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Trends in Plant Science Jun 2024Protein phosphorylation, the most common and essential post-translational modification, belongs to crucial regulatory mechanisms in plants, affecting their metabolism,... (Review)
Review
Protein phosphorylation, the most common and essential post-translational modification, belongs to crucial regulatory mechanisms in plants, affecting their metabolism, intracellular transport, cytoarchitecture, cell division, growth, development, and interactions with the environment. Protein kinases and phosphatases, two important families of enzymes optimally regulating phosphorylation, have now become important targets for gene editing in crops. We review progress on gene-edited protein kinases and phosphatases in crops using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). We also provide guidance for computational prediction of alterations and/or changes in function, activity, and binding of protein kinases and phosphatases as consequences of CRISPR/Cas9-based gene editing with its possible application in modern crop molecular breeding towards sustainable agriculture.
Topics: Gene Editing; Plant Breeding; Crops, Agricultural; Protein Kinases; CRISPR-Cas Systems; Phosphoric Monoester Hydrolases; Plant Proteins
PubMed: 38151445
DOI: 10.1016/j.tplants.2023.11.019 -
Journal of Experimental Botany Sep 2023Plant architecture imposes a large impact on crop yield. IDEAL PLANT ARCHITECTURE 1 (IPA1), which encodes a SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription...
Plant architecture imposes a large impact on crop yield. IDEAL PLANT ARCHITECTURE 1 (IPA1), which encodes a SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor, is a target of molecular design for improving grain yield. However, the roles of SPL transcription factors in regulating tomato (Solanum lycopersicum) plant architecture are unclear. Here, we show that the expression of SPL13 is down-regulated in the lateral buds of strigolactone (SL)-deficient ccd mutants and is induced by GR24 (a synthetic analog of SL). Knockout of SPL13 by CRISPR/Cas9 resulted in higher levels of cytokinins (CKs) and transcripts of the CK synthesis gene ISOPENTENYL TRANSFERASES 1 (IPT1) in the stem nodes, and more growth of lateral buds. GR24 suppresses CK synthesis and lateral bud growth in ccd mutants, but is not effective in spl13 mutants. On the other hand, silencing of the IPT1 gene inhibited bud growth of spl13 mutants. Interestingly, SL levels in root extracts and exudates are significantly increased in spl13 mutants. Molecular studies indicated that SPL13 directly represses the transcription of IPT1 and the SL synthesis genes CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7) and MORE AXILLARY GROWTH 1 (MAX1). The results demonstrate that SPL13 acts downstream of SL to suppress lateral bud growth by inhibiting CK synthesis in tomato. Tuning the expression of SPL13 is a potential approach for decreasing the number of lateral shoots in tomato.
Topics: Solanum lycopersicum; Transcription Factors; Plant Shoots; Gene Expression Regulation, Plant; Cytokinins; Lactones; Plant Proteins
PubMed: 37504507
DOI: 10.1093/jxb/erad303 -
International Journal of Molecular... Oct 2023The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory...
The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory roles in plant development and physiological processes, such as transcription regulation and signal transduction; it is also involved in anthocyanin biosynthesis. In rice, only was found to be associated with anthocyanin biosynthesis, and evolutionary analysis of the WD40 gene family in multiple species is less studied. Here, a genome-wide analysis of the subfamily belonging to WD40-TTG1 was performed in nine AA genome species: ssp. , ssp. , , , , , , , and . In this study, 383 WD40 genes in the genus were identified, and they were classified into four groups by phylogenetic analysis, with most members in group C and group D. They were found to be unevenly distributed across 12 chromosomes. A total of 39 collinear gene pairs were identified in the genus, and all were segmental duplications. WD40s had similar expansion patterns in the genus. Ka/Ks analyses indicated that they had undergone mainly purifying selection during evolution. Furthermore, WD40s in the genus have similar evolutionary patterns, so ssp. was used as a model species for further analysis. The cis-acting elements analysis showed that many genes were related to jasmonic acid and light response. Among them, contained elements of flavonoid synthesis, and had MYB binding sites, indicating that they might be related to anthocyanin synthesis. The expression profile analysis at different stages revealed that most were expressed in leaves, roots, and panicles. The expression of was further analyzed by qRT-PCR in 9311 (indica) under various hormone treatments and abiotic stresses. was found to be responsive to both phytohormones and abiotic stresses, suggesting that it might play an important role in plant stress resistance. And many might be more involved in cold stress tolerance. These findings contribute to a better understanding of the evolution of the WD40 subfamily. The analyzed candidate genes can be used for the exploration of practical applications in rice, such as cultivar culture for colored rice, stress tolerance varieties, and morphological marker development.
Topics: Oryza; Phylogeny; Anthocyanins; Genome, Plant; Cold-Shock Response; Gene Expression Regulation, Plant; Plant Proteins
PubMed: 37958759
DOI: 10.3390/ijms242115776 -
PloS One 2023Drought is the single greatest abiotic factor influencing crop yield worldwide. Plants remain in one area for extended periods, making them vulnerable to natural and...
Lupenone, a wonder chemical obtained from Euphorbia segetalis to boost affinity for the transcriptional factor escalating drought-tolerance in Solanum Lycopersicum: A cutting-edge computational biology approach.
Drought is the single greatest abiotic factor influencing crop yield worldwide. Plants remain in one area for extended periods, making them vulnerable to natural and man-made influences. Understanding plant drought responses will help us develop strategies for breeding drought-resistant crops. Large proteome analysis revealed that leaf and root tissue proteins respond to drought differently depending on the plant's genotype. Commonly known as tomatoes, Solanum Lycopersicum is a globally important vegetable crop. However, drought stress is one of the most significant obstacles to tomato production, making the development of cultivars adapted to dry conditions an essential goal of agricultural biotechnology. Breeders have put quite a lot of time and effort into the tomato to increase its productivity, adaptability, and resistance to biotic and abiotic challenges. However, conventional tomato breeding has only improved drought resistance due to the complexity of drought traits. The resilience of tomatoes under drought stress has been the subject of extensive study. Using contemporary sequencing approaches like genomics, transcriptomics, proteomics, and metabolomics has dramatically aided in discovering drought-responsive genes. One of the most prominent families of plant transcription factors, WRKY genes, plays a crucial role in plant growth and development in response to natural and abiotic stimuli. To develop plants that can withstand both biotic and abiotic stress, understanding the relationships between WRKY-proteins (transcription factors) and other proteins and ligands in plant cells is essential. This is despite the fact that tomatoes have a long history of domestication. This research aims to utilize Lupenone, a hormone produced in plant roots in response to stress, to increase drought resistance in plants. Lupenone exhibits a strong affinity for the WRKY protein at -9.64 kcal/mol. Molecular docking and modeling studies show that these polyphenols have a significant role in making Solanum Lycopersicum drought-resistant and improving the quality of its fruit. As a result of climate change, droughts are occurring more frequently and persisting for more extended periods, making it necessary to breed crops resistant to drought. While considerable variability for tolerance exists in wild cousins, little is known about the processes and essential genes influencing drought tolerance in cultivated tomato species.
Topics: Humans; Solanum lycopersicum; Droughts; Transcription Factors; Euphorbia; Molecular Docking Simulation; Plant Breeding; Stress, Physiological; Computational Biology; Plant Proteins; Gene Expression Regulation, Plant
PubMed: 37939107
DOI: 10.1371/journal.pone.0281293 -
International Journal of Molecular... May 2024Abiotic stressors, including drought, salt, cold, and heat, profoundly impact plant growth and development, forcing elaborate cellular responses for adaptation and... (Review)
Review
Abiotic stressors, including drought, salt, cold, and heat, profoundly impact plant growth and development, forcing elaborate cellular responses for adaptation and resilience. Among the crucial orchestrators of these responses is the CBL-CIPK pathway, comprising calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs). While CIPKs act as serine/threonine protein kinases, transmitting calcium signals, CBLs function as calcium sensors, influencing the plant's response to abiotic stress. This review explores the intricate interactions between the CBL-CIPK pathway and plant hormones such as ABA, auxin, ethylene, and jasmonic acid (JA). It highlights their role in fine-tuning stress responses for optimal survival and acclimatization. Building on previous studies that demonstrated the enhanced stress tolerance achieved by upregulating CBL and CIPK genes, we explore the regulatory mechanisms involving post-translational modifications and protein-protein interactions. Despite significant contributions from prior research, gaps persist in understanding the nuanced interplay between the CBL-CIPK system and plant hormone signaling under diverse abiotic stress conditions. In contrast to broader perspectives, our review focuses on the interaction of the pathway with crucial plant hormones and its implications for genetic engineering interventions to enhance crop stress resilience. This specialized perspective aims to contribute novel insights to advance our understanding of the potential of the CBL-CIPK pathway to mitigate crops' abiotic stress.
Topics: Signal Transduction; Stress, Physiological; Plant Growth Regulators; Plant Proteins; Gene Expression Regulation, Plant; Protein Serine-Threonine Kinases; Plants
PubMed: 38732261
DOI: 10.3390/ijms25095043 -
International Journal of Molecular... Jul 2023() is an important enzyme in the synthesis pathway of raffinose from sucrose and galactinol in higher plants and is involved in the regulation of seed development and...
() is an important enzyme in the synthesis pathway of raffinose from sucrose and galactinol in higher plants and is involved in the regulation of seed development and plant responses to abiotic stresses. In this study, we analyzed the families and profiled their alternative splicing patterns at the genome-wide scale from 10 grass species representing crops and grasses. A total of 73 genes were identified from grass species such as rice, maize, foxtail millet, and switchgrass. These genes were assigned to six groups based the phylogenetic analysis. We compared the gene structures, protein domains, and expression patterns of genes, and also unraveled the alternative transcripts of them. In addition, different conserved sequences were observed at these putative splice sites among grass species. The subcellular localization of suggested that the gene was expressed in the cytoplasm or cell membrane. Our findings provide comprehensive knowledge of the families in terms of genes and proteins, which will facilitate further functional characterization in grass species in response to abiotic stress.
Topics: Humans; Alternative Splicing; Phylogeny; Galactosyltransferases; Stress, Physiological; Setaria Plant; Gene Expression Regulation, Plant; Plant Proteins
PubMed: 37446297
DOI: 10.3390/ijms241311120 -
The Plant Cell Jan 2024
Topics: Phylogeny; Plant Proteins; Flowers
PubMed: 37943669
DOI: 10.1093/plcell/koad283 -
Genes Nov 2023Plant-specific YABBY transcription factors play an important role in lateral organ development and abiotic stress responses. However, the functions of the genes in...
Plant-specific YABBY transcription factors play an important role in lateral organ development and abiotic stress responses. However, the functions of the genes in quinoa remain elusive. In this study, twelve () genes were identified in the quinoa genome, and they were distributed on nine chromosomes. They were classified into FIL/YAB3, YAB2, YAB5, INO, and CRC clades. All genes consist of six or seven exons, and their proteins contain both N-terminal C2C2 zinc finger motifs and C-terminal YABBY domains. Ninety-three -regulatory elements were revealed in gene promoters, and they were divided into six groups, such as -elements involved in light response, hormone response, development, and stress response. Six genes were significantly upregulated by salt stress, while one was downregulated. Nine genes were upregulated under drought stress, whereas six genes were downregulated under cadmium treatment. Tissue expression profiles showed that nine genes were expressed in seedlings, leaves, and flowers, seven in seeds, and two specifically in flowers, but no expression was detected in roots. Furthermore, could rescue the mutant phenotype in but not , a paralog of , indicative of functional conservation and divergence among these genes. Taken together, these results lay a foundation for further functional analysis of genes in quinoa growth, development, and abiotic stress responses.
Topics: Plant Proteins; Chenopodium quinoa; Arabidopsis; Flowers; Plant Leaves
PubMed: 38003046
DOI: 10.3390/genes14112103 -
BMC Genomics Jul 2023Basic leucine zipper (bZIP) proteins are important transcription factors in plants. To study the role of bZIP transcription factors in walnut explant browning, this...
BACKGROUND
Basic leucine zipper (bZIP) proteins are important transcription factors in plants. To study the role of bZIP transcription factors in walnut explant browning, this study used bioinformatics software to analyze walnut bZIP gene family members, along with their transcript levels in different walnut tissues, to evaluate the transcriptional expression of this gene family during the primary culture of walnut explants and to reveal the mechanism of action of walnut bZIP genes in walnut explant browning.
RESULTS
The results identified 65 JrbZIP genes in the walnut genome, which were divided into 8 subfamilies and distributed on 16 chromosomes. The results of transcriptome data analysis showed that there were significant differences in the expression of four genes, namely, JrbZIP55, JrbZIP70, JrbZIP72, and JrbZIP88, under both vermiculite and agar culture conditions. There were multiple hormone (salicylic acid, abscisic acid, auxin, and gibberellin) signaling and regulatory elements that are responsive to stress (low temperature, stress, and defense) located in the promoter regions of JrbZIP55, JrbZIP70, JrbZIP72, and JrbZIP88. The walnut JrbZIP55 protein and Arabidopsis bZIP42 protein are highly homologous, and the proteins interacting with Arabidopsis bZIP42 include the AT2G19940 oxidoreductases, which act on aldehyde or oxygen-containing donors.
CONCLUSION
It is speculated that JrbZIP55 may participate in the regulation of browning in walnut explants.
Topics: Juglans; Arabidopsis; Gene Expression Profiling; Transcriptome; Genes, Plant; Basic-Leucine Zipper Transcription Factors; Gene Expression Regulation, Plant; Phylogeny; Plant Proteins
PubMed: 37407925
DOI: 10.1186/s12864-023-09492-1 -
Nature Communications Oct 2023Receptor-mediated transport of soluble proteins is nature's key to empowering eukaryotic cells to access a plethora of macromolecules, either by direct accumulation or...
Receptor-mediated transport of soluble proteins is nature's key to empowering eukaryotic cells to access a plethora of macromolecules, either by direct accumulation or as products from resulting biochemical pathways. The transport efficiency of these mechanisms results from the receptor's capability to capture, transport, and release ligands on the one hand and the cycling ability that allows for performing multiple rounds of ligand transport on the other. However, the plant VACUOLAR SORTING RECEPTOR (VSR) protein family is diverse, and their ligand-specificity and bidirectional trafficking routes and transport mechanisms remain highly controversial. Here we employ nanobody-epitope interaction-based molecular tools to assess the function of the VSR 7 in vivo. We demonstrate the specificity of the VSR7 for sequence-specific vacuolar sorting signals, and we trace its anterograde transport and retrograde recycling route. VSR7 localizes at the cis-Golgi apparatus at steady state conditions and transports ligands downstream to release them in the trans-Golgi network/early endosome (TGN/EE) before undergoing clathrin-dependent recycling from the TGN/EE back to the cis-Golgi.
Topics: trans-Golgi Network; Clathrin; Ligands; Golgi Apparatus; Protein Transport; Carrier Proteins; Plant Proteins; Endosomes
PubMed: 37903761
DOI: 10.1038/s41467-023-42331-1