants of two of these genes (named as EMO1 and EMO2 for ELP2-regulated Methylation in Orbit 1 and 2) showed enhanced root growth rate.

CONCLUSIONS

FENGC simplifies and reduces the cost of multiplexed, targeted, single-molecule profiling of methylation in plants, providing additional resolution along each DNA molecule that is not seen in population-based short-read data such as WGBS. This case study has revealed spaceflight-altered regional modification of cytosine methylation occurring within single DNA molecules of cell subpopulations, which were not identified by WGBS. The single-molecule survey by FENGC can lead to identification of novel functional genes. The newly identified EMO1 and EMO2 are root growth regulators which may be epigenetically involved in plant adaptation to spaceflight.

Rare earth elements perturb root architecture and ion homeostasis in Arabidopsis thaliana

Rare earth elements (REEs) are crucial elements for current high-technology and renewable energy advances. In addition to their increasing usage and their low recyclability leading to their release into the environment, REEs are also used as crop fertilizers. However, little is known regarding the cellular and molecular effects of REEs in plants, which is crucial for better risk assessment, crop safety and phytoremediation. Here, we analysed the ionome and transcriptomic response of Arabidopsis thaliana exposed to a light (lanthanum, La) and a heavy (ytterbium, Yb) REE. At the transcriptome level, we observed the contribution of ROS and auxin redistribution to the modified root architecture following REE exposure. We found indications for the perturbation of Fe homeostasis by REEs in both roots and leaves of Arabidopsis suggesting competition between REEs and Fe. Furthermore, we propose putative ways of entry of REEs inside cells through transporters of microelements. Finally, similar to REE accumulating species, organic acid homeostasis (e.g. malate and citrate) appears critical as a tolerance mechanism in response to REEs. By combining ionomics and transcriptomics, we elucidated essential patterns of REE uptake and toxicity response of Arabidopsis and provide new hypotheses for a better evaluation of the impact of REEs on plant homeostasis.

From genes to ecosystems: Decoding plant tolerance mechanisms to arsenic stress

Arsenic (As), a metalloid of considerable toxicity, has become increasingly bioavailable through anthropogenic activities, raising As contamination levels in groundwater and agricultural soils worldwide. This bioavailability has profound implications for plant biology and farming systems. As can detrimentally affect crop yield and pose risks of bioaccumulation and subsequent entry into the food chain. Upon exposure to As, plants initiate a multifaceted molecular response involving crucial signaling pathways, such as those mediated by calcium, mitogen-activated protein kinases, and various phytohormones (e.g., auxin, methyl jasmonate, cytokinin). These pathways, in turn, activate enzymes within the antioxidant system, which combat the reactive oxygen/nitrogen species (ROS and RNS) generated by As-induced stress. Plants exhibit a sophisticated genomic response to As, involving the upregulation of genes associated with uptake, chelation, and sequestration. Specific gene families, such as those coding for aquaglyceroporins and ABC transporters, are key in mediating As uptake and translocation within plant tissues. Moreover, we explore the gene regulatory networks that orchestrate the synthesis of phytochelatins and metallothioneins, which are crucial for As chelation and detoxification. Transcription factors, particularly those belonging to the MYB, NAC, and WRKY families, emerge as central regulators in activating As-responsive genes. On a post-translational level, we examine how ubiquitination pathways modulate the stability and function of proteins involved in As metabolism. By integrating omics findings, this review provides a comprehensive overview of the complex genomic landscape that defines plant responses to As. Knowledge gained from these genomic and epigenetic insights is pivotal for developing biotechnological strategies to enhance crop As tolerance.

Decrypting Molecular Mechanisms Involved in Counteracting Copper and Nickel Toxicity in Jack Pine (Pinus banksiana) Based on Transcriptomic Analysis

The remediation of copper and nickel-afflicted sites is challenged by the different physiological effects imposed by each metal on a given plant system. Pinus banksiana is resilient against copper and nickel, providing an opportunity to build a valuable resource to investigate the responding gene expression toward each metal. The objectives of this study were to (1) extend the analysis of the Pinus banksiana transcriptome exposed to nickel and copper, (2) assess the differential gene expression in nickel-resistant compared to copper-resistant genotypes, and (3) identify mechanisms specific to each metal. The Illumina platform was used to sequence RNA that was extracted from seedlings treated with each of the metals. There were 449 differentially expressed genes (DEGs) between copper-resistant genotypes (RGs) and nickel-resistant genotypes (RGs) at a high stringency cut-off, indicating a distinct pattern of gene expression toward each metal. For biological processes, 19.8% of DEGs were associated with the DNA metabolic process, followed by the response to stress (13.15%) and the response to chemicals (8.59%). For metabolic function, 27.9% of DEGs were associated with nuclease activity, followed by nucleotide binding (27.64%) and kinase activity (10.16%). Overall, 21.49% of DEGs were localized to the plasma membrane, followed by the cytosol (16.26%) and chloroplast (12.43%). Annotation of the top upregulated genes in copper RG compared to nickel RG identified genes and mechanisms that were specific to copper and not to nickel. NtPDR, AtHIPP10, and YSL1 were identified as genes associated with copper resistance. Various genes related to cell wall metabolism were identified, and they included genes encoding for HCT, CslE6, MPG, and polygalacturonase. Annotation of the top downregulated genes in copper RG compared to nickel RG revealed genes and mechanisms that were specific to nickel and not copper. Various regulatory and signaling-related genes associated with the stress response were identified. They included UGT, TIFY, ACC, dirigent protein, peroxidase, and glyoxyalase I. Additional research is needed to determine the specific functions of signaling and stress response mechanisms in nickel-resistant plants.

Genome-wide characterization of heavy metal-associated isoprenylated plant protein gene family from Citrus sinensis in response to huanglongbing

Introduction

Heavy metal-associated isoprenylated plant proteins (HIPPs) play vital roles in maintaining heavy metal balance and responding to both biotic and abiotic stresses in vascular plants. However, the role of HIPPs in the response to Huanglongbing (HLB), a harmful disease of citrus caused by the phloem-colonizing bacterium Candidatus Liberibacter asiaticus (CLas), has not been examined.

Methods and results

In this study, a total of 26 HIPP genes were identified in Citrus sinensis, and they were grouped into 5 clades. The CsHIPP genes are distributed on 8 chromosomes and exhibited considerable synteny with HIPPs found in Arabidopsis thaliana. Additionally, we analyzed the gene structure, conserved motifs and domains of the CsHIPPs. Various cis-acting elements related to plant hormones and stress responses were identified in the promoters of CsHIPPs. Public transcriptome data and RT-qPCR analysis showed that the expression level of CsHIPP03 was significantly reduced in samples infected by CLas and Xanthomonas citri ssp. citri (Xcc). Furthermore, silencing the homologous gene of CsHIPP03 in Nicotiana benthamiana increased the disease resistance of plants to bacteria.

Discussion

Our results provide a basis for functional studies of HIPP gene family in C. sinensis, highlighting their functions in bacterial resistance, and improve our understanding to the susceptibility mechanism of HLB.

Gene expression profiling of Jack Pine (Pinus banksiana) under copper stress: Identification of genes associated with copper resistance

Understanding the genetic response of plants to copper stress is a necessary step to improving the utility of plants for environmental remediation and restoration. The objectives of this study were to: 1) characterize the transcriptome of Jack Pine (Pinus banksiana) under copper stress, 2) analyze the gene expression profile shifts of genotypes exposed to copper ion toxicity, and 3) identify genes associated with copper resistance. Pinus banksiana seedlings were treated with 10 mmoles of copper and screened in a growth chamber. There were 6,213 upregulated and 29,038 downregulated genes expressed in the copper resistant genotypes compared to the susceptible genotypes at a high stringency based on the false discovery rate (FDR). Overall, 25,552 transcripts were assigned gene ontology. Among the top upregulated genes, the response to stress, the biosynthetic process, and the response to chemical stimuli terms represented the highest proportion of gene expression for the biological processes. For the molecular function category, the majority of expressed genes were associated with nucleotide binding followed by transporter activity, and kinase activity. The majority of upregulated genes were located in the plasma membrane while half of the total downregulated genes were associated with the extracellular region. Two candidate genes associated with copper resistance were identified including genes encoding for heavy metal-associated isoprenylated plant proteins (AtHIP20 and AtHIP26) and a gene encoding the pleiotropic drug resistance protein 1 (NtPDR1). This study represents the first report of transcriptomic responses of a conifer species to copper ions.

Physiological and transcriptomic response reveals new insight into manganese tolerance of Celosia argentea Linn

Celosia argentea is a manganese (Mn) hyperaccumulator with high ornamental value and strong stress resistance. It is important to understand the molecular mechanism of tolerance to heavy metals of hyperaccumulators to improve the efficiency of phytoremediation. In this study, the effects of different Mn concentrations (0, 0.8, 3, and 10 mM) on physiological characteristics and molecular changes were determined. Low concentrations of Mn increased the growth of C. argentea, while high concentrations of Mn suppressed its growth, A concentration up to 3 mM did not affect the growth of C. argentea, and the highest transfer factor (TF) was 6.16. Oxidative damage of different Mn level treatments in C. argentea was verified through relative water content, electrolyte leakage, MDA content, H2O2 content and superoxide contents. With an increase in Mn concentration, the contents of chlorophyll a, chlorophyll b, and carotenoids decreased. Our results indicated that low-concentration manganese treatment can reduce the reactive oxygen burst and MDA, soluble sugar and proline, making C. argentea have strong abiotic stress tolerance. The molecular mechanism of C. argentea after 10 mM Mn treatment was analysed through transcriptome analysis, and differentially expressed genes (DEGs) in these pathways were further verified by qRTPCR. Plantpathogen interactions, plant hormone signal transduction, the MAPK signalling pathway and the phenylpropanoid biosynthesis pathway were important in the response to Mn stress, and the heavy metal-associated isoprenylated plant protein, metal transporter Nramp, and zinc transporter play key roles in the strong ability of C. argentea to tolerate heavy metals. These results suggest that C. argentea exhibits strong manganese tolerance and provide new insight into the molecular mechanisms of plant responses to heavy metal stress.

Biological roles of soil microbial consortium on promoting safe crop production in heavy metal(loid) contaminated soil: A systematic review

Heavy metal(loid) (HM) pollution of agricultural soils is a growing global environmental concern that affects planetary health. Numerous studies have shown that soil microbial consortia can inhibit the accumulation of HMs in crops. However, our current understanding of the effects and mechanisms of inhibition is fragmented. In this review, we summarise extant studies and knowledge to provide a comprehensive view of HM toxicity on crop growth and development at the biological, cellular and the molecular levels. In a meta-analysis, we find that microbial consortia can improve crop resistance and reduce HM uptake, which in turn promotes healthy crop growth, demonstrating that microbial consortia are more effective than single microorganisms. We then review three main mechanisms by which microbial consortia reduce the toxicity of HMs to crops and inhibit HMs accumulation in crops: 1) reducing the bioavailability of HMs in soil (e.g. biosorption, bioaccumulation and biotransformation); 2) improving crop resistance to HMs (e.g. facilitating the absorption of nutrients); and 3) synergistic effects between microorganisms. Finally, we discuss the prospects of microbial consortium applications in simultaneous crop safety production and soil remediation, indicating that they play a key role in sustainable agricultural development, and conclude by identifying research challenges and future directions for the microbial consortium to promote safe crop production.

Malate production, sugar metabolism, and redox homeostasis in the leaf growth zone of Rye (Secale cereale) increase stress tolerance to aluminum stress: A biochemical and genome-wide transcriptional study

Global soil acidification is increasing, enlarging aluminum (Al) availability in soils, leading to reductions in plant growth. This study investigates the effect of Al stress on the leaf growth zones of Rye (Secale cereale, cv Beira). Kinematic analysis showed that the effect of Al on leaf growth rates was mainly due to a reduced cell production rate in the meristem. Transcriptomic analysis identified 2272 significantly (log2fold > |0.5| FDR < 0.05) differentially expressed genes (DEGs) for Al stress. There was a downregulation in several DEGs associated with photosynthetic processes and an upregulation in genes for heat/light response, and H2O2 production in all leaf zones. DEGs associated with heavy metals and malate transport were increased, particularly, in the meristem. To determine the putative function of these processes in Al tolerance, we performed biochemical analyses comparing the tolerant Beira with an Al sensitive variant RioDeva. Beira showed improved sugar metabolism and redox homeostasis, specifically in the meristem compared to RioDeva. Similarly, a significant increase in malate and citrate production, which are known to aid in Al detoxification in plants, was found in Beira. This suggests that Al tolerance in Rye is linked to its ability for Al exclusion from the leaf meristem.

N-acetyl-cysteine mitigates arsenic stress in lettuce: Molecular, biochemical, and physiological perspective

Agricultural land contaminated with heavy metals such as non-biodegradable arsenic (As) has become a serious global problem as it adversely affects agricultural productivity, food security and human health. Therefore, in this study, we investigated how the administration of N-acetyl-cysteine (NAC), regulates the physio-biochemical and gene expression level to reduce As toxicity in lettuce. According to our results, different NAC levels (125, 250 and 500 μM) significantly alleviated the growth inhibition and toxicity induced by As stress (20 mg/L). Shoot fresh weight, root fresh weight, shoot dry weight and root dry weight (33.05%, 55.34%, 17.97% and 46.20%, respectively) were decreased in plants grown in As-contaminated soils compared to lettuce plants grown in soils without the addition of As. However, NAC applications together with As stress increased these growth parameters. While the highest increase in shoot fresh and dry weight (58.31% and 37.85%, respectively) was observed in 250 μM NAC application, the highest increase in root fresh and dry weight (75.97% and 63.07%, respectively) was observed in 125 μM NAC application in plants grown in As-polluted soils. NAC application decreased the amount of ROS, MDA and H2O2 that increased with As stress, and decreased oxidative damage by regulating hormone levels, antioxidant and enzymes involved in nitrogen metabolism. According to gene expression profiles, LsHIPP28 and LsABC3 genes have shown important roles in reducing As toxicity in leaves. This study will provide insight for future studies on how NAC applications develop resistance to As stress in lettuce.

Effector-triggered susceptibility by the rice blast fungus Magnaporthe oryzae

Rice blast, the most destructive disease of cultivated rice world-wide, is caused by the filamentous fungus Magnaporthe oryzae. To cause disease in plants, M. oryzae secretes a diverse range of effector proteins to suppress plant defense responses, modulate cellular processes, and support pathogen growth. Some effectors can be secreted by appressoria even before host penetration, while others accumulate in the apoplast, or enter living plant cells where they target specific plant subcellular compartments. During plant infection, the blast fungus induces the formation of a specialized plant structure known as the biotrophic interfacial complex (BIC), which appears to be crucial for effector delivery into plant cells. Here, we review recent advances in the cell biology of M. oryzae-host interactions and show how new breakthroughs in disease control have stemmed from an increased understanding of effector proteins of M. oryzae are deployed and delivered into plant cells to enable pathogen invasion and host susceptibility.

Untying the regulatory roles of miRNAs in CuO-NPs stress response mechanism in maize: A genome-wide sRNA transcriptome analysis

MicroRNAs (miRNAs), a group of tiny non-coding RNAs play pivotal role in plant responses to environmental stress. The present small RNA transcriptome study aims to untie the role of miRNAs in CuO-NPs stress adaptation in maize seedlings. Restricted seedling growth, enhanced ROS generation and higher membrane damage were recorded under CuO-NPs [<50 nm, 8 mM] treatment. Deep sequencing reveals 7 up- and 36 down-regulated known miRNAs from CuO-NPs challenged leaves. Gene ontology study demonstrates involvement of CuO-NPs responsive miRNAs in a variety of biological processes including plant growth (miR159a, miR159b), redox homeostasis (miR156e, miR395a), detoxification of heavy metals (miR156e, miR827), signal transduction (miR156e, miR156d), and cell signalling (miR167b-3p, miR393a). Enhanced transcriptional abundance of ABC transporter G family member 41 isoform X2 and HM-associated isoprenylated plant protein 45 isoform X1 might be involved in sequestration and detoxification of excess Cu, essential for metal homeostasis in maize. The miR528-5p mediated up-regulation of superoxide dismutase does not give much protection against CuO-NPs induced oxidative stress damages as evident after histochemical staining with NBT. Moreover, CuO-NPs stress mediated down regulation of miR396 could be an underlying cause of the restricted seedling growth. Taken together, our findings provide insights into the miRNA-guided stress regulatory networks involved in plant's adaptive responses to CuO-NPs stress.

Physiological and molecular mechanisms of boron in alleviating cadmium toxicity in Capsicum annuum

Soil cadmium (Cd) contamination threatens food safety and human health, particularly in developing countries. Previously, we have proposed that boron (B) could reduce Cd uptake and accumulation in hot peppers (Capsicum annuum) by regulating the expression of genes related to Cd transport in roots. However, only few studies have examined the role of B in plant leaves under Cd stress. It is unclear how B induces the expression of relevant genes and metabolites in hot pepper leaves and to what extent B is involved in leaf growth and Cd accumulation. The purpose of this study was to investigate the effects of B on growth and Cd accumulation in hot pepper leaves by determining physiological parameters and transcriptome sequencing. The results showed that B application significantly improved the concentration of chlorophyll a and intercellular CO2, stomatal conductance, and photosynthetic and transpiration rates by 18-41 % in Cd-stressed plants. Moreover, B enhanced Cd retention in the cell wall by upregulating the expression levels of pectin-, lignin-, and callose-related genes and improving the activity of pectin methylesterase by 30 %, resulting in an approximate 31 % increase in Cd retention in the cell wall. Furthermore, B application not only enhanced the expression levels of genes related to antioxidant enzymes (superoxide dismutase, catalase, and peroxidase) and their activities by 28-40 %, thereby counteracting Cd-induced oxidative stress, but also improved Cd chelation, sequestration, and exclusion by upregulating the expression levels of genes related to sulfur metabolism, heavy metal-associated isoprenylated plant protein (HIPP), and transporters such as vacuolar cation/proton exchanger (CAX3), metal-nicotianamine transporter (YSL), ATP-binding cassette (ABC), zinc/iron transporters (ZIP) and oxic-compound detoxification (DTX), ultimately reinforcing Cd tolerance. Together, our results suggest that B application reduces the negative effects of Cd on leaf growth, promotes photosynthesis, and decreases Cd transfer to fruits through its sequestration and retention.

Recent Advances in Effector Research of Magnaporthe oryzae

Recalcitrant rice blast disease is caused by Magnaporthe oryzae, which has a significant negative economic reverberation on crop productivity. In order to induce the disease onto the host, M. oryzae positively generates many types of small secreted proteins, here named as effectors, to manipulate the host cell for the purpose of stimulating pathogenic infection. In M. oryzae, by engaging with specific receptors on the cell surface, effectors activate signaling channels which control an array of cellular activities, such as proliferation, differentiation and apoptosis. The most recent research on effector identification, classification, function, secretion, and control mechanism has been compiled in this review. In addition, the article also discusses directions and challenges for future research into an effector in M. oryzae.

Label-Free Quantitative Proteomics Reveal the Mechanisms of Young Wheat (Triticum aestivum L.) Ears' Response to Spring Freezing

Late spring frost is an important meteorological factor threatening the safe production of winter wheat in China. The young ear is the most vulnerable organ of the wheat plant to spring frost. To gain an insight into the mechanisms underpinning young wheat ears' tolerance to freezing, we performed a comparative proteome analysis of wheat varieties Xumai33 (XM33, freezing-sensitive) and Jimai22 (JM22, freezing-tolerant) under normal and freezing conditions using label-free quantitative proteomic techniques during the anther connective tissue formation phase (ACFP). Under freezing stress, 392 and 103 differently expressed proteins (DEPs) were identified in the young ears of XM33 and JM22, respectively, and among these, 30 proteins were common in both varieties. A functional characterization analysis revealed that these DEPs were associated with antioxidant capacity, cell wall modification, protein folding, dehydration response, and plant-pathogen interactions. The young ears of JM22 showed significantly higher expression levels of antioxidant enzymes, heat shock proteins, and dehydrin under normal conditions compared to those of XM33, which might help to prepare the young ears of JM22 for freezing stress. Our results lead to new insights into understanding the mechanisms in young wheat ears' response to freezing stress and provide pivotal potential candidate proteins required for improving young wheat ears' tolerance to spring frost.

Two QTL regions for spike length showing pleiotropic effects on Fusarium head blight resistance and thousand-grain weight in bread wheat (Triticum aestivum L.)

Spike length (SL) plays an important role in the yield improvement of wheat and is significantly associated with other traits. Here, we used a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) to construct a genetic linkage map and identify quantitative trait loci (QTL) for SL. A total of 5 QTL were identified for SL, among which QSl.yaas-3A and QSl.yaas-5B are two novel QTL for SL. The YZ1 alleles at QSl.yaas-2D and QSl.yaas-5A, and the YM12 alleles at QSl.yaas-2A, QSl.yaas-3A, and QSl.yaas-5B conferred increasing SL effects. Two major QTL QSl.yaas-5A and QSl.yaas-5B explained 9.11-15.85% and 9.01-12.85% of the phenotypic variations, respectively. Moreover, the positive alleles of QSl.yaas-5A and QSl.yaas-5B could significantly increase Fusarium head blight (FHB) resistance (soil surface inoculation and spray inoculation were used) and thousand-grain weight (TGW) in the RIL population. Kompetitive allele-specific PCR (KASP) markers for QSl.yaas-5A and QSl.yaas-5B were developed and validated in an additional panel of 180 wheat cultivars/lines. The cultivars/lines harboring both the positive alleles of QSl.yaas-5A and QSl.yaas-5B accounted for only 28.33% of the validation populations and had the longest SL, best FHB resistance (using spray inoculation), and highest TGW. A total of 358 and 200 high-confidence annotated genes in QSl.yaas-5A and QSl.yaas-5B were identified, respectively. Some of the genes in these two regions were involved in cell development, disease resistance, and so on. The results of this study will provide a basis for directional breeding of longer SL, higher TGW, and better FHB resistance varieties and a solid foundation for fine-mapping QSl.yaas-5A and QSl.yaas-5B in future.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01427-8.

Acetylcholine (ACh) enhances Cd tolerance through transporting ACh in vesicles and modifying Cd absorption in duckweed (Lemna turionifera 5511)

Acetylcholine (ACh), an important neurotransmitter, plays a role in resistance to abiotic stress. However, the role of ACh during cadmium (Cd) resistance in duckweed (Lemna turionifera 5511) remains uncharacterized. In this study, the changes of endogenous ACh in duckweed under Cd stress has been investigated. Also, how exogenous ACh affects duckweed's ability to withstand Cd stress was studied. The ACh sensor transgenic duckweed (ACh 3.0) showed the ACh signal response under Cd stress. And ACh was wrapped and released in vesicles. Cd stress promoted ACh content in duckweed. The gene expression analysis showed an improved fatty acid metabolism and choline transport. Moreover, exogenous ACh addition enhanced Cd tolerance and decreased Cd accumulation in duckweed. ACh supplement reduced the root abscission rate, alleviated leaf etiolation, and improved chlorophyll fluorescence parameters under Cd stress. A modified calcium (Ca2+) flux and improved Cd2+ absorption were present in conjunction with it. Thus, we speculate that ACh could improve Cd resistance by promoting the uptake and accumulation of Cd, as well as the response of the Ca2+ signaling pathway. Also, plant-derived extracellular vesicles (PDEVs) were extracted during Cd stress. Therefore, these results provide new insights into the response of ACh during Cd stress.

Overexpression of ApHIPP26 from the Hyperaccumulator Arabis paniculata Confers Enhanced Cadmium Tolerance and Accumulation to Arabidopsis thaliana

Cadmium (Cd) is a toxic heavy metal that seriously affects metabolism after accumulation in plants, and it also causes adverse effects on humans through the food chain. The HIPP gene family has been shown to be highly tolerant to Cd stress due to its special domain and molecular structure. This study described the Cd-induced gene ApHIPP26 from the hyperaccumulator Arabis paniculata. Its subcellular localization showed that ApHIPP26 was located in the nucleus. Transgenic Arabidopsis overexpressing ApHIPP26 exhibited a significant increase in main root length and fresh weight under Cd stress. Compared with wild-type lines, Cd accumulated much more in transgenic Arabidopsis both aboveground and underground. Under Cd stress, the expression of genes related to the absorption and transport of heavy metals underwent different changes in parallel, which were involved in the accumulation and distribution of Cd in plants, such as AtNRAMP6 and AtNRAMP3. Under Cd stress, the activities of antioxidant enzymes (superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase) in the transgenic lines were higher than those in the wild type. The physiological and biochemical indices showed that the proline and chlorophyll contents in the transgenic lines increased significantly after Cd treatment, while the malondialdehyde (MDA) content decreased. In addition, the gene expression profile analysis showed that ApHIPP26 improved the tolerance of Arabidopsis to Cd by regulating the changes of related genes in plant hormone signal transduction pathway. In conclusion, ApHIPP26 plays an important role in cadmium tolerance by alleviating oxidative stress and regulating plant hormones, which provides a basis for understanding the molecular mechanism of cadmium tolerance in plants and provides new insights for phytoremediation in Cd-contaminated areas.

Heavy Metal-Associated Isoprenylated Plant Proteins (HIPPs) at Plasmodesmata: Exploring the Link between Localization and Function

Heavy metal-associated isoprenylated plant proteins (HIPPs) are a metallochaperone-like protein family comprising a combination of structural features unique to vascular plants. HIPPs possess both one or two heavy metal-binding domains and an isoprenylation site, facilitating a posttranslational protein lipid modification. Recent work has characterized individual HIPPs across numerous different species and provided evidence for varied functionalities. Interestingly, a significant number of HIPPs have been identified in proteomes of plasmodesmata (PD)-nanochannels mediating symplastic connectivity within plant tissues that play pivotal roles in intercellular communication during plant development as well as responses to biotic and abiotic stress. As characterized functions of many HIPPs are linked to stress responses, plasmodesmal HIPP proteins are potentially interesting candidate components of signaling events at or for the regulation of PD. Here, we review what is known about PD-localized HIPP proteins specifically, and how the structure and function of HIPPs more generally could link to known properties and regulation of PD.

Functional analysis of a susceptibility gene (HIPP27) in the Arabidopsis thaliana-Meloidogyne incognita pathosystem by using a genome editing strategy

BACKGROUND

Plant-parasitic root-knot nematodes cause immense yield declines in crop plants that ultimately obviate global food security. They maintain an intimate relationship with their host plants and hijack the host metabolic machinery to their own advantage. The existing resistance breeding strategies utilizing RNAi and resistance (R) genes might not be particularly effective. Alternatively, knocking out the susceptibility (S) genes in crop plants appears to be a feasible approach, as the induced mutations in S genes are likely to be long-lasting and may confer broad-spectrum resistance. This could be facilitated by the use of CRISPR/Cas9-based genome editing technology that precisely edits the gene of interest using customizable guide RNAs (gRNAs) and Cas9 endonuclease.

RESULTS

Initially, we characterized the nematode-responsive S gene HIPP27 from Arabidopsis thaliana by generating HIPP27 overexpression lines, which were inoculated with Meloidogyne incognita. Next, two gRNAs (corresponding to the HIPP27 gene) were artificially synthesized using laboratory protocols, sequentially cloned into a Cas9 editor plasmid, mobilized into Agrobacterium tumefaciens strain GV3101, and transformed into Arabidopsis plants using the floral dip method. Apart from 1-3 bp deletions and 1 bp insertions adjacent to the PAM site, a long deletion of approximately 161 bp was documented in the T0 generation. Phenotypic analysis of homozygous, 'transgene-free' T2 plants revealed reduced nematode infection compared to wild-type plants. Additionally, no growth impairment was observed in gene-edited plants.

CONCLUSION

Our results suggest that the loss of function of HIPP27 in A. thaliana by CRISPR/Cas9-induced mutagenesis can improve host resistance to M. incognita.

Hub Gene Mining and Co-Expression Network Construction of Low-Temperature Response in Maize of Seedling by WGCNA

Weighted gene co-expression network analysis (WGCNA) is a research method in systematic biology. It is widely used to identify gene modules related to target traits in multi-sample transcriptome data. In order to further explore the molecular mechanism of maize response to low-temperature stress at the seedling stage, B144 (cold stress tolerant) and Q319 (cold stress sensitive) provided by the Maize Research Institute of Heilongjiang Academy of Agricultural Sciences were used as experimental materials, and both inbred lines were treated with 5 °C for 0 h, 12 h, and 24 h, with the untreated material as a control. Eighteen leaf samples were used for transcriptome sequencing, with three biological replicates. Based on the above transcriptome data, co-expression networks of weighted genes associated with low-temperature-tolerance traits were constructed by WGCNA. Twelve gene modules significantly related to low-temperature tolerance at the seedling stage were obtained, and a number of hub genes involved in low-temperature stress regulation pathways were discovered from the four modules with the highest correlation with target traits. These results provide clues for further study on the molecular genetic mechanisms of low-temperature tolerance in maize at the seedling stage.

Molecular engineering of plant immune receptors for tailored crop disease resistance

The specific recognition of pathogen effectors by intracellular nucleotide-binding and leucine-rich repeat domain receptors (NLRs) is an important component of plant immunity. Creating NLRs with new bespoke recognition specificities is a major goal in molecular plant pathology as it promises to provide unlimited resources for the resistance of crops against diseases. Recent breakthrough discoveries on the structure and molecular activity of NLRs begin to enable their knowledge-guided molecular engineering. First, studies succeeded to extend or change effector recognition specificities by modifying, in a structure-guided manner, the NLR domains that directly bind effectors. By modifying the LRR domain of the singleton NLR Sr35 or the unconventional decoy domains of the helper NLRs RGA5 or Pik-1, receptors that detected other or additional effectors were created.

OsHIPP17 is involved in regulating the tolerance of rice to copper stress

Introduction

Heavy metal-associated isoprenylated plant proteins (HIPPs) play vital roles in metal absorption, transport and accumulation in plants. However, so far, only several plant HIPPs have been functionally analyzed. In this study, a novel HIPP member OsHIPP17, which was involved in the tolerance to copper (Cu) was functionally characterized.

Methods

In this study, qRT-PCR, Yeast transgenic technology, Plant transgenic technology, ICP-MS and so on were used for research.

Results

OsHIPP17 protein was targeted to the nucleus. The Cu concentration reached 0.45 mg/g dry weight due to the overexpression of OsHIPP17 in yeast cells. Meanwhile, the overexpression of OsHIPP17 resulted in the compromised growth of Arabidopsis thaliana (Arabidopsis) under Cu stress. The root length of Oshipp17 mutant lines was also significantly reduced by 16.74- 24.36% under 25 mM Cu stress. The roots of Oshipp17 rice mutant showed increased Cu concentration by 7.25%-23.32%. Meanwhile, knockout of OsHIPP17 decreased the expression levels of OsATX1, OsZIP1, OsCOPT5 or OsHMA5, and increased the expression levels of OsCOPT1 or OsHMA4. Antioxidant enzyme activity was also reduced in rice due to the knockout of OsHIPP17. Moreover, the expression levels of cytokinin-related genes in plants under Cu stress were also affected by overexpression or knockout of OsHIPP17.

Discussion

These results implied that OsHIPP17 might play a role in plant Cu toxic response by affecting the expression of Cu transport genes or cytokinin-related genes. Simultaneously, our work may shed light on the underlying mechanism of how heavy metals affect the plant growth and provide a novel rice genetic source for phytoremediation of heavy metal-contaminated soil.

An analysis of differentially expressed and differentially m6A-modified transcripts in soybean roots treated with lead

Lead is one of the most common toxic heavy metal pollutants in nature, and exposure to lead can cause serious toxicity to many organisms. In this study, we collected root growth data from soybean plants exposed to lead for seven days and confirmed that lead significantly inhibited root growth. We performed a transcriptome-wide m6A methylation analysis to study the response of soybean RNA methylation groups to lead. The m6A modified regions were enriched near the 3'UTR region and stop codon, and m6A methylation was positively correlated with transcript abundance. In the presence of lead, the transcriptome range of m6A RNA methylation peaks increased, and we identified 1144 m6A modification peaks and 1094 differentially expressed genes. The integration of m6A methylation and transcriptomic results enabled us to identify 16 candidate genes whose transcripts were differentially methylated and differentially expressed under lead stress. Annotation results suggest that these genes may promote abiotic stress tolerance by impacting lead uptake, transport, and accumulation through ROS pathways, enzymes, transporters, and hormones. These results provide candidate genes for future studies of lead stress tolerance mechanisms in soybean roots and provide genetic resources for studying plant heavy metal stress in soybean breeding.

Metallochaperone protein OsHIPP17 regulates the absorption and translocation of cadmium in rice (Oryza sativa L.)

Heavy metal-associated isoprenylated plant proteins (HIPPs) play vital roles in regulating heavy metal responding activities in plants. Yet only a handful of studies have characterized the functions of HIPPs. In this study, a novel HIPP member OsHIPP17 was functionally characterized, which was involved in the tolerance of yeast and plants to cadmium (Cd). The Cd accumulation in yeast cells was increased due to the overexpression of OsHIPP17. Nevertheless, the overexpression of OsHIPP17 in Arabidopsis thaliana resulted in compromised growth under Cd stress. Meanwhile, the mutation of OsHIPP17 resulted in 38.9-40.9 % increase of Cd concentration in rice roots as well as 14.3-20.0 % decrease of Cd translocation factor. Further investigation of the genes responsible for Cd absorption and transporter indicated that the expression levels of these genes were also perturbed. In addition, two OsHIPP17-interacting proteins, OsHIPP24 and OsLOL3 were identified in a yeast two hybrid assay. Further analysis of their functions revealed that OsHIPP24 or OsLOL3 may be involved in the regulation of Cd tolerance by OsHIPP17 in rice. All above results implied that OsHIPP17 may affect Cd resistance by regulating the absorption and translocation of Cd in rice.

Structural mechanism of heavy metal-associated integrated domain engineering of paired nucleotide-binding and leucine-rich repeat proteins in rice

Plant nucleotide-binding and leucine-rich repeat (NLR) proteins are immune sensors that detect pathogen effectors and initiate a strong immune response. In many cases, single NLR proteins are sufficient for both effector recognition and signaling activation. These proteins possess a conserved architecture, including a C-terminal leucine-rich repeat (LRR) domain, a central nucleotide-binding (NB) domain, and a variable N-terminal domain. Nevertheless, many paired NLRs linked in a head-to-head configuration have now been identified. The ones carrying integrated domains (IDs) can recognize pathogen effector proteins by various modes; these are known as sensor NLR (sNLR) proteins. Structural and biochemical studies have provided insights into the molecular basis of heavy metal-associated IDs (HMA IDs) from paired NLRs in rice and revealed the co-evolution between pathogens and hosts by combining naturally occurring favorable interactions across diverse interfaces. Focusing on structural and molecular models, here we highlight advances in structure-guided engineering to expand and enhance the response profile of paired NLR-HMA IDs in rice to variants of the rice blast pathogen MAX-effectors (Magnaporthe oryzae AVRs and ToxB-like). These results demonstrate that the HMA IDs-based design of rice materials with broad and enhanced resistance profiles possesses great application potential but also face considerable challenges.

Root and Leaf Anatomy, Ion Accumulation, and Transcriptome Pattern under Salt Stress Conditions in Contrasting Genotypes of Sorghum bicolor

Roots from salt-susceptible ICSR-56 (SS) sorghum plants display metaxylem elements with thin cell walls and large diameter. On the other hand, roots with thick, lignified cell walls in the hypodermis and endodermis were noticed in salt-tolerant CSV-15 (ST) sorghum plants. The secondary wall thickness and number of lignified cells in the hypodermis have increased with the treatment of sodium chloride stress to the plants (STN). Lignin distribution in the secondary cell wall of sclerenchymatous cells beneath the lower epidermis was higher in ST leaves compared to the SS genotype. Casparian thickenings with homogenous lignin distribution were observed in STN roots, but inhomogeneous distribution was evident in SS seedlings treated with sodium chloride (SSN). Higher accumulation of K⁺ and lower Na⁺ levels were noticed in ST compared to the SS genotype. To identify the differentially expressed genes among SS and ST genotypes, transcriptomic analysis was carried out. Both the genotypes were exposed to 200 mM sodium chloride stress for 24 h and used for analysis. We obtained 70 and 162 differentially expressed genes (DEGs) exclusive to SS and SSN and 112 and 26 DEGs exclusive to ST and STN, respectively. Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis unlocked the changes in metabolic pathways in response to salt stress. qRT-PCR was performed to validate 20 DEGs in each SSN and STN sample, which confirms the transcriptomic results. These results surmise that anatomical changes and higher K⁺/Na⁺ ratios are essential for mitigating salt stress in sorghum apart from the genes that are differentially up- and downregulated in contrasting genotypes.

Metallochaperone OsHIPP9 is involved in the retention of cadmium and copper in rice

Metallochaperones are a unique class of proteins that play crucial roles in metal homoeostasis and detoxification. However, few metallochaperones have been functionally characterised in rice. Heterologous expression of Heavy metal-associated Isoprenylated Plant Protein 9 (OsHIPP9), a metallochaperone, altered yeast tolerance to cadmium (Cd) and copper (Cu). We investigated the physiological role of OsHIPP9 in rice. OsHIPP9 was primarily expressed in the root exodermis and xylem region of enlarged vascular bundles (EVB) at nodes. KO of OsHIPP9 increased the Cd concentrations of the upper nodes and panicle, but decreased Cd in expanded leaves. KO of OsHIPP9 decreased Cu uptake and accumulation in rice. Constitutive OX of OsHIPP9 increased Cd and Cu accumulation in aboveground tissues and brown rice. OsHIPP9 showed binding capacity for Cd and Cu. We propose that OsHIPP9 has dual metallochaperone roles, chelating Cd in the xylem region of EVB for Cd retention in the nodes and chelating Cu in rice roots to aid Cu uptake.

The heavy metal-associated isoprenylated plant protein (HIPP) gene family plays a crucial role in cadmium resistance and accumulation in the tea plant (Camellia sinensis L.)

Heavy metal-associated isoprenylated plant proteins (HIPPs) are only distributed in vascular plants, and are essential for the detoxification and vascular transport of heavy metals in plants. However, the HIPP gene family has not been thoroughly explored in the tea plant (Camellia sinensis). In this study, we systematically identified 56C. sinensis CsHIPP genes from five groups and characterized their phylogeny, structures, and the features of the encoded proteins. The expression patterns of CsHIPP genes in various tissues of C. sinensis were investigated based on a previous RNA-seq data analysis. The expression patterns of CsHIPP genes were explored in cadmium (Cd)-treated C. sinensis roots using our RNA-seq data. Three CsHIPP genes (CsHIPP22, CsHIPP24, and CsHIPP36) with high expression levels in Cd-treated C. sinensis roots were selected as candidate genes associated with Cd tolerance. Overexpression of CsHIPP22, CsHIPP24, and CsHIPP36 in a yeast mutant (ycf1) rescued Cd-sensitive ycf1 yeast and increased the yeast resistance to Cd stress, implying that these three CsHIPPs might be involved in Cd tolerance. These findings will enable the roles of HIPPs in Cd absorption and detoxification to be better understood as well as improving our understanding of the Cd-resistance and Cd-accumulation mechanisms in tea plant.

Physiological and transcriptional mechanisms associated with cadmium stress tolerance in Hibiscus syriacus L

BACKGROUND

Cadmium (Cd) pollution of soils is a global concern because its accumulation in plants generates severe growth retardation and health problems. Hibiscus syriacus is an ornamental plant that can tolerate various abiotic stresses, including Cd stress. Therefore, it is proposed as a plant material in Cd-polluted areas. However, the molecular mechanisms of H. syriacus tolerance to Cd are not yet understood.

RESULTS

This study investigated the physiological and transcriptional response of "Hongxing", a Cd2+-tolerant H. syriacus variety, grown on a substrate containing higher concentration of Cd (400 mg/kg). The Cd treatment induced only 28% of plant mortality, but a significant decrease in the chlorophyll content was observed. Malondialdehyde content and activity of the antioxidant enzymes catalase, peroxidase, and superoxide dismutase were significantly increased under Cd stress. Transcriptome analysis identified 29,921 differentially expressed genes (DEGs), including 16,729 down-regulated and 13,192 up-regulated genes, under Cd stress. Functional enrichment analyses assigned the DEGs mainly to plant hormone signal transduction, transport, nucleosome and DNA processes, mitogen-activated protein kinase signaling pathway, antioxidant process, fatty acid metabolism, and biosynthesis of secondary metabolites. Many MYB, EP2/ERF, NAC, WRKY family genes, and genes containing metal binding domains were up-regulated, implying that they are essential for the Cd-stress response in H. syriacus. The most induced genes were filtered out, providing valuable resources for future studies.

CONCLUSIONS

Our findings provide insights into the molecular responses to Cd stress in H. syriacus. Moreover, this study offers comprehensive and important resources for future studies toward improving the plant Cd tolerance and its valorization in phytoremediation.

Transcriptomic analysis reveals the molecular mechanisms of Boehmeria nivea L. in response to antimonite and antimonate stresses

Soil antimony (Sb) pollution is a global concern that threatens food security and human health. Boehmeria nivea L. (ramie) is a promising phytoremediation plant exhibiting high tolerance and enrichment capacity for Sb. To reveal the molecular mechanisms and thus enhance the ramie uptake, transport, and detoxification of Sb with practical strategies, a hydroponic experiment was conducted to compare the physiological and transcriptomic responses of ramie towards antimonite (Sb(Ⅲ)) and antimonate (Sb(Ⅴ)). Phenotypic results showed that Sb(Ⅲ) had a stronger inhibitory effect on the growth of ramie. Root Sb content under Sb(Ⅲ) was 2.43 times higher than that in Sb(Ⅴ) treatment. Based on the ribonucleic acid sequencing (RNA-Seq) technique, 3915 and 999 significant differentially expressed genes (DEGs) were identified under Sb(Ⅲ) and Sb(Ⅴ), respectively. Transcriptomic analysis revealed that ramie showed different adaptation strategies to Sb(Ⅲ) and Sb(V). Key DEGs and their involved pathways such as catalytic activity, carbohydrate metabolisms, phenylpropanoid biosynthesis, and cell wall modification were identified to perform crucial roles in Sb tolerance and detoxification. Two heavy metal-associated domain-type genes, six heavy metal-associated isoprenylated plant proteins, and nine ABC transporters showed possible roles in the transport and detoxification of Sb. The significant upregulation of NRAMP5 and three NIPs suggested their roles in the transport of Sb(V). This study is the basis for future research to identify the exact genes and biological processes that can effectively enhance Sb accumulation or improve plant tolerance to Sb, thereby promoting the phytoremediation of Sb-polluted soils.

Hexaploid Salix rehderiana is more suitable for remediating lead contamination than diploids, especially male plants

Willows are promising candidates for phytoremediation, but the lead (Pb) phytoremediation potential of different willow ploidy and sex has not yet been exploited. In this study, the Pb uptake, translocation and detoxification capacities of hexaploid and diploid, female and male Salix rehderiana were investigated. The results showed that Pb treatment inhibited biomass accumulation and gas exchange, caused ultrastructural and oxidative damage, and induced antioxidant, phytohormonal and transcriptional regulation in S. rehderiana. Absorbed Pb was mainly accumulated in the roots with restricted root-to-shoot transport. Despite lower biomass, greater transpiration, phytohormonal and transcriptional regulation indicated that hexaploid S. rehderiana had higher tissue Pb concentration, total accumulated Pb amount (4.39 mg, 6.19 mg, 6.60 mg and 10.83 mg in diploid and hexaploid females and males, respectively) as well as bioconcentration factors and translocation factors (0.412, 0.593, 0.921 and 1.320 for bioconcentration factors in roots, and 0.029, 0.032, 0.035 and 0.047 for translocation factors in diploid and hexaploid females and males, respectively) than diploids. Higher soil urease and acid phosphatase activities also favored hexaploids to use more available N and P than diploids in Pb-contaminated soils. Additionally, hexaploid S. rehderiana had stronger antioxidant, phytohormonal and transcriptional responses, and displayed less morphological and ultrastructural damage than diploids after Pb treatment, suggesting that hexaploids have greater Pb uptake, translocation and detoxification capacities than diploids. Moreover, S. rehderiana males had greater Pb uptake and translocation abilities, as well as stronger antioxidant, phytohormonal, and transcriptional regulation mediated Pb detoxification capacities than females. Therefore, hexaploid S. rehderiana are superior to diploids, and males are better than females in Pb phytoremediation. This study provides novel and valuable insights for selecting better willow materials to mitigate Pb contamination.

Genome-Wide Identification of Candidate Genes Associated with Heat Stress in Mulberry (Morus alba L.)

Mulberry (Morus alba L.) is an economically important plant for the silk industry and has the possibility of contributing immensely to Chinese pharmacopeia because of its health benefits. Domesticated silkworms feed only on mulberry leaves, meaning that the worms' survival depends on the mulberry tree. Mulberry production is threatened by climate change and global warming. However, the regulatory mechanisms of mulberry responses to heat are poorly understood. We performed transcriptome analysis of high-temperature-stressed (42 °C) M. alba seedlings using RNA-Seq technologies. A total of 703 differentially expressed genes (DEGs) were discovered from 18,989 unigenes. Among these, 356 were up-regulated, and 347 were down-regulated. KEGG analysis revealed that most DEGs were enriched in valine, leucine and isoleucine degradation, and in starch and sucrose metabolism, alpha-linolenic acid metabolism, carotenoid biosynthesis and galactose metabolism, among others. In addition, TFs such as the NAC, HSF, IAA1, MYB, AP2, GATA, WRKY, HLH and TCP families were actively involved in response to high temperatures. Moreover, we used RT-qPCR to confirm the expression changes of eight genes under heat stress observed in the RNA-Seq analysis. This study provides M. alba transcriptome profiles under heat stress and provides theoretical bases to researchers for better understanding mulberry heat response mechanisms and breeding heat-tolerant mulberry plants.

Effects of cadmium on transcription, physiology, and ultrastructure of two tobacco cultivars

Cadmium (Cd) is one of the most toxic heavy metal pollutants worldwide. Tobacco is an important cash crop; however, the accumulation of Cd in its biomass is very high. Cadmium may enter the body of smokers with contaminated tobacco and the surrounding environment via smoke. Therefore, it is important to understand the mechanisms of Cd accumulation and tolerance in tobacco plants, especially in the leaves. In this study, the effects of Cd on the growth, accumulation, and biochemical indices of two tobacco varieties, K326 (Cd resistant) and NC55 (Cd sensitive), were studied through transcriptomic and physiological experiments. Transcriptome and physiological analyses showed differences in the expression of Cd transport and Cd resistance related genes between NC55 and K326 under Cd stress. The root meristem cells of NC55 were more severely damaged. The antioxidant enzyme activity, ABA and ZT content, chlorophyll content, photosynthetic rate, and nitrogen metabolism enzyme activity in K326 leaves were higher than in NC55. These data elucidate the mechanisms of low Cd accumulation and high Cd tolerance in K326 leaves and provide a theoretical basis for cultivating tobacco varieties with low Cd accumulation and high Cd resistance.

Comprehensive Analysis of BrHMPs Reveals Potential Roles in Abiotic Stress Tolerance and Pollen–Stigma Interaction in Brassica rapa

Heavy metal-associated proteins (HMPs) participate in heavy metal detoxification. Although HMPs have been identified in several plants, no studies to date have identified the HMPs in Brassica rapa (B. rapa). Here, we identified 85 potential HMPs in B. rapa by bioinformatic methods. The promoters of the identified genes contain many elements associated with stress responses, including response to abscisic acid, low-temperature, and methyl jasmonate. The expression levels of BrHMP14, BrHMP16, BrHMP32, BrHMP41, and BrHMP42 were upregulated under Cu2+, Cd2+, Zn2+, and Pb2+ stresses. BrHMP06, BrHMP30, and BrHMP41 were also significantly upregulated after drought treatment. The transcripts of BrHMP06 and BrHMP11 increased mostly under cold stress. After applying salt stress, the expression of BrHMP02, BrHMP16, and BrHMP78 was induced. We observed increased BrHMP36 expression during the self-incompatibility (SI) response and decreased expression in the compatible pollination (CP) response during pollen–stigma interactions. These changes in expression suggest functions for these genes in HMPs include participating in heavy metal transport, detoxification, and response to abiotic stresses, with the potential for functions in sexual reproduction. We found potential co-functional partners of these key players by protein–protein interaction (PPI) analysis and found that some of the predicted protein partners are known to be involved in corresponding stress responses. Finally, phosphorylation investigation revealed many phosphorylation sites in BrHMPs, suggesting post-translational modification may occur during the BrHMP-mediated stress response. This comprehensive analysis provides important clues for the study of the molecular mechanisms of BrHMP genes in B. rapa, especially for abiotic stress and pollen–stigma interactions.

Transcriptomic mechanisms of reduced PM2.5-Pb retention in the leaves of the low-Pb-accumulation genotype of Chinese cabbage

Atmospheric fine particulate matter (PM_2.5) mainly contributes to Pb accumulation in the edible leaves of Chinese cabbage in North China. It was found that a low-Pb-accumulation (LPA) genotype of Chinese cabbage contained less Pb in leaves than high-Pb-accumulation (HPA) genotype exposed to PM_2.5-Pb. However, there are no data on the transcriptional regulatory mechanisms of foliar PM_2.5-Pb uptake by Chinese cabbage. The present study investigated the retention of PM_2.5-Pb in foliar apoplast and symplasm and the underlying molecular mechanisms of reduced Pb in LPA leaves. It appeared more Pb in apoplast and less Pb in symplasm of LPA leaves, whereas the pattern was opposite in HPA. There were 2646 and 3095 differentially expressed genes (DEGs) in LPA and HPA leaves under PM_2.5-Pb stress with clearly genotype-specific function, respectively. Furthermore, mRNA levels of XTH16 regulating cell wall thickening, PME2 and PME6 involved in cell wall remodification were significantly expressed in LPA, but not in HPA. Meanwhile, foliar PM_2.5-Pb stress downregulated expression of ZIP1, YSL1, and CNGC3 responsible for Pb influx to cell, and upregulated expression of ABCG36 regulated Pb efflux from symplasm in LPA leaves. These results improve our understanding to the mechanisms underlying foliar Pb uptake from PM_2.5-Pb at transcriptomic level.

'Garlic-lipo'4Plants: Liposome-Encapsulated Garlic Extract Stimulates ABA Pathway and PR Genes in Wheat (Triticum aestivum)

Recently, environmentally friendly crop improvements using next-generation plant biostimulants (PBs) come to the forefront in agriculture, regardless of whether they are used by scientists, farmers, or industries. Various organic and inorganic solutions have been investigated by researchers and producers, focusing on tolerance to abiotic and biotic stresses, crop quality, or nutritional deficiency. Garlic has been considered a universal remedy ever since antiquity. A supercritical carbon dioxide garlic extract encapsulated in nanoscale liposomes composed of plant-derived lipids was examined as a possible PB agent. The present study focused on the characterization of the genes associated with the pathways involved in defense response triggered by the liposome nanoparticles that were loaded with supercritical garlic extracts. This material was applied to Triticum aestivum in greenhouse experiments using foliar spraying. The effects were examined in a large-scale genome-wide transcriptional profiling experiment by collecting the samples four times (0 min, used as a control, and 15 min, 24 h, and 48 h after spraying). Based on a time-course expression analysis, the dynamics of the cellular response were determined by examining differentially expressed genes and applying a cluster analysis. The results suggested an enhanced expression of abscisic acid (ABA) pathway and pathogenesis-related (PR) genes, of which positive regulation was found for the AP2-, C2H2-, HD-ZIP-, and MYB-related transcription factor families.

The intertwining of Zn-finger motifs and abiotic stress tolerance in plants: Current status and future prospects

Environmental stresses such as drought, high salinity, and low temperature can adversely modulate the field crop's ability by altering the morphological, physiological, and biochemical processes of the plants. It is estimated that about 50% + of the productivity of several crops is limited due to various types of abiotic stresses either presence alone or in combination (s). However, there are two ways plants can survive against these abiotic stresses; a) through management practices and b) through adaptive mechanisms to tolerate plants. These adaptive mechanisms of tolerant plants are mostly linked to their signalling transduction pathway, triggering the action of plant transcription factors and controlling the expression of various stress-regulated genes. In recent times, several studies found that Zn-finger motifs have a significant function during abiotic stress response in plants. In the first report, a wide range of Zn-binding motifs has been recognized and termed Zn-fingers. Since the zinc finger motifs regulate the function of stress-responsive genes. The Zn-finger was first reported as a repeated Zn-binding motif, comprising conserved cysteine (Cys) and histidine (His) ligands, in Xenopus laevis oocytes as a transcription factor (TF) IIIA (or TFIIIA). In the proteins where Zn²⁺ is mainly attached to amino acid residues and thus espousing a tetrahedral coordination geometry. The physical nature of Zn-proteins, defining the attraction of Zn-proteins for Zn²⁺, is crucial for having an in-depth knowledge of how a Zn²⁺ facilitates their characteristic function and how proteins control its mobility (intra and intercellular) as well as cellular availability. The current review summarized the concept, importance and mechanisms of Zn-finger motifs during abiotic stress response in plants.

Transcriptome alterations of radish shoots exposed to cadmium can be interpreted in the context of leaf senescence

Till now few transcriptome studies have described shoot responses of heavy metal (HM)-sensitive plants to excess Cd and still a unifying model of Cd action is lacking. Using RNA-seq technique, the transcriptome responses of radish (Raphanus sativus L.) leaves to Cd stress were investigated in plants raised hydroponically under control and 5.0 mg L^-1 Cd. The element was mainly accumulated in roots and led to declined biomass and photosynthetic pigments, increased H₂O₂ and lipid peroxidation, and the accumulation of sugars, protein thiols, and phytochelatins. Out of 524 differentially expressed genes (DEGs), 244 and 280 upregulated and downregulated ones were assigned to 82 and 115 GO terms, respectively. The upregulated DEGs were involved in osmotic regulation, protein metabolism, chelators, and carbohydrate metabolisms, whereas downregulated DEGs were related to photosynthesis, response to oxidative stress, glucosinolate, and secondary metabolite biosynthesis. Our transcriptome data suggest that Cd triggers ROS production and photosynthesis decline associated with increased proteolysis through ubiquitin-proteasome system (UPS)- and chloroplast-proteases and in this way brings about re-mobilization of N and C stores into amino acids and sugars. Meanwhile, declined glucosinolate metabolism in favor of chelator synthesis and upregulation of dehydrins as inferred from transcriptome analysis confers shoots some tolerance to the HM-derived ionic/osmotic imbalances. Thus, the induction of leaf senescence might be a major long-term response of HM-sensitive plants to Cd toxicity.