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Toxins Dec 2023Ribosome-inactivating proteins (RIPs) are plant toxins that were identified for their ability to irreversibly damage ribosomes, thereby causing arrest of protein...
Ribosome-inactivating proteins (RIPs) are plant toxins that were identified for their ability to irreversibly damage ribosomes, thereby causing arrest of protein synthesis and induction of cell death. The RIPs purified from Adenia plants are the most potent ones. Here, we describe a novel toxic lectin from caudex, which has been named heterophyllin. Heterophyllin shows the enzymatic and lectin properties of type 2 RIPs. Interestingly, in immunoreactivity experiments, heterophyllin poorly cross-reacts with sera against all other tested RIPs. The cytotoxic effects and death pathways triggered by heterophyllin were investigated in three human-derived cell lines: NB100, T24, and MCF7, and compared to ricin, the most known and studied type 2 RIP. Heterophyllin was able to completely abolish cell viability at nM concentration. A strong induction of apoptosis, but not necrosis, and the involvement of oxidative stress and necroptosis were observed in all the tested cell lines. Therefore, the enzymatic, immunological, and biological activities of heterophyllin make it an interesting molecule, worthy of further in-depth analysis to verify its possible pharmacological application.
Topics: Humans; Plant Proteins; Ribosome Inactivating Proteins, Type 2; Ricin; Ribosome Inactivating Proteins; Ribosomes; Protein Biosynthesis
PubMed: 38276525
DOI: 10.3390/toxins16010001 -
BMC Biology May 2024Protein posttranslational modifications (PTMs) are fast and early responses to environmental changes, including pathogen infection. Jujube witches' broom (JWB) is a...
BACKGROUND
Protein posttranslational modifications (PTMs) are fast and early responses to environmental changes, including pathogen infection. Jujube witches' broom (JWB) is a phytoplasma disease causing great economic loss in jujube production. After phytoplasma infection, the transcriptional, translational, and metabolic levels in jujube were activated, enabling it to survive during phytoplasma invasion. However, no study has yet reported on PTMs in jujube. Lysine crotonylation (Kcr) and lysine succinylation (Ksu) have been popular studies in recent years and their function in plant phytoplasma-stress responses remains unclear.
RESULTS
Here, 1656 crotonylated and 282 succinylated jujube proteins were first identified under phytoplasma-stress, of which 198 were simultaneously crotonylated and succinylated. Comparative analysis revealed that 656 proteins, 137 crotonylated and 43 succinylated proteins in jujube were regulated by phytoplasma infection, suggesting that Kcr was more universal than Ksu. Kcr differentially expressed proteins (DEPs) were related to ribosomes, photosynthetic and carbon metabolism, while Ksu DEPs were mainly involved in carbon metabolism, the TCA cycle and secondary metabolite biosynthesis. The crosstalk network among proteome, crotonylome and succinylome showed that DEPs related to ribosomal, peroxidases and glutathione redox were enriched. Among them, ZjPOD51 and ZjPHGPX2 significantly increased at the protein and Kcr level under phytoplasma-stress. Notably, 7 Kcr sites were identified in ZjPHGPX2, a unique antioxidant enzyme. After inhibitor nicotinamide (NAM) treatment, GPX enzyme activity in jujube seedlings was reduced. Further, site-directed mutagenesis of key Kcr modification sites K130 and/or K135 in ZjPHGPX2 significantly reduced its activity.
CONCLUSIONS
This study firstly provided large-scale datasets of Kcr and Ksu in phytoplasma-infected jujube and revealed that Kcr modification in ZjPHGPX2 positively regulates its activity.
Topics: Ziziphus; Phytoplasma; Plant Proteins; Plant Diseases; Protein Processing, Post-Translational; Stress, Physiological; Lysine
PubMed: 38750524
DOI: 10.1186/s12915-024-01917-x -
Plant Signaling & Behavior Dec 2023set ornamental, edible, and medicinal plant with broad prospects for further application development. However, there are no reports on the YABBY transcription factor in...
set ornamental, edible, and medicinal plant with broad prospects for further application development. However, there are no reports on the YABBY transcription factor in . Identification and analysis of the gene family of using bioinformatics means. Six genes were identified and divided into five subgroups. Transcriptome data and qRT-PCR were used to analyze the expression patterns of genes exhibited organ-specific patterns in expression in . Upon salt stress and drought induction, presented different morphological and physiological changes with some dynamic changes. Under salt treatment, the gene family was down-regulated; was up-regulated in leaves at 24 h. In drought treatment, , and were down-regulated to varying degrees, but was significantly up-regulated in the roots. was up-regulated gradually after being down-regulated. was significantly up-regulated in stem and leaf at 48 h. was down-regulated at first and then significantly up-regulated. The dynamic changes of salt stress and drought stress can be regarded as the responses of plants to resist damage. During the whole process of salt and drought stress treatment, the protein content of each tissue part of changed continuously. At the same time, we found that the promoter region of the gene contains stress-resistant elements, and the regulatory role of YABBY transcription factor in the anti-stress mechanism of remains to be studied. , and may be involved in the regulation of saponins in may be involved in the drought resistance mechanism in stems and leaves. This study may provide a theoretical basis for studying the regulation of terpenoids by the YABBY transcription factor and its resistance to abiotic stress.
Topics: Platycodon; Plant Proteins; Plant Leaves; Plants, Medicinal; Transcription Factors; Gene Expression Regulation, Plant
PubMed: 36681901
DOI: 10.1080/15592324.2022.2163069 -
Plant Physiology Nov 2023Arabidopsis (Arabidopsis thaliana) high-affinity NITRATE TRANSPORTER2.1 (NRT2.1) plays a dominant role in the uptake of nitrate, the most important nitrogen (N) source...
Arabidopsis (Arabidopsis thaliana) high-affinity NITRATE TRANSPORTER2.1 (NRT2.1) plays a dominant role in the uptake of nitrate, the most important nitrogen (N) source for most terrestrial plants. The nitrate-inducible expression of NRT2.1 is regulated by NIN-LIKE PROTEIN (NLP) family transcriptional activators and NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR1 (NIGT1) family transcriptional repressors. Phosphorus (P) availability also affects the expression of NRT2.1 because the PHOSPHATE STARVATION RESPONSE1 transcriptional activator activates NIGT1 genes in P-deficient environments. Here, we show a biology-based mathematical understanding of the complex regulation of NRT2.1 expression by multiple transcription factors using 2 different approaches: a microplate-based assay for the real-time measurement of temporal changes in NRT2.1 promoter activity under different nutritional conditions, and an ordinary differential equation (ODE)-based mathematical modeling of the NLP- and NIGT1-regulated expression patterns of NRT2.1. Both approaches consistently reveal that NIGT1 stabilizes the amplitude of NRT2.1 expression under a wide range of nitrate concentrations. Furthermore, the ODE model suggests that parameters such as the synthesis rate of NIGT1 mRNA and NIGT1 proteins and the affinity of NIGT1 proteins for the NRT2.1 promoter substantially influence the temporal expression patterns of NRT2.1 in response to nitrate. These results suggest that the NLP-NIGT1 feedforward loop allows a precise control of nitrate uptake. Hence, this study paves the way for understanding the complex regulation of nutrient acquisition in plants, thus facilitating engineered nutrient uptake and plant response patterns using synthetic biology approaches.
Topics: Anion Transport Proteins; Arabidopsis; Arabidopsis Proteins; Gene Expression Regulation, Plant; Nitrates; Plant Proteins; Transcription Factors
PubMed: 37595050
DOI: 10.1093/plphys/kiad458 -
International Journal of Molecular... Feb 2024Members of the phloem protein 16 (PP16) gene family are induced by elicitors in rice and the corresponding proteins from cucurbits, which display RNA binding and...
Members of the phloem protein 16 (PP16) gene family are induced by elicitors in rice and the corresponding proteins from cucurbits, which display RNA binding and intercellular transport activities, are accumulated in phloem sap. These proteins facilitate the movement of protein complexes through the phloem translocation flow and may be involved in the response to water deficit, among other functions. However, there is scant information regarding their function in other plants, including the identification of paralog genes in non-vascular plants and chlorophytes. In the present work, an evolutionary and structural analysis of the PP16 family in green plants (Viridiplantae) was carried out. Data mining in different databases indicated that likely originated from a larger gene present in an ancestral lineage that gave rise to chlorophytes and multicellular plants. This gene encodes a protein related to synaptotagmin, which is involved in vesicular transport in animal systems, although other members of this family play a role in lipid turnover in endomembranes and organelles. These proteins contain a membrane-binding C2 domain shared with PP16 proteins in vascular plants. In silico analysis of the predicted structure of the PP16 protein family identified several β-sheets, one α-helix, and intrinsically disordered regions. PP16 may have been originally involved in vesicular trafficking and/or membrane maintenance but specialized in long-distance signaling during the emergence of the plant vascular system.
Topics: Plant Proteins; Phloem; Plants; Biological Transport; Viridiplantae
PubMed: 38474088
DOI: 10.3390/ijms25052839 -
International Journal of Molecular... Dec 2023Though conserved in higher plants, the WOX transcription factors play crucial roles in plant growth and development of Lour., which shows pioneer position in land...
Though conserved in higher plants, the WOX transcription factors play crucial roles in plant growth and development of Lour., which shows pioneer position in land ecosystem formation and produces nutritional fruits. Identifying the family genes in is imperative for elucidating its growth and development mechanisms. However, the genes in have not yet been characterized. In this study, by identification 22 genes in based on current genome data, we classified family genes into three clades and nine types with homeodomains. We highlighted gene duplications of , which offered evidences of whole-genome duplication events. Promoter analysis illustrated that cis-regulatory elements related to light and stress responses and plant growth were enriched. Expression pattern and RT-qPCR results demonstrated that the majority of genes exhibited expression in the stem. displayed highest expression across various tissues. displayed a specific expression in the stem. Collectively, our study provided foundations for elucidating gene functions and further molecular design breeding in .
Topics: Multigene Family; Ecosystem; Gene Duplication; Transcription Factors; Promoter Regions, Genetic; Phylogeny; Gene Expression Regulation, Plant; Plant Proteins
PubMed: 38139178
DOI: 10.3390/ijms242417349 -
International Journal of Molecular... Nov 2023The glutelins are a family of abundant plant proteins comprised of four glutelin subfamilies (GluA, GluB, GluC, and GluD) encoded by 15 genes. In this study, expression...
The glutelins are a family of abundant plant proteins comprised of four glutelin subfamilies (GluA, GluB, GluC, and GluD) encoded by 15 genes. In this study, expression of subsets of rice glutelins were suppressed using CRISPR-Cas9 gene-editing technology to generate three transgenic rice variant lines, , , and . Suppression of the targeted glutelin genes was confirmed by SDS-PAGE, Western blot, and q-RT-PCR. Transgenic rice variants GluA1, GluB2, and GluC1 showed reduced amylose and starch content, increased prolamine content, reduced grain weight, and irregularly shaped protein aggregates/protein bodies in mature seeds. Targeted transcriptional profiling of immature seeds was performed with a focus on genes associated with grain quality, starch content, and grain weight, and the results were analyzed using the Pearson correlation test (requiring correlation coefficient absolute value ≥ 0.7 for significance). Significantly up- or down-regulated genes were associated with gene ontology (GO) and KEGG pathway functional annotations related to RNA processing (spliceosomal RNAs, group II catalytic introns, small nucleolar RNAs, microRNAs), as well as protein translation (transfer RNA, ribosomal RNA and other ribosome and translation factors). These results suggest that rice glutelin genes may interact during seed development with genes that regulate synthesis of starch and seed storage proteins and modulate their expression via post-transcriptional and translational mechanisms.
Topics: Glutens; Seed Storage Proteins; Oryza; Down-Regulation; CRISPR-Cas Systems; Gene Editing; Plant Proteins; Edible Grain; Seeds; Starch; Gene Expression Regulation, Plant
PubMed: 38069264
DOI: 10.3390/ijms242316941 -
Plant Physiology Dec 2023Nitrogen (N) is essential for plant growth and development. Therefore, understanding its utilization is essential for improving crop productivity. However, much remains...
Nitrogen (N) is essential for plant growth and development. Therefore, understanding its utilization is essential for improving crop productivity. However, much remains to be learned about plant N sensing and signaling. Here, rice (Oryza sativa) NUCLEAR FACTOR-YA5 (OsNF-YA5) expression was tightly regulated by N status and induced under N-deficient conditions. Overexpression (OE) of OsNF-YA5 in rice resulted in increased chlorophyll levels and delayed senescence compared to control plants under normal N conditions. Agronomic traits were significantly improved in OE plants and impaired in knockout mutants under N-deficient conditions. Using a dexamethasone-inducible system, we identified the putative targets of OsNF-YA5 that include amino acid, nitrate/peptide transporters, and NITRATE TRANSPORTER 1.1A (OsNRT1.1A), which functions as a key transporter in rice. OsNF-YA5 directly enhanced OsNRT1.1A expression and N uptake rate under N-deficient conditions. Besides, overexpression of OsNF-YA5 also enhanced the expression of GLUTAMINE SYNTHETASE 1/2 (GS1/2) and GLUTAMINE OXOGLUTARATE AMINOTRANSFERASE 1/2 (GOGAT1/2), increasing free amino acid contents under N-deficient conditions. Osa-miR169a expression showed an opposite pattern with OsNF-YA5 depending on N status. Further analysis revealed that osa-miR169a negatively regulates OsNF-YA5 expression and N utilization, demonstrating that an OsNF-YA5/osa-miR169a module tightly regulates rice N utilization for adaptation to N status.
Topics: Plant Proteins; Oryza; Nitrogen; Nitrate Transporters; Amino Acids; Gene Expression Regulation, Plant
PubMed: 37723121
DOI: 10.1093/plphys/kiad504 -
Scientific Reports Dec 2023Abiotic stresses are a significant constraint to plant production globally. Identifying stress-related genes can aid in the development of stress-tolerant elite...
Abiotic stresses are a significant constraint to plant production globally. Identifying stress-related genes can aid in the development of stress-tolerant elite genotypes and facilitate trait and crop manipulation. The primary aim of this study was to conduct whole transcriptome analyses of the salt-tolerant faba bean genotype, Hassawi-2, under different durations of salt stress (6 h, 12 h, 24 h, 48 h, and 72 h) at the early vegetative stage, to better understand the molecular basis of salt tolerance. After de novo assembly, a total of 140,308 unigenes were obtained. The up-regulated differentially expressed genes (DEGs) were 2380, 2863, 3057, 3484, and 4820 at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. Meanwhile, 1974, 3436, 2371, 3502, and 5958 genes were downregulated at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. These DEGs encoded various regulatory and functional proteins, including kinases, plant hormone proteins, transcriptional factors (TFs) basic helix-loop-helix (bHLH), Myeloblastosis (MYB), and (WRKY), heat shock proteins (HSPs), late embryogenesis abundant (LEA) proteins, dehydrin, antioxidant enzymes, and aquaporin proteins. This suggests that the faba bean genome possesses an abundance of salinity resistance genes, which trigger different adaptive mechanisms under salt stress. Some selected DEGs validated the RNA sequencing results, thus confirming similar gene expression levels. This study represents the first transcriptome analysis of faba bean leaves subjected to salinity stress offering valuable insights into the mechanisms governing salt tolerance in faba bean during the vegetative stage. This comprehensive investigation enhances our understanding of precise gene regulatory mechanisms and holds promise for the development of novel salt-tolerant faba bean salt-tolerant cultivars.
Topics: Salt Tolerance; Transcriptome; Salinity; Salt Stress; Gene Expression Profiling; Genotype; Plant Proteins; Gene Expression Regulation, Plant
PubMed: 38040745
DOI: 10.1038/s41598-023-48118-0 -
International Journal of Molecular... Jul 2023Cotton is a valuable cash crop in many countries. Cotton fiber is a trichome that develops from a single epidermal cell and serves as an excellent model for...
Cotton is a valuable cash crop in many countries. Cotton fiber is a trichome that develops from a single epidermal cell and serves as an excellent model for understanding cell differentiation and other life processes. Alternative splicing (AS) of genes is a common post-transcriptional regulatory process in plants that is essential for plant growth and development. The process of AS during cotton fiber formation, on the other hand, is mainly unknown. A substantial number of multi-exon genes were discovered to be alternatively spliced during cotton fiber formation in this study, accounting for 23.31% of the total number of genes in . Retention intron (RI) is not necessarily the most common AS type, indicating that AS genes and processes during fiber development are very temporal and tissue-specific. When compared to fiber samples, AS is more prevalent at the fiber initiation stages and in the ovule, indicating that development stages and tissues use different AS strategies. Genes involved in fiber development have gone through stage-specific AS, demonstrating that AS regulates cotton fiber development. Furthermore, AS can be regulated by trans-regulation elements such as splicing factor and cis-regulation elements such as gene length, exon numbers, and GC content, particularly at exon-intron junction sites. Our findings also suggest that increased DNA methylation may aid in the efficiency of AS, and that gene body methylation is key in AS control. Finally, our research will provide useful information about the roles of AS during the cotton fiber development process.
Topics: Alternative Splicing; Genes, Plant; Gene Expression Profiling; Gossypium; Cotton Fiber; Gene Expression Regulation, Plant; Plant Proteins
PubMed: 37511571
DOI: 10.3390/ijms241411812