-
International Journal of Molecular... Oct 2019In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial... (Review)
Review
In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial roles. Among them, atlas analysis of plants under different abiotic stresses, including salinity, drought, and toxic conditions, has become more important for uncovering the potential key genes and proteins in different plant tissues. High-quality genomic data and integrated analyses of transcriptomic, proteomic, metabolomics, and phenomic patterns provide a deeper understanding of how plants grow and survive under environmental stresses. This editorial mini-review aims to synthesize the 27 papers including two timely reviews that have contributed to this Special Issue, which focuses on concluding the recent progress in the Protein and Proteome Atlas in plants under different stresses. It covers various aspects of plant proteins ranging from agricultural proteomics, structure and function of proteins, novel techniques and approaches for gene and protein identification, protein quantification, proteomics for post-translational modifications (PTMs), and new insights into proteomics. The proteomics-based results in this issue will help the readers to gain novel insights for the understanding of complicated physiological processes in crops and other important plants in response to stressed conditions. Furthermore, these target genes and proteins that are important candidates for further functional validation in economic plants and crops can be studied.
Topics: Atlases as Topic; Gene Expression Regulation, Plant; Plant Physiological Phenomena; Plant Proteins; Protein Conformation; Proteomics; Stress, Physiological
PubMed: 31640274
DOI: 10.3390/ijms20205222 -
Plant Physiology Jun 2017Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined three-dimensional structure. The study of IDPs is a rapidly growing area as the...
Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined three-dimensional structure. The study of IDPs is a rapidly growing area as the crucial biological functions of more of these proteins are uncovered. In plants, IDPs are implicated in plant stress responses, signaling, and regulatory processes. A superfamily of cell wall proteins, the hydroxyproline-rich glycoproteins (HRGPs), have characteristic features of IDPs. Their protein backbones are rich in the disordering amino acid proline, they contain repeated sequence motifs and extensive posttranslational modifications (glycosylation), and they have been implicated in many biological functions. HRGPs are evolutionarily ancient, having been isolated from the protein-rich walls of chlorophyte algae to the cellulose-rich walls of embryophytes. Examination of HRGPs in a range of plant species should provide valuable insights into how they have evolved. Commonly divided into the arabinogalactan proteins, extensins, and proline-rich proteins, in reality, a continuum of structures exists within this diverse and heterogenous superfamily. An inability to accurately classify HRGPs leads to inconsistent gene ontologies limiting the identification of HRGP classes in existing and emerging omics data sets. We present a novel and robust motif and amino acid bias (MAAB) bioinformatics pipeline to classify HRGPs into 23 descriptive subclasses. Validation of MAAB was achieved using available genomic resources and then applied to the 1000 Plants transcriptome project (www.onekp.com) data set. Significant improvement in the detection of HRGPs using multiple-mer transcriptome assembly methodology was observed. The MAAB pipeline is readily adaptable and can be modified to optimize the recovery of IDPs from other organisms.
Topics: Amino Acid Motifs; Arabidopsis Proteins; Computational Biology; Glycoproteins; Hydroxyproline; Intrinsically Disordered Proteins; Plant Proteins; Proteome; Reproducibility of Results; Transcriptome
PubMed: 28446635
DOI: 10.1104/pp.17.00294 -
Bioengineered Apr 2022Owing to various undesirable health effects of sugar overconsumption, joint efforts are being made by industrial sectors and regulatory authorities to reduce sugar... (Review)
Review
Owing to various undesirable health effects of sugar overconsumption, joint efforts are being made by industrial sectors and regulatory authorities to reduce sugar consumption practices, worldwide. Artificial sweeteners are considered potential substitutes in several products, e.g., sugar alcohols (polyols), high-fructose corn syrup, powdered drink mixes, and other beverages. Nevertheless, their long-standing health effects continue to be debatable. Consequently, growing interest has been shifted in producing non-caloric sweetenersfrom renewable resources to meet consumers' dietary requirements. Except for the lysozyme protein, various sweet proteins including thaumatin, mabinlin, brazzein, monellin, miraculin, pentadin, and curculin have been identified in tropical plants. Given the high cost and challenging extortion of natural resources, producing these sweet proteins using engineered microbial hosts, such as and represents an appealing choice. Engineering techniques can be applied for large-scale biosynthesis of proteins, which can be used in biopharmaceutical, food, diagnostic, and medicine industries. Nevertheless, extensive work needs to be undertaken to address technical challenges in microbial production of sweet-tasting proteins in bulk. This review spotlights historical aspects, physicochemical properties (taste, safety, stability, solubility, and cost), and recombinant biosynthesis of sweet proteins. Moreover, future opportunities for process improvement based on metabolic engineering strategies are also discussed.
Topics: Bioprospecting; Biotechnology; Plant Proteins; Recombinant Proteins; Sweetening Agents; Taste
PubMed: 35435127
DOI: 10.1080/21655979.2022.2061147 -
Nature Communications Sep 2023Adapted plant pathogens from various microbial kingdoms produce hundreds of unrelated small secreted proteins (SSPs) with elusive roles. Here, we used AlphaFold-Multimer...
Adapted plant pathogens from various microbial kingdoms produce hundreds of unrelated small secreted proteins (SSPs) with elusive roles. Here, we used AlphaFold-Multimer (AFM) to screen 1879 SSPs of seven tomato pathogens for interacting with six defence-related hydrolases of tomato. This screen of 11,274 protein pairs identified 15 non-annotated SSPs that are predicted to obstruct the active site of chitinases and proteases with an intrinsic fold. Four SSPs were experimentally verified to be inhibitors of pathogenesis-related subtilase P69B, including extracellular protein-36 (Ecp36) and secreted-into-xylem-15 (Six15) of the fungal pathogens Cladosporium fulvum and Fusarium oxysporum, respectively. Together with a P69B inhibitor from the bacterial pathogen Xanthomonas perforans and Kazal-like inhibitors of the oomycete pathogen Phytophthora infestans, P69B emerges as an effector hub targeted by different microbial kingdoms, consistent with a diversification of P69B orthologs and paralogs. This study demonstrates the power of artificial intelligence to predict cross-kingdom interactions at the plant-pathogen interface.
Topics: Artificial Intelligence; Peptide Hydrolases; Endopeptidases; Solanum lycopersicum; Plant Proteins; Plant Diseases
PubMed: 37758696
DOI: 10.1038/s41467-023-41721-9 -
International Journal of Molecular... Mar 2021Studies implicating an important role for apyrase (NTPDase) enzymes in plant growth and development began appearing in the literature more than three decades ago. After... (Review)
Review
Studies implicating an important role for apyrase (NTPDase) enzymes in plant growth and development began appearing in the literature more than three decades ago. After early studies primarily in potato, and legumes, especially important discoveries that advanced an understanding of the biochemistry, structure and function of these enzymes have been published in the last half-dozen years, revealing that they carry out key functions in diverse other plants. These recent discoveries about plant apyrases include, among others, novel findings on its crystal structures, its biochemistry, its roles in plant stress responses and its induction of major changes in gene expression when its expression is suppressed or enhanced. This review will describe and discuss these recent advances and the major questions about plant apyrases that remain unanswered.
Topics: Apyrase; Catalytic Domain; Chemical Phenomena; Drug Discovery; Enzyme Inhibitors; Gene Expression Regulation, Plant; Models, Molecular; Plant Proteins; Protein Conformation; Structure-Activity Relationship
PubMed: 33807069
DOI: 10.3390/ijms22063283 -
Plant, Cell & Environment Jun 2021Salicylic acid (SA) plays pivotal role in plant defense against biotrophic and hemibiotrophic pathogens. Tremendous progress has been made in the field of SA... (Review)
Review
Salicylic acid (SA) plays pivotal role in plant defense against biotrophic and hemibiotrophic pathogens. Tremendous progress has been made in the field of SA biosynthesis and SA signaling pathways over the past three decades. Among the key immune players in SA signaling pathway, NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1) functions as a master regulator of SA-mediated plant defense. The function of NPR1 as an SA receptor has been controversial; however, after years of arguments among several laboratories, NPR1 has finally been proven as one of the SA receptors. The function of NPR1 is strictly regulated via post-translational modifications and transcriptional regulation that were recently found. More recent advances in NPR1 biology, including novel functions of NPR1 and the structure of SA receptor proteins, have brought this field forward immensely. Therefore, based on these recent discoveries, this review acts to provide a full picture of how NPR1 functions in plant immunity and how NPR1 gene and NPR1 protein are regulated at multiple levels. Finally, we also discuss potential challenges in future studies of SA signaling pathway.
Topics: Arabidopsis Proteins; Gene Expression Regulation, Plant; Phosphorylation; Plant Immunity; Plant Proteins; Salicylic Acid; Sumoylation; Ubiquitination
PubMed: 33495996
DOI: 10.1111/pce.14003 -
International Journal of Molecular... Jun 2021Plant abiotic stress responses are tightly regulated by different players at multiple levels. At transcriptional or post-transcriptional levels, several RNA binding... (Review)
Review
Plant abiotic stress responses are tightly regulated by different players at multiple levels. At transcriptional or post-transcriptional levels, several RNA binding proteins (RBPs) regulate stress response genes through RNA metabolism. They are increasingly recognized as critical modulators of a myriad of biological processes, including stress responses. Plant RBPs are heterogeneous with one or more conservative RNA motifs that constitute canonical/novel RNA binding domains (RBDs), which can bind to target RNAs to determine their regulation as per the plant requirements at given environmental conditions. Given its biological significance and possible consideration as a potential tool in genetic manipulation programs to improve key agronomic traits amidst frequent episodes of climate anomalies, studies concerning the identification and functional characterization of RBP candidate genes are steadily mounting. This paper presents a comprehensive overview of canonical and novel RBPs and their functions in major abiotic stresses including drought, heat, salt, and cold stress conditions. To some extent, we also briefly describe the basic motif structure of RBPs that would be useful in forthcoming studies. Additionally, we also collected RBP genes that were modulated by stress, but that lacked functional characterization, providing an impetus to conduct further research.
Topics: Cold-Shock Response; Droughts; Heat-Shock Response; Plant Proteins; Protein Domains; RNA-Binding Proteins; Salinity; Salt Stress; Stress, Physiological
PubMed: 34201749
DOI: 10.3390/ijms22136731 -
The New Phytologist Jan 2020Strigolactones are an important class of plant signalling molecule with both external rhizospheric and internal hormonal functions in flowering plants. The past decade... (Review)
Review
Strigolactones are an important class of plant signalling molecule with both external rhizospheric and internal hormonal functions in flowering plants. The past decade has seen staggering progress in strigolactone biology, permitting highly detailed understanding of their signalling, synthesis and biological roles - or so it seems. However, phylogenetic analyses show that strigolactone signalling mediated by the D14-SCF -SMXL7 complex is only one of a number of closely related signalling pathways, and is much less ubiquitous in land plants than might be expected. The existence of closely related pathways, such as the KAI2-SMAX1 module, challenges many of our assumptions about strigolactones, and in particular emphasises how little we understand about the specificity of strigolactone signalling with respect to related signalling pathways. In this review, we examine recent advances in strigolactone signalling, taking a holistic evolutionary view to identify the ambiguities and uncertainties in our understanding. We highlight that while we now have highly detailed molecular models for the core mechanism of D14-SMXL7 signalling, we still do not understand the ligand specificity of D14, the specificity of its interaction with SMXL7, nor the specificity of SMXL7 function. Our analysis therefore identifies key areas requiring further study.
Topics: Lactones; Phylogeny; Plant Development; Plant Proteins; Receptors, Cell Surface; Signal Transduction
PubMed: 31442309
DOI: 10.1111/nph.16135 -
Molecular Plant Pathology Nov 2023The susceptibility factor TOBAMOVIRUS MULTIPLICATION 1 (TOM1) is required for efficient multiplication of tobacco mosaic virus (TMV). Although some phylogenetic and...
The susceptibility factor TOBAMOVIRUS MULTIPLICATION 1 (TOM1) is required for efficient multiplication of tobacco mosaic virus (TMV). Although some phylogenetic and functional analyses of the TOM1 family members have been conducted, a comprehensive analysis of the TOM1 homologues based on phylogeny from the most ancient to the youngest representatives within the plant kingdom, analysis of support for tobamovirus accumulation and interaction with other host and viral proteins has not been reported. In this study, using Nicotiana benthamiana and TMV as a model system, we functionally characterized the TOM1 homologues from N. benthamiana and other plant species from different plant lineages. We modified a multiplex genome editing tool and generated a sextuple mutant in which TMV multiplication was dramatically inhibited. We showed that TOM1 homologues from N. benthamiana exhibited variable capacities to support TMV multiplication. Evolutionary analysis revealed that the TOM1 family is restricted to the plant kingdom and probably originated in the Chlorophyta division, suggesting an ancient origin of the TOM1 family. We found that the TOM1 family acquired the ability to promote TMV multiplication after the divergence of moss and spikemoss. Moreover, the capacity of TOM1 orthologues from different plant species to promote TMV multiplication and the interactions between TOM1 and TOM2A and between TOM1 and TMV-encoded replication proteins are highly conserved, suggesting a conserved nature of the TOM2A-TOM1-TMV Hel module in promoting TMV multiplication. Our study not only revealed a conserved nature of a gene module to promote tobamovirus multiplication, but also provides a valuable strategy for TMV-resistant crop development.
Topics: Tobacco Mosaic Virus; Tobamovirus; Phylogeny; Plant Proteins; Nicotiana; Plant Diseases
PubMed: 37443447
DOI: 10.1111/mpp.13375 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Jan 2022Salt stress may cause primary osmotic stress and ion toxicity, as well as secondary oxidative stress and nutritional stress in plants, which hampers the agricultural... (Review)
Review
Salt stress may cause primary osmotic stress and ion toxicity, as well as secondary oxidative stress and nutritional stress in plants, which hampers the agricultural production. Salt stress-responsive transcription factors can mitigate the damage of salt stress to plants through regulating the expression of downstream target genes. Based on the soil salinization and its damage to plants, and the central regulatory role of transcription factors in the plant salt stress-responsive signal transduction network, this review summarized the salt stress-responsive signal transduction pathways that the transcription factors are involved, and the application of salt stress-responsive transcription factors to enhance the salt tolerance of plants. We also reviewed the transcription factors-regulated complex downstream gene network which is formed by forming homo- or heterodimers between transcription factors and by forming complexes with regulatory proteins. This paper provides a theoretical basis for understanding the role of salt stress-responsive transcription factors in the salt stress regulatory network, which may facilitate the molecular breeding for improved stress resistance.
Topics: Gene Expression Regulation, Plant; Osmotic Pressure; Plant Proteins; Plants, Genetically Modified; Salt Stress; Salt Tolerance; Stress, Physiological; Transcription Factors
PubMed: 35142118
DOI: 10.13345/j.cjb.210135