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The Plant Cell May 2024Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic... (Review)
Review
Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic and complex program that involves interactions between mRNAs, transfer RNAs, and the ribosome machinery through both cis- and trans-regulation while integrating internal and external signals. Translational control can act in a global (transcriptome-wide) or mRNA-specific manner. Recent advances in genome-wide techniques, particularly ribosome profiling and proteomics, have led to numerous exciting discoveries in both global and mRNA-specific translation. In this review, we aim to provide a "primer" that introduces readers to this fascinating yet complex cellular process and provide a big picture of how essential components connect within the network. We begin with an overview of mRNA translation, followed by a discussion of the experimental approaches and recent findings in the field, focusing on unannotated translation events and translational control through cis-regulatory elements on mRNAs and trans-acting factors, as well as signaling networks through 3 conserved translational regulators TOR, SnRK1, and GCN2. Finally, we briefly touch on the spatial regulation of mRNAs in translational control. Here, we focus on cytosolic mRNAs; translation in organelles and viruses is not covered in this review.
Topics: Protein Biosynthesis; Gene Expression Regulation, Plant; Plants; RNA, Messenger; Ribosomes; Plant Proteins; Signal Transduction
PubMed: 37437121
DOI: 10.1093/plcell/koad197 -
Planta Medica Jun 2024Peptides have emerged as key regulators in various physiological processes, including growth, development, stress, and defense responses within plants as well as... (Review)
Review
Peptides have emerged as key regulators in various physiological processes, including growth, development, stress, and defense responses within plants as well as ecological interactions of plants with microbes and animals. Understanding and harnessing plant peptides can lead to the development of innovative strategies for crop improvement, increasing agricultural productivity, and enhancing resilience to environmental challenges such as drought, pests, and diseases. Moreover, some plant peptides have shown promise in human health applications, with potential therapeutic benefits as ingredients in herbal medicines as well as novel drug leads. The exploration of plant peptides is essential for unraveling the mysteries of plant biology and advancing peptide drug discovery. This short personal commentary provides a very brief overview about the field of plant-derived peptides and a personal word of motivation to increase the number of scientists in pharmacognosy working with these fascinating biomolecules.
Topics: Drug Discovery; Biological Products; Peptides; Humans; Plant Proteins; Plants; Animals
PubMed: 38843800
DOI: 10.1055/a-2219-9724 -
BMC Plant Biology Oct 2023Mechanosensitive (MS) ion channels provide efficient molecular mechanism for transducing mechanical forces into intracellular ion fluxes in all kingdoms of life. The...
Mechanosensitive (MS) ion channels provide efficient molecular mechanism for transducing mechanical forces into intracellular ion fluxes in all kingdoms of life. The mechanosensitive channel of small conductance (MscS) was one of the best-studied MS channels and its homologs (MSL, MscS-like) were widely distributed in cell-walled organisms. However, the origin, evolution and expansion of MSL proteins in plants are still not clear. Here, we identified more than 2100 MSL proteins from 176 plants and conducted a broad-scale phylogenetic analysis. The phylogenetic tree showed that plant MSL proteins were divided into three groups (I, II and III) prior to the emergence of chlorophytae algae, consistent with their specific subcellular localization. MSL proteins were distributed unevenly into each of plant species, and four parallel expansion was identified in angiosperms. In Brassicaceae, most MSL duplicates were derived by whole-genome duplication (WGD)/segmental duplications. Finally, a hypothetical evolutionary model of MSL proteins in plants was proposed based on phylogeny. Our studies illustrate the evolutionary history of the MSL proteins and provide a guide for future functional diversity analyses of these proteins in plants.
Topics: Phylogeny; Plants; Ion Channels; Plant Proteins; Evolution, Molecular
PubMed: 37794319
DOI: 10.1186/s12870-023-04479-2 -
The EMBO Journal Sep 2023In virus-host interactions, nucleic acid-directed first lines of defense that allow viral clearance without compromising growth are of paramount importance. Plants use...
In virus-host interactions, nucleic acid-directed first lines of defense that allow viral clearance without compromising growth are of paramount importance. Plants use the RNA interference pathway as a basal antiviral immune system, but additional RNA-based mechanisms of defense also exist. The infectivity of a plant positive-strand RNA virus, alfalfa mosaic virus (AMV), relies on the demethylation of viral RNA by the recruitment of the cellular N6-methyladenosine (m A) demethylase ALKBH9B, but how demethylation of viral RNA promotes AMV infection remains unknown. Here, we show that inactivation of the Arabidopsis cytoplasmic YT521-B homology domain (YTH)-containing m A-binding proteins ECT2, ECT3, and ECT5 is sufficient to restore AMV infectivity in partially resistant alkbh9b mutants. We further show that the antiviral function of ECT2 is distinct from its previously demonstrated function in the promotion of primordial cell proliferation: an ect2 mutant carrying a small deletion in its intrinsically disordered region is partially compromised for antiviral defense but not for developmental functions. These results indicate that the m A-YTHDF axis constitutes a novel branch of basal antiviral immunity in plants.
Topics: Antiviral Agents; Plant Proteins; RNA-Binding Proteins; Arabidopsis; RNA, Viral; RNA Viruses; Arabidopsis Proteins; Intracellular Signaling Peptides and Proteins
PubMed: 37431920
DOI: 10.15252/embj.2022113378 -
Plant Signaling & Behavior Dec 2023The mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved plant cell signaling pathway that plays an important role in plant growth and...
The mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved plant cell signaling pathway that plays an important role in plant growth and development and stress response. Currently, MAPK cascade genes have been identified and reported in a variety of plants including , , and , but have not been identified in foxtail millet (). In this study, a total of 93 MAPK cascade genes, including 15 , 10 and 68 genes, were identified by genome-wide analysis of foxtail millet, and these genes were distributed on nine chromosomes of foxtail millet. Using phylogenetic analysis, we divided the and into four subgroups, respectively, and the into three subgroups (Raf, ZIK, and MEKK). Whole-genome duplication analysis revealed that there are 14 duplication pairs in the MAPK cascade family in foxtail millet, and they are expanded by segmental replication events. Results from quantitative real-time PCR (qRT-PCR) revealed that the expression levels of most and were changed under both exogenous hormone and abiotic stress treatments, with and being induced under almost all treatments, while the expression of was repressed. In a nutshell, this study will shed some light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to hormonal and abiotic stress signaling pathways in foxtail millet ().
Topics: Setaria Plant; Plant Proteins; Phylogeny; Stress, Physiological; Multigene Family; Arabidopsis; Gene Expression Regulation, Plant
PubMed: 37585594
DOI: 10.1080/15592324.2023.2246228 -
Nature Chemical Biology Aug 2023Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection of transcripts and metabolites at the level of single cells...
Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection of transcripts and metabolites at the level of single cells and high-resolution determination of gene regulatory features. Here, using a complementary, multi-omics approach, we interrogated the monoterpene indole alkaloid (MIA) biosynthetic pathway in Catharanthus roseus, a source of leading anticancer drugs. We identified clusters of genes involved in MIA biosynthesis on the eight C. roseus chromosomes and extensive gene duplication of MIA pathway genes. Clustering was not limited to the linear genome, and through chromatin interaction data, MIA pathway genes were present within the same topologically associated domain, permitting the identification of a secologanin transporter. Single-cell RNA-sequencing revealed sequential cell-type-specific partitioning of the leaf MIA biosynthetic pathway that, when coupled with a single-cell metabolomics approach, permitted the identification of a reductase that yields the bis-indole alkaloid anhydrovinblastine. We also revealed cell-type-specific expression in the root MIA pathway.
Topics: Catharanthus; Plants, Medicinal; Multiomics; Indole Alkaloids; Antineoplastic Agents; Monoterpenes; Gene Expression Regulation, Plant; Plant Proteins
PubMed: 37188960
DOI: 10.1038/s41589-023-01327-0 -
Current Biology : CB Jul 2023Cell polarity-broadly defined as the asymmetric distribution of cellular activities and subcellular components within a cell-determines the geometry of cell growth and...
Cell polarity-broadly defined as the asymmetric distribution of cellular activities and subcellular components within a cell-determines the geometry of cell growth and division during development. RHO GTPase proteins regulate the establishment of cell polarity and are conserved among eukaryotes. RHO of plant (ROP) proteins are a subgroup of RHO GTPases that are required for cellular morphogenesis in plants. However, how ROP proteins modulate the geometry of cell growth and division during the morphogenesis of plant tissues and organs is not well understood. To investigate how ROP proteins function during tissue development and organogenesis, we characterized the function of the single-copy ROP gene of the liverwort Marchantia polymorpha (MpROP). M. polymorpha develops morphologically complex three-dimensional tissues and organs exemplified by air chambers and gemmae, respectively. Mprop loss-of-function mutants form defective air chambers and gemmae, indicating ROP function is required for tissue development and organogenesis. During air chamber and gemma development in wild type, the MpROP protein is enriched to sites of polarized growth at the cell surface and accumulates at the expanding cell plate of dividing cells. Consistent with these observations, polarized cell growth is lost and cell divisions are misoriented in Mprop mutants. We propose that ROP regulates both polarized cell growth and cell division orientation in a coordinated manner to orchestrate tissue development and organogenesis in land plants.
Topics: rho GTP-Binding Proteins; Cell Division; Plants; Plant Proteins; Morphogenesis; Marchantia
PubMed: 37385256
DOI: 10.1016/j.cub.2023.06.015 -
Molecules (Basel, Switzerland) Dec 2023Repeated exposure to pathogens leads to evolutionary selection of adaptive traits. Many species transfer immunological memory to their offspring to counteract future...
Repeated exposure to pathogens leads to evolutionary selection of adaptive traits. Many species transfer immunological memory to their offspring to counteract future immune challenges. Transfer factors such as those found in the colostrum are among the many mechanisms where transfer of immunologic memory from one generation to the next can be achieved for an enhanced immune response. Here, a library of 100 plants with high protein contents was screened to find plant-based proteins that behave like a transfer factor moiety to boost human immunity. Aqueous extracts from candidate plants were tested in a human peripheral blood mononuclear cell (PBMC) cytotoxicity assay using human cancerous lymphoblast cells-with K562 cells as a target and natural killer cells as an effector. Plant extracts that caused PBMCs to exhibit enhanced killing beyond the capability of the colostrum-based transfer factor were considered hits. Primary screening yielded an 11% hit rate. The protein contents of these hits were tested via a Bradford assay and Coomassie-stained SDS-PAGE, where three extracts were confirmed to have high protein contents. Plants with high protein contents underwent C18 column fractionation using methanol gradients followed by membrane ultrafiltration to isolate protein fractions with molecular weights of <3 kDa, 3-30 kDa, and >30 kDa. It was found that the 3-30 kDa and >30 kDa fractions had high activity in the PBMC cytotoxicity assay. The 3-30 kDa ultrafiltrates from the top two hits, seeds from and , were then selected for protein identification by mass spectrometry. The majority of the proteins in the fractions were found to be seed storage proteins, with a low abundance of proteins involved in plant defense and stress response. These findings suggest that or extracts could be considered for further characterization and immune functional exploration with a possibility of supplemental use to bolster recipients' immune response.
Topics: Humans; Plant Proteins; Leukocytes, Mononuclear; Transfer Factor; Plants; Mustard Plant; Raphanus
PubMed: 38138452
DOI: 10.3390/molecules28247961 -
International Journal of Molecular... Aug 2023WUSCHEL-related homeobox (WOX) proteins are very important in controlling plant development and stress responses. However, the WOX family members and their role in...
WUSCHEL-related homeobox (WOX) proteins are very important in controlling plant development and stress responses. However, the WOX family members and their role in response to abiotic stresses are largely unknown in melon ( L.). In this study, 11 WOX (CmWOX) transcript factors with conserved WUS and homeobox motif were identified and characterized, and subdivided into modern clade, ancient clade and intermediate clade based on bioinformatic and phylogenetic analysis. Evolutionary analysis revealed that the CmWOX family showed protein variations in Arabidopsis, tomato, cucumber, melon and rice. Alignment of protein sequences uncovered that all CmWOXs had the typical homeodomain, which consisted of conserved amino acids. -element analysis showed that genes may response to abiotic stress. RNA-seq and qRT-PCR results further revealed that the expression of partially genes are associated with cold and drought. and were constitutively expressed under abiotic stresses, may play a role in abiotic processes during plant development. Taken together, this study offers new perspectives on the CmWOX family's interaction and provides the framework for research on the molecular functions of genes.
Topics: Genes, Homeobox; Cucumis melo; Phylogeny; Cucurbitaceae; Multigene Family; Genes, Plant; Arabidopsis; Gene Expression Regulation, Plant; Plant Proteins; Homeodomain Proteins; Arabidopsis Proteins
PubMed: 37569702
DOI: 10.3390/ijms241512326 -
International Journal of Molecular... Sep 2023Expansin proteins, a crucial class of intracellular proteins, are known to play a vital role in facilitating processes like cell wall relaxation and cell growth. Recent...
Expansin proteins, a crucial class of intracellular proteins, are known to play a vital role in facilitating processes like cell wall relaxation and cell growth. Recent discoveries have revealed that expansin proteins also have significant functions in plant growth, development, and response to resistance. However, the expansin gene family, particularly in emmer wheat, has not been thoroughly studied, particularly in terms of evolution. In this study, we identified 63 and 49 from the latest genome versions of wild emmer wheat (WEW) and durum wheat (DW), respectively. The physicochemical properties of the encoded expansin proteins exhibited minimal differences, and the gene structures remained relatively conserved. Phylogenetic analysis categorized the proteins into three subfamilies, namely EXPA, EXPB, and EXLA, in addition to the EXLB subfamily. Furthermore, codon preference analysis revealed an increased usage frequency of the nucleotide "T" in expansin proteins throughout the evolution of WEW and DW. Collinearity analysis demonstrated higher orthology between the expansin proteins of WEW and DW, with a Ka/Ks ratio ranging from 0.4173 to 0.9494, indicating purifying selection during the evolution from WEW to DW. Haplotype analysis of the expansin gene family identified five genes in which certain haplotypes gradually became dominant over the course of evolution, enabling adaptation for survival and improvement. Expression pattern analysis indicated tissue-specific expression of expansin genes in emmer wheat, and some of these genes were quantified through qRT-PCR to assess their response to salt stress. These comprehensive findings present the first systematic analysis of the expansin protein gene family during the evolution from WEW to DW, providing a foundation for further understanding the functions and biological roles of expansin protein genes in emmer wheat.
Topics: Triticum; Phylogeny; Plant Proteins; Genes, Plant; Multigene Family; Gene Expression Regulation, Plant
PubMed: 37762423
DOI: 10.3390/ijms241814120