A mutation in the essential and widely conserved DAMAGED DNA BINDING1-Cullin4 ASSOCIATED FACTOR gene OZS3 causes hypersensitivity to zinc excess, cold and UV stress in Arabidopsis thaliana

Unveiling key mechanisms: Transcriptomic meta-analysis of diverse nanomaterial applications addressing biotic and abiotic stresses in Arabidopsis Thaliana

The potential applications of nanomaterials in agriculture for alleviating diverse biotic and abiotic stresses have garnered significant attention. The reported mechanisms encompass promoting plant growth and development, alleviating oxidative stress, inducing defense responses, modulating plant-microbe interactions, and more. However, individual studies may not fully uncover the common pathways or distinguish the effects of different nanostructures. We examined Arabidopsis thaliana transcriptomes exposed to biotic, abiotic, and metal or carbon-based nanomaterials, utilizing 24 microarray chipsets and 17 RNA-seq sets. The results showed that: 1) from the perspective of different nanostructures, all metal nanomaterials relieved biotic/abiotic stresses via boosting metal homeostasis, particularly zinc and iron. Carbon nanomaterials induce hormone-related immune responses in the presence of both biotic and abiotic stressors. 2) Considering the distinct features of various nanostructures, metal nanomaterials displayed unique characteristics in seed priming for combating abiotic stresses. In contrast, carbon nanomaterials exhibited attractive features in alleviating water deprivation and acting as signaling amplifiers during biotic stress. 3) For shared pathway analysis, response to hypoxia emerges as the predominant and widely shared regulatory mechanism governing diverse stress responses, including those induced by nanomaterials. By deciphering shared and specific pathways and responses, this research opens new avenues for precision nano-agriculture, offering innovative strategies to optimize plant resilience, improve stress management, and advance sustainable crop production practices.

Unveiling Innovative Approaches to Mitigate Metals/Metalloids Toxicity for Sustainable Agriculture

Due to anthropogenic activities, environmental pollution of heavy metals/metalloids (HMs) has increased and received growing attention in recent decades. Plants growing in HM-contaminated soils have slower growth and development, resulting in lower agricultural yield. Exposure to HMs leads to the generation of free radicals (oxidative stress), which alters plant morpho-physiological and biochemical pathways at the cellular and tissue levels. Plants have evolved complex defense mechanisms to avoid or tolerate the toxic effects of HMs, including HMs absorption and accumulation in cell organelles, immobilization by forming complexes with organic chelates, extraction via numerous transporters, ion channels, signaling cascades, and transcription elements, among others. Nonetheless, these internal defensive mechanisms are insufficient to overcome HMs toxicity. Therefore, unveiling HMs adaptation and tolerance mechanisms is necessary for sustainable agriculture. Recent breakthroughs in cutting-edge approaches such as phytohormone and gasotransmitters application, nanotechnology, omics, and genetic engineering tools have identified molecular regulators linked to HMs tolerance, which may be applied to generate HMs-tolerant future plants. This review summarizes numerous systems that plants have adapted to resist HMs toxicity, such as physiological, biochemical, and molecular responses. Diverse adaptation strategies have also been comprehensively presented to advance plant resilience to HMs toxicity that could enable sustainable agricultural production.

Populus cathayana genome and population resequencing provide insights into its evolution and adaptation

Populus cathayana Rehder, an indigenous poplar species of ecological and economic importance, is widely distributed in a high-elevation range from southwest to northeast China. Further development of this species as a sustainable poplar resource has been hindered by a lack of genome information the at the population level. Here, we produced a chromosome-level genome assembly of P. cathayana, covering 406.55 Mb (scaffold N50 = 20.86 Mb) and consisting of 19 chromosomes, with 35 977 protein-coding genes. Subsequently, we made a genomic variation atlas of 438 wild individuals covering 36 representative geographic areas of P. cathayana, which were divided into four geographic groups. It was inferred that the Northwest China regions served as the genetic diversity centers and a population bottleneck happened during the history of P. cathayana. By genotype-environment association analysis, 947 environment-association loci were significantly associated with temperature, solar radiation, precipitation, and altitude variables. We identified local adaptation genes involved in DNA repair and UV radiation response, among which UVR8, HY5, and CUL4 had key roles in high-altitude adaptation of P. cathayana. Predictions of adaptive potential under future climate conditions showed that P. cathayana populations in areas with drastic climate change were anticipated to have greater maladaptation risk. These results provide comprehensive insights for understanding wild poplar evolution and optimizing adaptive potential in molecular breeding.

Auxin-cytokinin interplay shapes root functionality under low-temperature stress

Low-temperature stress alters root system architecture. In particular, changes in the levels and response to auxin and cytokinin determine the fate of root architecture and function under stress because of their vital roles in regulating root cell division, differentiation, and elongation. An intricate nexus of genes encoding components of auxin and cytokinin biosynthesis, signaling, and transport components operate to counteract stress and facilitate optimum development. We review the role of auxin transport and signaling and its regulation by cytokinin during root development and stem cell maintenance under low-temperature stress. We highlight intricate mechanisms operating in root stem cells to minimize DNA damage by altering phytohormone levels, and discuss a working model for cytokinin in low-temperatures stress response.

A long non-coding RNA PelncRNA1 is involved in Phyllostachys edulis response to UV-B stress

Phyllostachys edulis (moso bamboo) is China's most widespread bamboo species, with significant economic and ecological values. Long non-coding RNA (lncRNA) is a type of regulatory RNA that is longer than 200 nucleotides and incapable of encoding proteins, and is frequently involved in regulating biotic and abiotic stress and plant development. However, the biological functions of lncRNA in moso bamboo are unknown. In this study, a lncRNA (named PelncRNA1) differentially expressed following UV-B treatment was discovered in the whole transcriptome sequencing database of moso bamboo. The target genes were filtered and defined by correlation analysis of PelncRNA1 and gene expression pattern. The expression levels of PelncRNA1 and its target genes were verified using qRT-PCR. The results demonstrated that the expression levels of PelncRNA1 and its target genes increased during UV-B treatment. In Arabidopsis transgenic seedlings and moso bamboo protoplasts, PelncRNA1 was discovered to influence the expression of its target genes when overexpressed. In addition, transgenic Arabidopsis showed higher tolerance to UV-B stress. These results suggest that PelncRNA1 and its target genes are involved in the response of moso bamboo to UV-B stress. The novel findings would contribute to our understanding of how lncRNAs regulate the response to abiotic stresses in moso bamboo.

State-of-the-art OMICS strategies against toxic effects of heavy metals in plants: A review

Environmental pollution of heavy metals (HMs), mainly due to anthropogenic activities, has received growing attention in recent decades. HMs, especially the non-essential carcinogenic ones, including chromium (Cr), cadmium (Cd), mercury (Hg), aluminum (Al), lead (Pb), and arsenic (As), have appeared as the most significant air, water, and soil pollutants, which adversely affect the quantity, quality, and security of plant-based food all over the world. Plants exposed to HMs could experience significant decline in growth and yield. To avoid or tolerate the toxic effects of HMs, plants have developed complicated defense mechanisms, including absorption and accumulation of HMs in cell organelles, immobilization by forming complexes with organic chelates, extraction by using numerous transporters, ion channels, signalling cascades, and transcription elements, among others. OMICS strategies have developed significantly to understand the mechanisms of plant transcriptomics, genomics, proteomics, metabolomics, and ionomics to counter HM-mediated stress stimuli. These strategies have been considered to be reliable and feasible for investigating the roles of genomics (genomes), transcriptomic (coding), mRNA transcripts (non-coding), metabolomics (metabolites), and ionomics (metal ions) to enhance stress resistance or tolerance in plants. The recent developments in the mechanistic understandings of the HMs-plant interaction in terms of their absorption, translocation, and toxicity invasions at the molecular and cellular levels, as well as plants' response and adaptation strategies against these stressors, are summarized in the present review. Transcriptomics, genomics, metabolomics, proteomics, and ionomics for plants against HMs toxicities are reviewed, while challenges and future recommendations are also discussed.

Expression of BRCA1, BRCA2, RAD51, and other DSB repair factors is regulated by CRL4WDR70

Double-strand break (DSB) repair relies on DNA damage response (DDR) factors including BRCA1, BRCA2, and RAD51, which promote homology-directed repair (HDR); 53BP1, which affects single-stranded DNA formation; and proteins that mediate end-joining. Here we show that the CRL4/DDB1/WDR70 complex (CRL4WDR70) controls the expression of DDR factors. Auxin-mediated degradation of WDR70 led to reduced expression of BRCA1, BRCA2, RAD51, and other HDR factors; 53BP1 and its downstream effectors; and other DDR factors. In contrast, cNHEJ factors were generally unaffected. WDR70 loss abrogated the localization of HDR factors to DSBs and elicited hallmarks of genomic instability, although 53BP1/RIF1 foci still formed. Mutation of the DDB1-binding WD40 motif, disruption of DDB1, or inhibition of cullins phenocopied WDR70 loss, consistent with CRL4, DDB1, and WDR70 functioning as a complex. RNA-sequencing revealed that WDR70 degradation affects the mRNA levels of DDR and many other factors. The data indicate that CRL4WDR70 is critical for expression of myriad genes including BRCA1, BRCA2, and RAD51.

Advances in "Omics" Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants' demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.