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

Integrated transcriptomics, metabolomics and physiological analyses reveal the regulatory mechanism of dopamine in Nicotiana tabacum response to cadmium stress

Cadmium (Cd) pollution is a serious threat to many plants. Dopamine (DOPA) can potentially alleviate abiotic stress in plants, however, the effects of DOPA on Cd biotoxicity remain largely elusive. This study explored the beneficial effects of DOPA on Cd tolerance and detoxification in tobacco using transcriptomics and metabolomics combined with physiological and biochemical analyses. The results showed that applying DOPA reduced Cd absorption in tobacco plants, altered its subcellular distribution, decreased the soluble Cd proportion within cells and organelles, and increased the soluble Cd proportion associated with the cell wall. Analysis of Cd chemical forms revealed that DOPA decreased the concentrations of inorganic Cd and water-soluble Cd (with limited mobility), while increased the Cd complexed with pectin, proteins, and phosphate in the cell walls and vacuoles. Furthermore, DOPA enhanced CAT, SOD, POD, APX activity, decreased Cd-induced O2·-, H2O2, and MDA accumulation and damage, and preserved cell wall structural integrity, thereby improved the plant photosynthetic capacity (Fv/Fm, Gs, Tr, Pn). Comprehensive transcriptome and metabolome analyses revealed that DOPA modulated amino acid and lipid metabolism, and upregulated the expression of genes involved in cell wall synthesis (PME, XTH et al.), Cd uptake and detoxification (FROs, HIPPs et al.), as well as light-harvesting protein (Psa, Psb, LHC et al.). This study establishes a theoretical foundation for understanding how DOPA enhances plant tolerance to Cd stress and elucidates the fundamental regulatory mechanisms involved.

Genome-wide identification of the HIPPs gene family and functional validation of MsHIPP12 in enhancing cadmium tolerance in Medicago sativa

Heavy metal-associated isoprenylated plant proteins (HIPPs) are crucial for metal ion homeostasis and stress responses in plants exposed to heavy metals. They bind heavy metal ions via their HMA domains, sequestering them to prevent cellular toxicity. The C-terminal isoprenylation enhances interactions with membrane proteins, aiding in ion transport and compartmentalization. In Medicago sativa (alfalfa), we identified 23 MsHIPP genes containing conserved HMA domains and C-terminal isoprenylation motifs using bioinformatics tools. Phylogenetic analysis classified these genes into five clades, indicating functional diversity and evolutionary divergence. Promoter analysis revealed cis-regulatory elements associated with responses to light, drought, cold, abscisic acid (ABA), salicylic acid (SA), and auxin, suggesting roles in environmental adaptation. Expression profiling under drought, cold, salt, cadmium (Cd), ABA, and indole-3-acetic acid (IAA) treatments demonstrated the involvement of MsHIPPs in abiotic stress responses. Notably, overexpression of MsHIPP12 in Arabidopsis thaliana enhanced Cd tolerance by increasing antioxidant enzyme activities (APX, CAT, SOD), reducing malondialdehyde (MDA) levels, and attenuating chlorophyll degradation. These findings identify MsHIPP12 as a promising candidate gene for enhancing stress tolerance in M. sativa. This work provides valuable insights for molecular breeding strategies and phytoremediation approaches to address cadmium-contaminated soils.

Integrative analysis of RNA-Seq data and machine learning approaches to identify Biomarkers for Rhizoctonia solani resistance in sugar beet

Rhizoctonia solani is a significant pathogen that causes crown and root rot in sugar beet (Beta vulgaris), leading to considerable yield losses. To develop resilient cultivars, it is crucial to understand the molecular mechanisms underlying both resistance and susceptibility. In this study, we employed RNA-Seq analysis alongside machine learning techniques to identify key biomarkers associated with resistance to R. solani. We ranked differentially expressed genes (DEGs) using feature-weighting algorithms, such as Relief and kernel-based methods, to model expression patterns between sensitive and tolerant cultivars. Our integrative approach identified several candidate genes, including Bv5g001004 (encoding Ethylene-responsive transcription factor 1A), Bv8g000842 (encoding 5'-adenylylsulfate reductase 1), and Bv7g000949 (encoding Heavy metal-associated isoprenylated plant protein 5). These genes are involved in stress signal transduction, sulfur metabolism, and disease resistance pathways. Graphical visualizations of the Random Forest and Decision Tree models illustrated the decision-making processes and gene interactions, enhancing our understanding of the complex relationships between sensitive and tolerant genotypes. This study demonstrates the effectiveness of integrating RNA-Seq and machine learning techniques for biomarker discovery and highlights potential targets for developing R. solani-resistant sugar beet cultivars. The findings provide a robust framework for improving crop enhancement strategies and contribute to sustainable agricultural practices by increasing stress resilience in economically important crops.

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.

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.

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.