Plant Glycine-Rich Proteins in Stress Response: An Emerging, Still Prospective Story

Exploring the mechanism of seed shattering in Psathyrostachys juncea through histological analysis and comparative transcriptomics

BACKGROUND

Seed shattering (SS) negatively impacts seed yield in Psathyrostachys juncea. Understanding and improving the SS trait requires elucidating the regulatory mechanisms of SS and identifying the key genes involved.

RESULTS

This study presents a comprehensive analysis of the abscission zone (AZ) structures at four developmental stages in two P. juncea genotypes. High-SS P. juncea (H) exhibited a significantly higher SS rate than low-SS P. juncea (L) at all four developmental stages. Anatomical analysis revealed that the degree of lignification in the AZ cell walls is related to the integrity of the abscission structure. The degradation of the AZ in H occurred earlier and was more severe compared to L. At different developmental stages of the AZ, H exhibited higher cellulase and polygalacturonase activities and higher abscisic acid contents compared to L. Conversely, L showed higher lignin, cytokinin, auxin, and gibberellin contents than H. Transcriptomic analysis identified key metabolic pathways related to SS in P. juncea, such as phenylpropanoid biosynthesis, fructose and mannose metabolism, galactose metabolism, and pentose and glucuronate interconversions. The integration of morphological, histological, physiochemical, and metabolic data led to the identification of critical genes, including AUX1, CKX, ABF, GH3, 4CL, CCoAOMT, BGAL, Gal, and PG. The roles of these genes were involved in the regulation of plant hormones and in the synthesis and degradation of cell walls within the AZ.

CONCLUSIONS

This study provides an in-depth understanding of the regulatory mechanisms of SS in P. juncea through comparative transcriptomic analysis. The SS in P. juncea may result from the degradation of the cell wall regulated by cell wall hydrolases genes. The genes identified in this study provide a basis for the genetic improvement of SS traits and serve as a reference for research on other grass species.

Transcriptome and molecular evidence of HvMORF8 conferring drought-tolerance in barley

Drought is one of the most devastating abiotic stresses worldwide, which severely limits crop yield. Tibetan wild barley is a treasure trove of useful genes for crop improvement including drought tolerance. Here, we detected large-scale changes of gene expression in response to drought stress with a substantial difference among contrasting Tibetan barley genotypes XZ5 (drought-tolerant), XZ54 (drought-sensitive) and cv. Tadmor (drought-tolerant). Drought stress led to upregulations of 142 genes involved in transcription, metabolism, protein synthesis, stress defense, transport and signal transduction in XZ5, but those genes were down-regulated or unchanged in XZ54 and Tadmor. We identified and functionally characterized a novel multiple organellar RNA editing factors 8 (HvMORF8), which was up-regulated by drought stress in XZ5, but unchanged in XZ54 and Tadmor under drought stress. Phylogenetic analysis showed that orthologues of HvMORF8 can be traced back to the closest gymnosperm species such as Cycas micholitzii, implicating a potential evolutionary origin for MORF8 from a common ancestor in early seed plants. Virus-induced HvMORF8 silencing in XZ5 led to hypersensitivity to drought stress, demonstrating it is a positive regulator of drought tolerance in barley. RNA sequencing of BSMV:HvMORF8 and control plants reveals that silencing of HvMORF8 suppresses genes involved in osmolytes transport, cell wall modification and antioxidants, resulting in water metabolism disorder and overaccumulation of reactive oxygen species (ROS) under drought stress. Therefore, we propose HvMORF8-mediated regulatory drought tolerance mechanisms at transcriptomic level in XZ5, providing new insight into the genetic basis of plastid RNA editing function of HvMORF8 for barley drought tolerance.

Photorespiratory Metabolism and Its Regulatory Links to Plant Defence Against Pathogens

When plants face biotic stress, the induction of defence responses imposes a massive demand for carbon and energy resources, which could decrease the reserves allocated towards growth. These growth-defence trade-offs have important implications for plant fitness and productivity and influence the outcome of plant-pathogen interactions. Biotic stress strongly affects plant cells' primary metabolism, including photosynthesis and respiration, the main source of energy and carbon skeletons for plant growth, development, and defence. Although the nature of photosynthetic limitations imposed by pathogens is variable, infection often increases photorespiratory pressure, generating conditions that promote ribulose-1,5-bisphosphate oxygenation, leading to a metabolic shift from assimilation to photorespiration. Photorespiration, the significant metabolic flux following photosynthesis, protects the photosynthetic apparatus from photoinhibition. However, recent studies reveal that its role is far beyond photoprotection. The intermediates of the photorespiratory cycle regulate photosynthesis, and photorespiration interacts with the metabolic pathways of nitrogen and sulphur, shaping the primary metabolism for stress responses. This work aims to present recent insights into the integration of photorespiration within the network of primary metabolism under biotic stress. It also explores the potential implications of regulating photosynthetic-photorespiratory metabolism for plant defence against bacterial and fungal pathogens.

Structural basis of nucleic acid recognition by the N-terminal cold shock domain of the plant glycine-rich protein AtGRP2

AtGRP2 is a glycine-rich, RNA-binding protein that plays pivotal roles in abiotic stress response and flowering time regulation in Arabidopsis thaliana. AtGRP2 consists of an N-terminal cold shock domain (CSD) and two C-terminal CCHC-type zinc knuckles interspersed with glycine-rich regions. Here, we investigated the structure, dynamics, and nucleic acid-binding properties of AtGRP2-CSD. The 2D [1H,15N] heteronuclear single quantum coherence spectrum of AtGRP2-CSD1-79 revealed the presence of a partially folded intermediate in equilibrium with the folded state. The addition of 11 residues at the C terminus stabilized the folded conformation. The three-dimensional structure of AtGRP2-CSD1-90 unveiled a β-barrel composed of five antiparallel β-strands and a 310 helical turn, along with an ordered C-terminal extension, a conserved feature in eukaryotic CSDs. Direct contacts between the C-terminal extension and the β3-β4 loop further stabilized the CSD fold. AtGRP2-CSD1-90 exhibited nucleic acid binding via solvent-exposed residues on strands β2 and β3, as well as the β3-β4 loop, with higher affinity for DNA over RNA, particularly favoring pyrimidine-rich sequences. Furthermore, DNA binding induced rigidity in the β3-β4 loop, evidenced by 15N-{1H} NOE values. Mutation of residues W17, F26, and F37, in the central β-sheet, completely abolished DNA binding, highlighting the significance of π-stacking interactions in the binding mechanism. These results shed light on the mechanism of nucleic acid recognition employed by AtGRP2, creating a framework for the development of biotechnological strategies aimed at enhancing plant resistance to abiotic stresses.

Genome of Halimeda opuntia reveals differentiation of subgenomes and molecular bases of multinucleation and calcification in algae

Algae mostly occur either as unicellular (microalgae) or multicellular (macroalgae) species, both being uninucleate. There are important exceptions, however, as some unicellular algae are multinucleate and macroscopic, some of which inhabit tropical seas and contribute to biocalcification and coral reef robustness. The evolutionary mechanisms and ecological significance of multinucleation and associated traits (e.g., rapid wound healing) are poorly understood. Here, we report the genome of Halimeda opuntia, a giant multinucleate unicellular chlorophyte characterized by interutricular calcification. We achieve a high-quality genome assembly that shows segregation into four subgenomes, with evidence for polyploidization concomitant with historical sea level and climate changes. We further find myosin VIII missing in H. opuntia and three other unicellular multinucleate chlorophytes, suggesting a potential mechanism that may underpin multinucleation. Genome analysis provides clues about how the unicellular alga could survive fragmentation and regenerate, as well as potential signatures for extracellular calcification and the coupling of calcification with photosynthesis. In addition, proteomic alkalinity shifts were found to potentially confer plasticity of H. opuntia to ocean acidification (OA). Our study provides crucial genetic information necessary for understanding multinucleation, cell regeneration, plasticity to OA, and different modes of calcification in algae and other organisms, which has important implications in reef conservation and bioengineering.

1H NMR analysis of metabolites from leaf tissue of resistant and susceptible oil palm breeding materials against Ganoderma boninense

INTRODUCTION

Breeding for oil palm resistance against basal stem rot caused by Ganoderma boninense is challenging and time-consuming. Advanced oil palm gene pools are very limited, hence it is assumed that parental palms have experienced genetic drift and lost their resistance genes against Ganoderma. High-throughput selection criteria should be developed. Metabolomic analysis using 1H nuclear magnetic resonance (NMR) spectroscopy is easy, and the resulting metabolite can be used as a diagnostic tool for detecting disease in various host-pathogen combinations.

OBJECTIVES

The objective of this study was to identify metabolite variations in Dura (D) and Pisifera (P) parental palms with different resistance levels against Ganoderma and moderately resistant DxP using 1H NMR analysis.

METHODS

Leaf tissues of seven different oil palm categories consisting of: resistant, moderate, and susceptible Dura (D); moderate and susceptible Pisifera (P); resistant Tenera/Pisifera (T/P) parental palms; and moderately resistant DxP variety progenies, were sampled and their metabolites were determined using NMR spectroscopy.

RESULTS

Twenty-nine types of metabolites were identified, and most of the metabolites fall in the monosaccharides, amino acids, and fatty acids compound classes. The PCA, PLS-DA, and heatmap multivariate analysis indicated two identified groups of resistance based on their metabolites. The first group consisted of resistant T/P, moderate P, resistant D, and moderately resistant DxP. In contrast, the second group consisted of susceptible P, moderate D, and susceptible D. Glycerol and ascorbic acid were detected as biomarker candidates by OPLS-DA to differentiate moderately resistant DxP from susceptible D and P. The pathway analysis suggested that glycine, serine, and threonine metabolism and taurine and hypotaurine metabolism were involved in the oil palm defense mechanism against Ganoderma.

CONCLUSION

A metabolomic study with 1H NMR was able to describe the metabolite composition that could differentiate the characteristics of oil palm resistance against basal stem rot (BSR) caused by G. boninense. These metabolites revealed in this study have enormous potential to become support tools for breeding new oil palm varieties with higher resistance against BSR.

Fast-track adaptive laboratory evolution of Cupriavidus necator H16 with divalent metal cations

Microbial strain improvement through adaptive laboratory evolution (ALE) has been a key strategy in biotechnology for enhancing desired phenotypic traits. In this Biotech Method paper, we present an accelerated ALE (aALE) workflow and its successful implementation in evolving Cupriavidus necator H16 for enhanced tolerance toward elevated glycerol concentrations. The method involves the deliberate induction of genetic diversity through controlled exposure to divalent metal cations, enabling the rapid identification of improved variants. Through this approach, we observed the emergence of robust variants capable of growing in high glycerol concentration environments, demonstrating the efficacy of our aALE workflow. When cultivated in 10% v/v glycerol, the adapted variant Mn-C2-B11, selected through aALE, achieved a final OD600 value of 56.0 and a dry cell weight of 15.2 g L-1, compared to the wild type (WT) strain's final OD600 of 39.1 and dry cell weight of 8.4 g L-1. At an even higher glycerol concentration of 15% v/v, Mn-C2-B11 reached a final OD600 of 48.9 and a dry cell weight of 12.7 g L-1, in contrast to the WT strain's final OD600 of 9.0 and dry cell weight of 3.1 g L-1. Higher glycerol consumption by Mn-C2-B11 was also confirmed by high-performance liquid chromatography (HPLC) analysis. This adapted variant consumed 34.5 times more glycerol compared to the WT strain at 10% v/v glycerol. Our method offers several advantages over other reported ALE approaches, including its independence from genetically modified strains, specialized genetic tools, and potentially carcinogenic DNA-modifying agents. By utilizing divalent metal cations as mutagens, we offer a safer, more efficient, and cost-effective alternative for expansion of genetic diversity. With its ability to foster rapid microbial evolution, aALE serves as a valuable addition to the ALE toolbox, holding significant promise for the advancement of microbial strain engineering and bioprocess optimization.

A genome-wide association study of panicle blast resistance to Magnaporthe oryzae in rice

Rice blast, caused by Magnaporthe oryzae (M. oryzae), is one of the most serious diseases worldwide. Developing blast-resistant rice varieties is an effective strategy to control the spread of rice blast and reduce the reliance on chemical pesticides. In this study, 477 sequenced rice germplasms from 48 countries were inoculated and assessed at the booting stage. We found that 23 germplasms exhibited high panicle blast resistance against M. oryzae. Genome-wide association analysis (GWAS) identified 43 quantitative trait loci (QTLs) significantly associated (P < 1.0 × 10-4) with resistance to rice panicle blast. These QTL intervals encompass four genes (OsAKT1, OsRACK1A, Bsr-k1 and Pi25/Pid3) previously reported to contribute to rice blast resistance. We selected QTLs with -Log10 (P-value) greater than 6.0 or those detected in two-year replicates, amounting to 12 QTLs, for further candidate gene analysis. Three blast resistance candidate genes (Os06g0316800, Os06g0320000, Pi25/Pid3) were identified based on significant single nucleotide polymorphisms (SNP) distributions within annotated gene sequences across these 12 QTLs and the differential expression levels among blast-resistant varieties after 72 h of inoculation. Os06g0316800 encodes a glycine-rich protein, OsGrp6, an important component of plant cell walls involved in cellular stress responses and signaling. Os06g0320000 encodes a protein with unknown function (DUF953), part of the thioredoxin-like family, which is crucial for maintaining reactive oxygen species (ROS) homeostasis in vivo, named as OsTrxl1. Lastly, Pi25/Pid3 encodes a disease resistance protein, underscoring its potential importance in plant biology. By analyzing the haplotypes of these three genes, we identified favorable haplotypes for blast resistance, providing valuable genetic resources for future rice blast resistance breeding programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01486-5.

Exploring glycine root uptake dynamics in phosphorus and iron deficient tomato plants during the initial stages of plant development

BACKGROUND

Phosphorus (P) and iron (Fe) deficiencies are relevant plants nutritional disorders, prompting responses such as increased root exudation to aid nutrient uptake, albeit at an energy cost. Reacquiring and reusing exudates could represent an efficient energy and nitrogen saving strategy. Hence, we investigated the impact of plant development, Fe and P deficiencies on this process. Tomato seedlings were grown hydroponically for 3 weeks in Control, -Fe, and -P conditions and sampled twice a week. We used Isotope Ratio Mass-Spectrometry to measure δ13C in roots and shoots after a 2-h exposure to 13C-labeled glycine (0, 50, or 500 μmol L-1). Plant physiology was assessed with an InfraRed Gas Analyzer and ionome with an Inductively Coupled Plasma Mass-Spectrometry.

RESULTS

Glycine uptake varied with concentration, suggesting an involvement of root transporters with different substrate affinities. The uptake decreased over time, with -Fe and -P showing significantly higher values as compared to the Control. This highlights its importance during germination and in nutrient-deficient plants. Translocation to shoots declined over time in -P and Control but increased in -Fe plants, suggesting a role of Gly in the Fe xylem transport.

CONCLUSIONS

Root exudates, i.e. glycine, acquisition and their subsequent shoot translocation depend on Fe and P deficiency. The present findings highlight the importance of this adaptation to nutrient deficiencies, that can potentially enhance plants fitness. A thorough comprehension of this trait holds potential significance for selecting cultivars that can better withstand abiotic stresses.

Divergence in regulatory mechanisms of GR-RBP genes in different plants under abiotic stress

The IVa subfamily of glycine-rich proteins (GRPs) comprises a group of glycine-rich RNA binding proteins referred to as GR-RBPa here. Previous studies have demonstrated functions of GR-RBPa proteins in regulating stress response in plants. However, the mechanisms responsible for the differential regulatory functions of GR-RBPa proteins in different plant species have not been fully elucidated. In this study, we identified and comprehensively studied a total of 34 GR-RBPa proteins from five plant species. Our analysis revealed that GR-RBPa proteins were further classified into two branches, with proteins in branch I being relatively more conserved than those in branch II. When subjected to identical stresses, these genes exhibited intensive and differential expression regulation in different plant species, corresponding to the enrichment of cis-acting regulatory elements involving in environmental and internal signaling in these genes. Unexpectedly, all GR-RBPa genes in branch I underwent intensive alternative splicing (AS) regulation, while almost all genes in branch II were only constitutively spliced, despite having more introns. This study highlights the complex and divergent regulations of a group of conserved RNA binding proteins in different plants when exposed to identical stress conditions. These species-specific regulations may have implications for stress responses and adaptations in different plant species.

Functional annotation of proteins in Catharanthus roseus shoot cultures under biogenic zinc nanotreatment

Nano-interactions are well known for their positive as well as negative impacts on the morphological and physiological systems of plants. Keeping in mind, the conformational changes in plant proteins as one of the key mechanisms for stress adaptation responses, the current project was designed to explore the effect of glutathione-capped and uncapped zinc nano-entities on Catharanthus roseus shoot cultures. Zinc nanotreatment (0.05 μg/mL) significantly induced ester production in C. roseus shoots as detected by Gas Chromatography-Mass spectrometry. These nanotreated shoots were further subjected to peptide-centric nano-LC-MS/MS analysis. Mass spectrometry followed by a Heat map revealed a significant effect of zinc nanoparticles on 59 distinct classes of proteins as compared to control. Proteins involved in regulating stress scavenging, transport, and secondary metabolite biosynthesis were robustly altered under capped zinc nanotreatment. UniProt database identified majority of the localization of the abundantly altered protein in cell membranes and chloroplasts. STRING and Cytoscape analysis assessed inter and intra coordination of triosephosphate isomerase with other identified proteins and highlighted its role in the regulation of protein abundance under applied stress. This study highlights the understanding of complex underlying mechanisms and regulatory networks involved in proteomic alterations and interactions within the plant system to cope with the nano-effect.

Glycine-Rich RNA-Binding Protein AtGRP7 Functions in Nickel and Lead Tolerance in Arabidopsis

Plant glycine-rich RNA-binding proteins (GRPs) play crucial roles in the response to environmental stresses. However, the functions of AtGRP7 in plants under heavy metal stress remain unclear. In the present study, in Arabidopsis, the transcript level of AtGRP7 was markedly increased by Ni but was decreased by Pb. AtGRP7-overexpressing plants improved Ni tolerance, whereas the knockout mutant (grp7) was more susceptible than the wild type to Ni. In addition, grp7 showed greatly enhanced Pb tolerance, whereas overexpression lines showed high Pb sensitivity. Ni accumulation was reduced in overexpression lines but increased in grp7, whereas Pb accumulation in grp7 was lower than that in overexpression lines. Ni induced glutathione synthase genes GS1 and GS2 in overexpression lines, whereas Pb increased metallothionein genes MT4a and MT4b and phytochelatin synthase genes PCS1 and PCS2 in grp7. Furthermore, Ni increased CuSOD1 and GR1 in grp7, whereas Pb significantly induced FeSOD1 and FeSOD2 in overexpression lines. The mRNA stability of GS2 and PCS1 was directly regulated by AtGRP7 under Ni and Pb, respectively. Collectively, these results indicate that AtGRP7 plays a crucial role in Ni and Pb tolerance by reducing Ni and Pb accumulation and the direct or indirect post-transcriptional regulation of genes related to heavy metal chelators and antioxidant enzymes.

Comprehensive Genome-Wide Identification of the RNA-Binding Glycine-Rich Gene Family and Expression Profiling under Abiotic Stress in Brassica oleracea

The RNA-binding glycine-rich proteins (RBGs) of the glycine-rich protein family play vital roles in regulating gene expression both at the transcriptional and post-transcriptional levels. However, the members and functions in response to abiotic stresses of the RBG gene family remain unclear in Brassica oleracea. In this study, a total of 19 BoiRBG genes were identified through genome-wide analysis in broccoli. The characteristics of BoiRBG sequences and their evolution were examined. An analysis of synteny indicated that the expansion of the BoiRBG gene family was primarily driven by whole-genome duplication and tandem duplication events. The BoiRBG expression patterns revealed that these genes are involved in reaction to diverse abiotic stress conditions (i.e., simulated drought, salinity, heat, cold, and abscisic acid) and different organs. In the present research, the up-regulation of BoiRBGA13 expression was observed when subjected to both NaCl-induced and cold stress conditions in broccoli. Moreover, the overexpression of BoiRBGA13 resulted in a noteworthy reduction in taproot lengths under NaCl stress, as well as the inhibition of seed germination under cold stress in broccoli, indicating that RBGs play different roles under various stresses. This study provides insights into the evolution and functions of BoiRBG genes in Brassica oleracea and other Brassicaceae family plants.

Genome-Wide Identification and Analysis of MYB Transcription Factors in Pyropia yezoensis

MYB transcription factors are one of the largest transcription factor families in plants, and they regulate numerous biological processes. Red algae are an important taxonomic group and have important roles in economics and research. However, no comprehensive analysis of the MYB gene family in any red algae, including Pyropia yezoensis, has been conducted. To identify the MYB gene members of Py. yezoensis, and to investigate their family structural features and expression profile characteristics, a study was conducted. In this study, 3 R2R3-MYBs and 13 MYB-related members were identified in Py. yezoensis. Phylogenetic analysis indicated that most red algae MYB genes could be clustered with green plants or Glaucophyta MYB genes, inferring their ancient origins. Synteny analysis indicated that 13 and 5 PyMYB genes were orthologous to Pyropia haitanensis and Porphyra umbilicalis, respectively. Most Bangiaceae MYB genes contain several Gly-rich motifs, which may be the result of an adaptation to carbon limitations and maintenance of important regulatory functions. An expression profile analysis showed that PyMYB genes exhibited diverse expression profiles. However, the expression patterns of different members appeared to be diverse, and PyMYB5 was upregulated in response to dehydration, low temperature, and Pythium porphyrae infection. This is the first comprehensive study of the MYB gene family in Py. Yezoensis and it provides vital insights into the functional divergence of MYB genes.

The Glycine-Rich RNA-Binding Protein Is a Vital Post-Transcriptional Regulator in Crops

Glycine-rich RNA binding proteins (GR-RBPs), a branch of RNA binding proteins (RBPs), play integral roles in regulating various aspects of RNA metabolism regulation, such as RNA processing, transport, localization, translation, and stability, and ultimately regulate gene expression and cell fate. However, our current understanding of GR-RBPs has predominantly been centered on Arabidopsis thaliana, a model plant for investigating plant growth and development. Nonetheless, an increasing body of literature has emerged in recent years, shedding light on the presence and functions of GRPs in diverse crop species. In this review, we not only delineate the distinctive structural domains of plant GR-RBPs but also elucidate several contemporary mechanisms of GR-RBPs in the post-transcriptional regulation of RNA. These mechanisms encompass intricate processes, including RNA alternative splicing, polyadenylation, miRNA biogenesis, phase separation, and RNA translation. Furthermore, we offer an exhaustive synthesis of the diverse roles that GR-RBPs fulfill within crop plants. Our overarching objective is to provide researchers and practitioners in the field of agricultural genetics with valuable insights that may inform and guide the application of plant genetic engineering for enhanced crop development and sustainable agriculture.

GARP: A family of glycine and alanine-rich proteins that helps spider mites feed on plants

Spider mites (Tetranychidae) are destructive agricultural pests which have evolved strategies to overcome plant defenses, such as the ability to puncture the leaves of their hosts to feed. The expression of many genes with unknown functions is altered during feeding, but little is known about the role of these genes in plant-mite interactions. Here, we identified 3 novel gene families through analysis of genomic and transcriptomic data from 3 spider mite species. These GARP family genes encode glycine and alanine-rich proteins; they are present in mites (Acariformes) but absent in ticks (Parasitiformes) in the subclass Acari, indicating that these genes have undergone a significant expansion in spider mites and thus play important adaptive roles. Transcriptomic analysis revealed that the expression of GARP genes is strongly correlated with feeding and the transfer to new hosts. We used RNA interference to silence GARP1d in the two-spotted spider mite Tetranychus urticae, which inhibited feeding and egg laying and significantly increased mortality when the mites were transferred to soybean shoots; a similar effect was observed after TuVATPase was silenced. However, no changes in mite mortality were observed after TuGARP1d-silenced mites were placed on an artificial diet, which was different from the effect of TuVATPase silencing. Our results indicate that GARP family members play important roles in mite-plant interactions. Additional studies are needed to clarify the mechanisms underlying these interactions.

Functional Meta-Analysis of the Proteomic Responses of Arabidopsis Seedlings to the Spaceflight Environment Reveals Multi-Dimensional Sources of Variability across Spaceflight Experiments

The human quest for sustainable habitation of extraterrestrial environments necessitates a robust understanding of life's adaptability to the unique conditions of spaceflight. This study provides a comprehensive proteomic dissection of the Arabidopsis plant's responses to the spaceflight environment through a meta-analysis of proteomics data from four separate spaceflight experiments conducted on the International Space Station (ISS) in different hardware configurations. Raw proteomics LC/MS spectra were analyzed for differential expression in MaxQuant and Perseus software. The analysis of dissimilarities among the datasets reveals the multidimensional nature of plant proteomic responses to spaceflight, impacted by variables such as spaceflight hardware, seedling age, lighting conditions, and proteomic quantification techniques. By contrasting datasets that varied in light exposure, we elucidated proteins involved in photomorphogenesis and skotomorphogenesis in plant spaceflight responses. Additionally, with data from an onboard 1 g control experiment, we isolated proteins that specifically respond to the microgravity environment and those that respond to other spaceflight conditions. This study identified proteins and associated metabolic pathways that are consistently impacted across the datasets. Notably, these shared proteins were associated with critical metabolic functions, including carbon metabolism, glycolysis, gluconeogenesis, and amino acid biosynthesis, underscoring their potential significance in Arabidopsis' spaceflight adaptation mechanisms and informing strategies for successful space farming.

Lilium Gray Mold Suppression Conferred by the Host Antimicrobial Protein LsGRP1 Involves Main Pathogen-Targeted Manipulation of the Nonantimicrobial Region LsGRP1N

Antimicrobial protein LsGRP1 protects Lilium from gray mold mainly caused by the destructive pathogen Botrytis elliptica; however, its nonantimicrobial region LsGRP1N conversely promotes spore germination of this fungus. By assaying the effects of LsGRP1N, LsGRP1, and the combination of LsGRP1N and the antimicrobial region LsGRP1C on fungal spore germination, hyphal growth, and Lilium gray mold development, LsGRP1N was found to improve the LsGRP1C sensitivity of B. elliptica and disease suppression by LsGRP1C. B. elliptica cell vitality assays indicated that LsGRP1N pretreatment uniquely enhanced the lethal efficiency of LsGRP1C compared to the control peptides. In addition, LsGRP1N-treated B. elliptica was demonstrated to lower infection-related gene expression and increase host-defense-eliciting activity, as indicated by reverse transcription quantitative polymerase chain reaction and histochemical-staining-based callose detection results, respectively. Therefore, LsGRP1N showed a novel mode of action for antimicrobial proteins by manipulating the main pathogen, which facilitated the development of target-specific and dormant microbe-eradicating antimicrobial agents.

Temporal transcriptomic profiling elucidates sorghum defense mechanisms against sugarcane aphids

BACKGROUND

The sugarcane aphid (SCA; Melanaphis sacchari) has emerged as a key pest on sorghum in the United States that feeds from the phloem tissue, drains nutrients, and inflicts physical damage to plants. Previously, it has been shown that SCA reproduction was low and high on sorghum SC265 and SC1345 plants, respectively, compared to RTx430, an elite sorghum male parental line (reference line). In this study, we focused on identifying the defense-related genes that confer resistance to SCA at early and late time points in sorghum plants with varied levels of SCA resistance.

RESULTS

We used RNA-sequencing approach to identify the global transcriptomic responses to aphid infestation on RTx430, SC265, and SC1345 plants at early time points 6, 24, and 48 h post infestation (hpi) and after extended period of SCA feeding for 7 days. Aphid feeding on the SCA-resistant line upregulated the expression of 3827 and 2076 genes at early and late time points, respectively, which was relatively higher compared to RTx430 and SC1345 plants. Co-expression network analysis revealed that aphid infestation modulates sorghum defenses by regulating genes corresponding to phenylpropanoid metabolic pathways, secondary metabolic process, oxidoreductase activity, phytohormones, sugar metabolism and cell wall-related genes. There were 187 genes that were highly expressed during the early time of aphid infestation in the SCA-resistant line, including genes encoding leucine-rich repeat (LRR) proteins, ethylene response factors, cell wall-related, pathogenesis-related proteins, and disease resistance-responsive dirigent-like proteins. At 7 days post infestation (dpi), 173 genes had elevated expression levels in the SCA-resistant line and were involved in sucrose metabolism, callose formation, phospholipid metabolism, and proteinase inhibitors.

CONCLUSIONS

In summary, our results indicate that the SCA-resistant line is better adapted to activate early defense signaling mechanisms in response to SCA infestation because of the rapid activation of the defense mechanisms by regulating genes involved in monolignol biosynthesis pathway, oxidoreductase activity, biosynthesis of phytohormones, and cell wall composition. This study offers further insights to better understand sorghum defenses against aphid herbivory.

NGS transcriptomic analysis uncovers the possible resistance mechanisms of olive to Spilocea oleagina leaf spot infection

Spilocea oleagina is a dangerous obligate fungal pathogen of olive, feared in the Mediterranean countries, causing Peacock's eye or leaf spot infection, which can lead to a serious yield loss of approximately 20% or higher depending on climatic conditions. Coping with this disease is much more problematic for organic farms. To date, knowledge on the genetic control of possible mechanisms of resistance/low susceptibility is quite limited. In this work, comparative transcriptomic analysis (RNA-seq) was conducted in leaf tissues of a low susceptible cultivar Koroneiki and a high susceptible cultivar Nocellara del Belice, both tested in the field using the NaOH test, considering two stages-"zero sign of disease" and "evident sign of infection". Cultivars showed a very large number of differentially expressed genes (DEGs) in both stages. 'Koroneiki' showed an extensive hormonal crosstalk, involving Abscisic acid (ABA) and ethylene synergistically acting with Jasmonate, with early signaling of the disease and remarkable defense responses against Spilocea through the over-expression of many resistance gene analogs or pathogenesis-related (PR) genes: non-specific lipid-transfer genes (nsLTPs), LRR receptor-like serine/threonine-protein kinase genes, GDSL esterase lipase, defensin Ec-AMP-D2-like, pathogenesis-related leaf protein 6-like, Thaumatin-like gene, Mildew resistance Locus O (MLO) gene, glycine-rich protein (GRP), MADS-box genes, STH-21-like, endochitinases, glucan endo-1,3-beta-glucosidases, and finally, many proteinases. Numerous genes involved in cell wall biogenesis, remodeling, and cell wall-based defense, including lignin synthesis, were also upregulated in the resistant cultivar, indicating the possible role of wall composition in disease resistance. It was remarkable that many transcription factors (TS), some of which involved in Induced Systemic Resistance (ISR), as well as some also involved in abiotic stress response, were found to be uniquely expressed in 'Koroneiki', while 'Nocellara del Belice' was lacking an effective system of defense, expressing genes that overlap with wounding responses, and, to a minor extent, genes related to phenylpropanoid and terpenoid pathways. Only a Thaumatin-like gene was found in both cultivars showing a similar expression. In this work, the genetic factors and mechanism underlying the putative resistance trait against this fungal pathogen were unraveled for the first time and possible target genes for breeding resistant olive genotypes were found.

Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean

Soybean is a high oil and protein-rich legume with several production constraints. Globally, several fungi, viruses, nematodes, and bacteria cause significant yield losses in soybean. Coniothyrium glycines (CG), the causal pathogen for red leaf blotch disease, is the least researched and causes severe damage to soybean. The identification of resistant soybean genotypes and mapping of genomic regions associated with resistance to CG is critical for developing improved cultivars for sustainable soybean production. This study used single nucleotide polymorphism (SNP) markers generated from a Diversity Arrays Technology (DArT) platform to conduct a genome-wide association (GWAS) analysis of resistance to CG using 279 soybean genotypes grown in three environments. A total of 6395 SNPs was used to perform the GWAS applying a multilocus model Fixed and random model Circulating Probability Unification (FarmCPU) with correction of the population structure and a statistical test p-value threshold of 5%. A total of 19 significant marker-trait associations for resistance to CG were identified on chromosomes 1, 5, 6, 9, 10, 12, 13, 15, 16, 17, 19, and 20. Approximately 113 putative genes associated with significant markers for resistance to red leaf blotch disease were identified across soybean genome. Positional candidate genes associated with significant SNP loci-encoding proteins involved in plant defense responses and that could be associated with soybean defenses against CG infection were identified. The results of this study provide valuable insight for further dissection of the genetic architecture of resistance to CG in soybean. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving resistance traits in soybean.

Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association

RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.

Long-term cold, freezing and drought: overlapping and specific regulatory mechanisms and signal transduction in tea plant (Camellia sinensis (L.) Kuntze)

Introduction

Low temperatures and drought are two main environmental constraints reducing the yield and geographical distribution of horticultural crops worldwide. Understanding the genetic crosstalk between stress responses has potential importance for crop improvement.

Methods

In this study, Illumina RNA-seq and Pac-Bio genome resequencing were used to annotate genes and analyze transcriptome dynamics in tea plants under long-term cold, freezing, and drought.

Results

The highest number of differentially expressed genes (DEGs) was identified under long-term cold (7,896) and freezing (7,915), with 3,532 and 3,780 upregulated genes, respectively. The lowest number of DEGs was observed under 3-day drought (47) and 9-day drought (220), with five and 112 genes upregulated, respectively. The recovery after the cold had 6.5 times greater DEG numbers as compared to the drought recovery. Only 17.9% of cold-induced genes were upregulated by drought. In total, 1,492 transcription factor genes related to 57 families were identified. However, only 20 transcription factor genes were commonly upregulated by cold, freezing, and drought. Among the 232 common upregulated DEGs, most were related to signal transduction, cell wall remodeling, and lipid metabolism. Co-expression analysis and network reconstruction showed 19 genes with the highest co-expression connectivity: seven genes are related to cell wall remodeling (GATL7, UXS4, PRP-F1, 4CL, UEL-1, UDP-Arap, and TBL32), four genes are related to calcium-signaling (PXL1, Strap, CRT, and CIPK6), three genes are related to photo-perception (GIL1, CHUP1, and DnaJ11), two genes are related to hormone signaling (TTL3 and GID1C-like), two genes are involved in ROS signaling (ERO1 and CXE11), and one gene is related to the phenylpropanoid pathway (GALT6).

Discussion

Based on our results, several important overlapping mechanisms of long-term stress responses include cell wall remodeling through lignin biosynthesis, o-acetylation of polysaccharides, pectin biosynthesis and branching, and xyloglucan and arabinogalactan biosynthesis. This study provides new insight into long-term stress responses in woody crops, and a set of new target candidate genes were identified for molecular breeding aimed at tolerance to abiotic stresses.

1 H, 15 N, and 13 C backbone and side chain resonance assignments of the cold shock domain of the Arabidopsis thaliana glycine-rich protein AtGRP2

AtGRP2 (Arabidopsis thaliana glycine-rich protein 2) is a 19-kDa RNA-binding glycine-rich protein that regulates key processes in A. thaliana. AtGRP2 is a nucleo-cytoplasmic protein with preferential expression in developing tissues, such as meristems, carpels, anthers, and embryos. AtGRP2 knockdown leads to an early flowering phenotype. In addition, AtGRP2-silenced plants exhibit a reduced number of stamens and abnormal development of embryos and seeds, suggesting its involvement in plant development. AtGRP2 expression is highly induced by cold and abiotic stresses, such as high salinity. Moreover, AtGRP2 promotes double-stranded DNA/RNA denaturation, indicating its role as an RNA chaperone during cold acclimation. AtGRP2 is composed of an N-terminal cold shock domain (CSD) followed by a C-terminal flexible region containing two CCHC-type zinc fingers interspersed with glycine-rich sequences. Despite its functional relevance in flowering time regulation and cold adaptation, the molecular mechanisms employed by AtGRP2 are largely unknown. To date, there is no structural information regarding AtGRP2 in the literature. Here, we report the ¹H, ¹⁵N, and ¹³C backbone and side chain resonance assignments, as well as the chemical shift-derived secondary structure propensities, of the N-terminal cold shock domain of AtGRP2, encompassing residues 1-90. These data provide a framework for AtGRP2-CSD three-dimensional structure, dynamics, and RNA binding specificity investigation, which will shed light on its mechanism of action.

Recent progress and perspectives on physiological and molecular mechanisms underlying cold tolerance of tea plants

Tea is one of the most consumed and widely planted beverage plant worldwide, which contains many important economic, healthy, and cultural values. Low temperature inflicts serious damage to tea yields and quality. To cope with cold stress, tea plants have evolved a cascade of physiological and molecular mechanisms to rescue the metabolic disorders in plant cells caused by the cold stress; this includes physiological, biochemical changes and molecular regulation of genes and associated pathways. Understanding the physiological and molecular mechanisms underlying how tea plants perceive and respond to cold stress is of great significance to breed new varieties with improved quality and stress resistance. In this review, we summarized the putative cold signal sensors and molecular regulation of the CBF cascade pathway in cold acclimation. We also broadly reviewed the functions and potential regulation networks of 128 cold-responsive gene families of tea plants reported in the literature, including those particularly regulated by light, phytohormone, and glycometabolism. We discussed exogenous treatments, including ABA, MeJA, melatonin, GABA, spermidine and airborne nerolidol that have been reported as effective ways to improve cold resistance in tea plants. We also present perspectives and possible challenges for functional genomic studies on cold tolerance of tea plants in the future.

The Phytophthora sojae effector PsFYVE1 modulates immunity-related gene expression by targeting host RZ-1A protein

Oomycete pathogens secrete numerous effectors to manipulate plant immunity and promote infection. However, relatively few effector types have been well characterized. In this study, members of an FYVE domain-containing protein family that are highly expanded in oomycetes were systematically identified, and one secreted protein, PsFYVE1, was selected for further study. PsFYVE1 enhanced Phytophthora capsici infection in Nicotiana benthamiana and was necessary for Phytophthora sojae virulence. The FYVE domain of PsFYVE1 had PI3P-binding activity that depended on four conserved amino acid residues. Furthermore, PsFYVE1 targeted RNA-binding proteins RZ-1A/1B/1C in N. benthamiana and soybean (Glycine max), and silencing of NbRZ-1A/1B/1C genes attenuated plant immunity. NbRZ-1A was associated with the spliceosome complex that included three important components, glycine-rich RNA-binding protein 7 (NbGRP7), glycine-rich RNA-binding protein 8 (NbGRP8), and a specific component of the U1 small nuclear ribonucleoprotein complex (NbU1-70K). Notably, PsFYVE1 disrupted NbRZ-1A-NbGRP7 interaction. RNA-seq and subsequent experimental analysis demonstrated that PsFYVE1 and NbRZ-1A not only modulated pre-mRNA alternative splicing (AS) of the necrotic spotted lesions 1 (NbNSL1) gene, but also co-regulated transcription of hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (NbHCT), ethylene insensitive 2 (NbEIN2), and sucrose synthase 4 (NbSUS4) genes, which participate in plant immunity. Collectively, these findings indicate that the FYVE domain-containing protein family includes potential uncharacterized effector types and also highlight that plant pathogen effectors can regulate plant immunity-related genes at both AS and transcription levels to promote disease.

Molecular Analysis of MgO Nanoparticle-Induced Immunity against Fusarium Wilt in Tomato

Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici (FOL), is a devastating soilborne disease in tomatoes. Magnesium oxide nanoparticles (MgO NPs) induce strong immunity against Fusarium wilt in tomatoes. However, the mechanisms underlying this immunity remain poorly understood. Comparative transcriptome analysis and microscopy of tomato roots were performed to determine the mechanism of MgO NP-induced immunity against FOL. Eight transcriptomes were prepared from tomato roots treated under eight different conditions. Differentially expressed genes were compared among the transcriptomes. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that in tomato roots pretreated with MgO NPs, Rcr3 encoding apoplastic protease and RbohD encoding NADPH oxidase were upregulated when challenge-inoculated with FOL. The gene encoding glycine-rich protein 4 (SlGRP4) was chosen for further analysis. SlGRP4 was rapidly transcribed in roots pretreated with MgO NPs and inoculated with FOL. Immunomicroscopy analysis showed that SlGRP4 accumulated in the cell walls of epidermal and vascular vessel cells of roots pretreated with MgO NPs, but upon FOL inoculation, SlGRP4 further accumulated in the cell walls of cortical tissues within 48 h. The results provide new insights into the probable mechanisms of MgO NP-induced tomato immunity against Fusarium wilt.

Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China

Understanding adaptive genetic variation of plant populations and their vulnerabilities to climate change are critical to preserve biodiversity and subsequent management interventions. To this end, landscape genomics may represent a cost-efficient approach for investigating molecular signatures underlying local adaptation. Tetrastigma hemsleyanum is, in its native habitat, a widespread perennial herb of warm-temperate evergreen forest in subtropical China. Its ecological and medicinal values constitute a significant revenue for local human populations and ecosystem. Using 30,252 single nucleotide polymorphisms (SNPs) derived from reduced-representation genome sequencing in 156 samples from 24 sites, we conducted a landscape genomics study of the T. hemsleyanum to elucidate its genomic variation across multiple climate gradients and genomic vulnerability to future climate change. Multivariate methods identified that climatic variation explained more genomic variation than that of geographical distance, which implied that local adaptation to heterogeneous environment might represent an important source of genomic variation. Among these climate variables, winter precipitation was the strongest predictor of the contemporary genetic structure. F _ST outlier tests and environment association analysis totally identified 275 candidate adaptive SNPs along the genetic and environmental gradients. SNP annotations of these putatively adaptive loci uncovered gene functions associated with modulating flowering time and regulating plant response to abiotic stresses, which have implications for breeding and other special agricultural aims on the basis of these selection signatures. Critically, modelling revealed that the high genomic vulnerability of our focal species via a mismatch between current and future genotype-environment relationships located in central-northern region of the T. hemsleyanum's range, where populations require proactive management efforts such as assistant adaptation to cope with ongoing climate change. Taken together, our results provide robust evidence of local climate adaption for T. hemsleyanum and further deepen our understanding of adaptation basis of herbs in subtropical China.

Unique and Shared Proteome Responses of Rice Plants (Oryza sativa) to Individual Abiotic Stresses

Food safety of staple crops such as rice is of global concern and is at the top of the policy agenda worldwide. Abiotic stresses are one of the main limitations to optimizing yields for sustainability, food security and food safety. We analyzed proteome changes in Oryza sativa cv. Nipponbare in response to five adverse abiotic treatments, including three levels of drought (mild, moderate, and severe), soil salinization, and non-optimal temperatures. All treatments had modest, negative effects on plant growth, enabling us to identify proteins that were common to all stresses, or unique to one. More than 75% of the total of differentially abundant proteins in response to abiotic stresses were specific to individual stresses, while fewer than 5% of stress-induced proteins were shared across all abiotic constraints. Stress-specific and non-specific stress-responsive proteins identified were categorized in terms of core biological processes, molecular functions, and cellular localization.

Responses of transcriptome and metabolome in the roots of Pugionium cornutum (L.) Gaertn to exogenously applied phthalic acid

BACKGROUND

The yield and quality of Pugionium cornutum (L.) Gaertn., a healthy, green vegetable with low sugar and high protein contents and high medicinal value, is severely affected by autotoxicity, which is a leading factor in the formation of plant disease. To help characterize the autotoxicity mechanism of P. cornutum (L.) Gaertn., we performed transcriptomic and metabolic analysis of the roots of P. cornutum (L.) Gaertn. response to phthalic acid, an autotoxin from P. cornutum (L.) Gaertn.

RESULTS

In this study, high-throughput sequencing of nine RNA-seq libraries generated from the roots.of P. cornutum (L.) Gaertn. under different phthalic acid treatments yielded 37,737 unigenes. In total, 1085 (703 upregulated and 382 downregulated) and 5998 (4385 upregulated and 1613 downregulated) DEGs were identified under 0.1 and 10 mmol·L^- 1 phthalic acid treatment, respectively, compared with the control treatment. Glutathione metabolism was among the top five important enriched pathways. In total, 457 and 435 differentially accumulated metabolites were detected under 0.1 and 10 mmol·L^- 1 phthalic acid treatment compared with the control, respectively, of which 223 and 253, respectively, increased in abundance. With the increase in phthalic acid concentration, the accumulation of ten metabolites increased significantly, while that of four metabolites decreased significantly, and phthalic acid, dambonitol, 4-hydroxy-butyric acid, homocitrulline, and ethyl β-D-glucopyranoside were 100 times more abundant under the 10 mmol·L^- 1 phthalic acid treatment than under the control. Seventeen differentially expressed genes significantly associated with phthalic acid content were identified. In addition, the L-histidinol content was highest under 0.1 mmol·L^- 1 phthalic acid, and a total of eleven differentially expressed genes were significantly positively correlated with the L-histidinol content, all of which were annotated to heat shock proteins, aquaporins and cysteine proteases.

CONCLUSIONS

Accumulation of autotoxins altered the metabolic balance in P. cornutum (L.) Gaertn. and influenced water absorption and carbon and nitrogen metabolism. These important results provide insights into the formation mechanisms of autotoxicity and for the subsequent development of new control measures to improve the production and quality of replanted plants.

Comparative Seeds Storage Transcriptome Analysis of Astronium fraxinifolium Schott, a Threatened Tree Species from Brazil

Astronium fraxinifolium Schott (Anacardiaceae), also known as a 'gonçalo-alves', is a tree of the American tropics, with distribution in Mexico, part of Central America, Argentina, Bolivia, Brazil and Paraguay. In Brazil it is an endangered species that occurs in the Cerrado, Caatinga and in the Amazon biomes. In support of ex situ conservation, this work aimed to study two accessions with different longevity (p50) of A. fraxinifolium collected from two different geographic regions, and to evaluate the transcriptome during aging of the seeds in order to identify genes related to seed longevity. Artificial ageing was performed at a constant temperature of 45 °C and 60% relative humidity. RNA was extracted from 100 embryonic axes exposed to control and aging conditions for 21 days. The transcriptome analysis revealed differentially expressed genes such as Late Embryogenesis Abundant (LEA) genes, genes involved in the photosystem, glycine rich protein (GRP) genes, and several transcription factors associated with embryo development and ubiquitin-conjugating enzymes. Thus, these results contribute to understanding which genes play a role in seed ageing, and may serve as a basis for future functional characterization of the seed aging process in A. fraxinifolium.

Molecular basis of genetic plasticity to varying environmental conditions on growing rice by dry/direct-sowing and exposure to drought stress: Insights for DSR varietal development

Rice requires plenty of water for its cultivation by transplanting. This poses several challenges to its cultivation due to erratic rainfall resulting in drought, flood, and other abiotic stresses of varying intensity. Dry/direct-sown rice (DSR) has emerged as a water-saving/climate-smart alternative to transplanted rice (TPR). The performance of a rice cultivar on growing by different methods of planting under varying environmental conditions varies considerably. However, the molecular basis of the observed phenotypic plasticity of rice to varying environmental conditions is still elusive. Resilience to various environmental fluctuations is important to ensure sustainable rice production in the present era of global climate change. Our observations on exclusively up-regulated genes in leaf of Nagina 22 (N 22) grown by dry/direct-sowing and subjected to drought stress at panicle initiation stage (compared to that in leaf of IR 64), and another set of genes exclusively down-regulated in leaf of N 22 (compared to that in leaf of IR 64) indicate important roles of leaf in stress resilience. A large number of genes down-regulated exclusively in root of N 22 on dry/direct-sowing subjected to drought stress indicates a major contribution of roots in stress tolerance. The genes for redox-homeostasis, transcription factors, stress signaling, carbohydrate metabolism, and epigenetic modifications play important roles in making N 22 better adapted to DSR conditions. More importantly, the involvement of genes in rendering genetic plasticity to N 22 under changing environmental conditions was confirmed by reversal of the method of planting. To the best of our knowledge, this is the first report on decoding the molecular basis of genetic plasticity of rice grown by two different methods of planting subjected to drought stress at the reproductive stage of plant growth. This might help in DSR varietal development program to enhance water-productivity, conserve natural resources, and minimize the emission of greenhouse gases, thus achieving the objectives of negative-emission agriculture.

Proteomic analysis of T. qataranse exposed to lead (Pb) stress reveal new proteins with potential roles in Pb tolerance and detoxification mechanism

Soil lead (Pb) contamination is one of the environmental problems facing the modern world. Sources of Pb in soil include industrial activities such as mining and smelting processes, agricultural activities such as application of insecticide and municipal sewage sludges, and urban activities such as use of lead in gasoline, paints, and other materials. Phytoremediation is the direct use of living green plants and is an effective, cheap, non-invasive, and environmentally friendly technique used to transfer or stabilize all the toxic metals and environmental pollutants in polluted soil or groundwater. Current work in this area is invested in elucidating mechanisms that underpin toxic-metal tolerance and detoxification mechanisms. The present study aims to gain insight into the mechanisms of Pb tolerance in T. qataranse by comparative proteomics. MALDI-TOF/MS and in silico proteome analysis showed differential protein expression between treated (50 mg kg^⎯1 Pb) and untreated (0 mg kg^⎯1 Pb) T. qataranse. A total of eighty-six (86) differentially expressed proteins, most of which function in ion and protein binding, antioxidant activity, transport, and abiotic response stress, were identified. In addition, essential stress-regulating metabolic pathways, including glutathione metabolism, cellular response to stress, and regulation of HSF1-mediated heat shock response, were also enriched. Also, at 52- and 49-kDa MW band areas, up to six hypothetical proteins with unknown functions were identified. Of these, protein AXX17_AT2G26660 is highly rich in glycine amino acid residues (up to 76%), suggesting that it is a probable glycine-rich protein (GRP) member. Although GRPs are known to be involved in plant defense against abiotic stress, including salinity and drought, there is no report on their role on Pb tolerance and or detoxification in plants. Further enrichment analysis in the current study reveals that the hypothetical proteins do not interact with known proteins and are not part of any enriched pathway. However, additional research is needed to functionally validate the role of the identified proteins in Pb detoxification mechanism.

BcGRP23: A novel gene involved in the chlorophyll metabolic pathway that is activated by BES1 in flowering Chinese cabbage

Glycine-rich proteins (GRPs) are a large family of proteins that play vital roles in cell wall remodeling, metabolism and development, and abiotic stress response. Although the functions of GRPs in cell wall remodeling have been extensively characterized, only a few studies have explored their effects on chlorophyll metabolism and hormone response. Accordingly, we aimed to determine the molecular mechanism of BcGRP23 and its role in chlorophyll metabolism and the BRI1-EMS-SUPPRESSOR 1 (BES1) signaling pathway in flowering Chinese cabbage. The expression levels of BcGRP23 in the leaves and stems gradually decreased with increasing growth and development of flowering Chinese cabbage, while BcGRP23 was barely expressed after flowering. As plant growth continued, the GUS (β-glucuronidase) stain gradually became lighter in hypocotyls and was largely free of growth points. The petioles and stems of BcGRP23-silenced plants lost their green color, and the contents of chlorophyll a (Chl a) and Chl b were significantly reduced. Further research revealed that the expression levels of chlorophyll degradation-related genes were significantly increased in silenced plants compared with the control; however, the opposite was noted for the BcGRP23-overexpressing lines. The BcGRP23 promoter sequence contains numerous hormone-responsive elements. In fact, the expression of BcGRP23 was upregulated in flowering Chinese cabbage following treatment with the hormones indole-3-acetic acid (IAA), gibberellin (GA), 6-benzylaminopurine (6-BA), methyl jasmonate (MeJA), and brassinosteroid (BR). Treatment with BR led to the most significant upregulation. BES1, in response to BRs, directly activated the BcGRP23 promoter. Overall, BcGRP23 regulated the expression of chlorophyll degradation-related genes, thereby affecting the chlorophyll content. Furthermore, the expression of BcGRP23 was significantly regulated by exogenous BR application and was directly activated by BES1. These findings preliminarily suggest the molecular mechanism and regulatory pathway of BcGRP23 in the growth and development of flowering Chinese cabbage plants and their response to environmental stress.

A GBS-based genome-wide association study reveals the genetic basis of salinity tolerance at the seedling stage in bread wheat (Triticum aestivum L.)

High salinity levels affect 20% of the cultivated area and 9%–34% of the irrigated agricultural land worldwide, ultimately leading to yield losses of crops. The current study evaluated seven salt tolerance-related traits at the seedling stage in a set of 138 pre-breeding lines (PBLs) and identified 63 highly significant marker-trait associations (MTAs) linked to salt tolerance. Different candidate genes were identified in in silico analysis, many of which were involved in various stress conditions in plants, including glycine-rich cell wall structural protein 1-like, metacaspase-1, glyceraldehyde-3-phosphate dehydrogenase GAPA1, and plastidial GAPA1. Some of these genes coded for structural protein and participated in cell wall structure, some were linked to programmed cell death, and others were reported to show abiotic stress response roles in wheat and other plants. In addition, using the Multi-Trait Genotype-Ideotype Distance Index (MGIDI) protocol, the best-performing lines under salt stress were identified. The SNPs identified in this study and the genotypes with favorable alleles provide an excellent source to impart salt tolerance in wheat.

Effects of exogenous calcium on the drought response of the tea plant (Camellia sinensis (L.) Kuntze)

Background

Drought is one of the major factors reducing the yield of many crops worldwide, including the tea crop (Camellia sinensis (L.) Kuntze). Calcium participates in most of cellular signaling processes, and its important role in stress detection and triggering a response has been shown in many crops. The aim of this study was to evaluate possible effects of calcium on the tea plant response to drought.

Methods

Experiments were conducted using 3-year-old potted tea plants of the best local cultivar Kolkhida. Application of ammonium nitrate (control treatment) or calcium nitrate (Ca treatment) to the soil was performed before drought induction. Next, a 7-day drought was induced in both groups of plants. The following physiological parameters were measured: relative electrical conductivity, pH of cell sap, and concentrations of cations, sugars, and amino acids. In addition, relative expression levels of 40 stress-related and crop quality-related genes were analyzed.

Results

Under drought stress, leaf electrolyte leakage differed significantly, indicating greater damage to cell membranes in control plants than in Ca-treated plants. Calcium application resulted in greater pH of cell sap; higher accumulation of tyrosine, methionine, and valine; and a greater Mg²⁺ content as compared to control plants. Drought stress downregulated most of the quality-related genes in both groups of tea plants. By contrast, significant upregulation of some genes was observed, namely CRK45, NAC26, TPS11, LOX1, LOX6, Hydrolase22, DREB26, SWEET2, GS, ADC, DHN2, GOLS1, GOLS3, and RHL41. Among them, three genes (LOX1, RHL41, and GOLS1) showed 2-3 times greater expression in Ca-treated plants than in control plants. Based on these results, it can be speculated that calcium affects galactinol biosynthesis and participates in the regulation of stomatal aperture not only through activation of abscisic-acid signaling but also through jasmonic-acid pathway activation. These findings clarify calcium-mediated mechanisms of drought defense in tree crops. Thus, calcium improves the drought response in the tea tree.

Plant-Derived Antimicrobial Peptides: Novel Preservatives for the Food Industry

Food spoilage is a widespread issue brought on by the undesired growth of microbes in food products. Thousands of tons of usable food or food products are wasted every day due to rotting in different parts of the world. Several food preservation techniques are employed to prevent food from rotting, including the use of natural or manufactured chemicals or substances; however, the issue persists. One strategy for halting food deterioration is the use of plant-derived antimicrobial peptides (AMPs), which have been investigated for possible bioactivities against a range of human, plant, and food pathogens. The food industry may be able to benefit from the development of synthetic AMPs, produced from plants that have higher bioactivity, better stability, and decreased cytotoxicity as a means of food preservation. In order to exploit plant-derived AMPs in various food preservation techniques, in this review, we also outline the difficulties in developing AMPs for use as commercial food preservatives. Nevertheless, as technology advances, it will soon be possible to fully explore the promise of plant-derived AMPs as food preservatives.

Glycine-rich RNA-binding cofactor RZ1AL is associated with tomato ripening and development

Tomato ripening is a complex and dynamic process coordinated by many regulatory elements, including plant hormones, transcription factors, and numerous ripening-related RNAs and proteins. Although recent studies have shown that some RNA-binding proteins are involved in the regulation of the ripening process, understanding of how RNA-binding proteins affect fruit ripening is still limited. Here, we report the analysis of a glycine-rich RNA-binding protein, RZ1A-Like (RZ1AL), which plays an important role in tomato ripening, especially fruit coloring. To analyze the functions of RZ1AL in fruit development and ripening, we generated knockout cr-rz1al mutant lines via the CRISPR/Cas9 gene-editing system. Knockout of RZ1AL reduced fruit lycopene content and weight in the cr-rz1al mutant plants. RZ1AL encodes a nucleus-localized protein that is associated with Cajal-related bodies. RNA-seq data demonstrated that the expression levels of genes that encode several key enzymes associated with carotenoid biosynthesis and metabolism were notably downregulated in cr-rz1al fruits. Proteomic analysis revealed that the levels of various ribosomal subunit proteins were reduced. This could affect the translation of ripening-related proteins such as ZDS. Collectively, our findings demonstrate that RZ1AL may participate in the regulation of carotenoid biosynthesis and metabolism and affect tomato development and fruit ripening.

SlRBP1 promotes translational efficiency via SleIF4A2 to maintain chloroplast function in tomato

Many glycine-rich RNA-binding proteins (GR-RBPs) have critical functions in RNA processing and metabolism. Here, we describe a role for the tomato (Solanum lycopersicum) GR-RBP SlRBP1 in regulating mRNA translation. We found that SlRBP1 knockdown mutants (slrbp1) displayed reduced accumulation of total chlorophyll and impaired chloroplast ultrastructure. These phenotypes were accompanied by deregulation of the levels of numerous key transcripts associated with chloroplast functions in slrbp1. Furthermore, native RNA immunoprecipitation-sequencing (nRIP-seq) recovered 61 SlRBP1-associated RNAs, most of which are involved in photosynthesis. SlRBP1 binding to selected target RNAs was validated by nRIP-qPCR. Intriguingly, the accumulation of proteins encoded by SlRBP1-bound transcripts, but not the mRNAs themselves, was reduced in slrbp1 mutants. Polysome profiling followed by RT-qPCR assays indicated that the polysome occupancy of target RNAs was lower in slrbp1 plants than in wild-type. Furthermore, SlRBP1 interacted with the eukaryotic translation initiation factor SleIF4A2. Silencing of SlRBP1 significantly reduced SleIF4A2 binding to SlRBP1-target RNAs. Taking these observations together, we propose that SlRBP1 binds to and channels RNAs onto the SleIF4A2 translation initiation complex and promotes the translation of its target RNAs to regulate chloroplast functions.

OsGRP3 Enhances Drought Resistance by Altering Phenylpropanoid Biosynthesis Pathway in Rice (Oryza sativa L.)

As a sessile organism, rice often faces various kinds of abiotic stresses, such as drought stress. Drought stress seriously harms plant growth and damages crop yield every year. Therefore, it is urgent to elucidate the mechanisms of drought resistance in rice. In this study, we identified a glycine-rich RNA-binding protein, OsGRP3, in rice. Evolutionary analysis showed that it was closely related to OsGR-RBP4, which was involved in various abiotic stresses. The expression of OsGRP3 was shown to be induced by several abiotic stress treatments and phytohormone treatments. Then, the drought tolerance tests of transgenic plants confirmed that OsGRP3 enhanced drought resistance in rice. Meanwhile, the yeast two-hybrid assay, bimolecular luminescence complementation assay and bimolecular fluorescence complementation assay demonstrated that OsGRP3 bound with itself may affect the RNA chaperone function. Subsequently, the RNA-seq analysis, physiological experiments and histochemical staining showed that OsGRP3 influenced the phenylpropanoid biosynthesis pathway and further modulated lignin accumulation. Herein, our findings suggested that OsGRP3 enhanced drought resistance in rice by altering the phenylpropanoid biosynthesis pathway and further increasing lignin accumulation.

Effects of Salt Stress on Transcriptional and Physiological Responses in Barley Leaves with Contrasting Salt Tolerance

Salt stress negatively impacts crop production worldwide. Genetic diversity among barley (Hordeum vulgare) landraces adapted to adverse conditions should provide a valuable reservoir of tolerance genes for breeding programs. To identify molecular and biochemical differences between barley genotypes, transcriptomic and antioxidant enzyme profiles along with several morpho-physiological features were compared between salt-tolerant (Boulifa) and salt-sensitive (Testour) genotypes subjected to salt stress. Decreases in biomass, photosynthetic parameters, and relative water content were low in Boulifa compared to Testour. Boulifa had better antioxidant protection against salt stress than Testour, with greater antioxidant enzymes activities including catalase, superoxide dismutase, and guaiacol peroxidase. Transcriptome assembly for both genotypes revealed greater accumulation of differentially expressed transcripts in Testour compared to Boulifa, emphasizing the elevated transcriptional response in Testour following salt exposure. Various salt-responsive genes, including the antioxidant catalase 3, the osmoprotectant betaine aldehyde dehydrogenase 2, and the transcription factors MYB20 and MYB41, were induced only in Boulifa. By contrast, several genes associated with photosystems I and II, and light receptor chlorophylls A and B, were more repressed in Testour. Co-expression network analysis identified specific gene modules correlating with differences in genotypes and morpho-physiological traits. Overall, salinity-induced differential transcript accumulation underlies the differential morpho-physiological response in both genotypes and could be important for breeding salt tolerance in barley.

Sugar metabolism during pre- and post-fertilization events in plants under high temperature stress

High temperature challenges global crop production by limiting the growth and development of the reproductive structures and seed. It impairs the developmental stages of male and female gametogenesis, pollination, fertilization, endosperm formation and embryo development. Among these, the male reproductive processes are highly prone to abnormalities under high temperature at various stages of development. The disruption of source-sink balance is the main constraint for satisfactory growth of the reproductive structures which is disturbed at the level of sucrose import and utilization within the tissue. Seed development after fertilization is affected by modulation in the activity of enzymes involved in starch metabolism. In addition, the alteration in the seed-filling rate and its duration affects the seed weight and quality. The present review critically discusses the role of sugar metabolism in influencing the various stages of gamete and seed development under high temperature stress. It also highlights the interaction of the sugars with hormones that mediate the transport of sugars to sink tissues. The role of transcription factors for the regulation of sugar availability under high temperature has also been discussed. Further, the omics-based systematic investigation has been suggested to understand the synergistic or antagonistic interactions between sugars, hormones and reactive oxygen species at various points of sucrose flow from source to sink under high temperature stress.

Comparative proteomics for an in-depth understanding of bioadhesion mechanisms and evolution across metazoans

Bioadhesion is a critical process for many marine and freshwater invertebrate animals. Bioadhesives mainly made of proteins have remarkable adhesive ability underwater. Unraveling the molecular composition of bioadhesives is fundamental to understanding their physiological roles as well as their potential for biotechnology applications and antibiofouling strategies. With the development of high-throughput methods such as proteomics, bioadhesive protein data in diverse taxa are rapidly accumulating, but the common mechanism across species is elusive due to the vast variety of bioadhesives. In this review, bioadhesive proteins from various taxa are reviewed, with the aim of facilitating researchers to appreciate the diversity of bioadhesive proteins (mostly 20-40) across species. By comparing proteomes across species, it was found that glycine-rich, epidermal growth factor, peroxidase, and DOPA together with typical extracellular domains are the most commonly used domains. Additionally, permanent and temporary adhesion show obvious differences in terms of domains or proteins. A basic recipe for bioadhesives composed of six components is proposed: structural elements, extracellular domains, modification enzymes, proteinase inhibitors, cytoskeletal proteins, and others. The extracellular domains are mostly related to interactions with other macromolecules (proteins, carbohydrates, and lipids), suggesting that domain shuffling and macromolecule interaction might be fundamental for bioadhesive evolution.

Functional Characterization of Tomato Phytochrome A and B1B2 Mutants in Response to Heat Stress

Heat stress (HS) is a prevalent negative factor affecting plant growth and development, as it is predominant worldwide and threatens agriculture on a large scale. PHYTOCHROMES (PHYs) are photoreceptors that control plant growth and development, and the stress signaling response partially interferes with their activity. PHYA, B1, and B2 are the most well-known PHY types in tomatoes. Our study aimed to identify the role of tomato 'Money Maker' phyA and phyB1B2 mutants in stable and fluctuating high temperatures at different growth stages. In the seed germination and vegetative growth stages, the phy mutants were HS tolerant, while during the flowering stage the phy mutants revealed two opposing roles depending on the HS exposure period. The response of the phy mutants to HS during the fruiting stage showed similarity to WT. The most obvious stage that demonstrated phy mutants' tolerance was the vegetative growth stage, in which a high degree of membrane stability and enhanced water preservation were achieved by the regulation of stomatal closure. In addition, both mutants upregulated the expression of heat-responsive genes related to heat tolerance. In addition to lower malondialdehyde accumulation, the phyA mutant enhanced proline levels. These results clarified the response of tomato phyA and phyB1B2 mutants to HS.

Alternative Splicing Regulation of Glycine-Rich Proteins via Target of Rapamycin-Reactive Oxygen Species Pathway in Arabidopsis Seedlings Upon Glucose Stress

Glucose can serve as both the source of energy and regulatory signaling molecule in plant. Due to the environmental and metabolic change, sugar levels could affect various developmental processes. High glucose environment is hardly conductive to the plant growth but cause development arrest. Increasing evidence indicate that alternative splicing (AS) plays a pivotal role in sugar signaling. However, the regulatory mechanism upon glucose stress remains unclear. The full-length transcriptomes were obtained from the samples of Arabidopsis seedlings with 3% glucose and mock treatment, using Oxford Nanopore sequencing technologies. Further analysis indicated that many genes involved in photosynthesis were significantly repressed and many genes involved in glycolysis, mitochondrial function, and the response to oxidative stress were activated. In total, 1,220 significantly differential alternative splicing (DAS) events related to 619 genes were identified, among which 75.74% belong to intron retention (IR). Notably, more than 20% of DAS events come from a large set of glycine-rich protein (GRP) family genes, such as GRP7, whose AS types mostly belong to IR. Besides the known productive GRP transcript isoforms, we identified a lot of splicing variants with diverse introns spliced in messenger RNA (mRNA) region coding the glycine-rich (GR) domain. The AS pattern of GRPs changed and particularly, the productive GRPs increased upon glucose stress. These ASs of GRP pre-mRNAs triggered by glucose stress could be abolished by AZD-8055, which is an ATP competitive inhibitor for the target of rapamycin (TOR) kinase but could be mimicked by H₂O₂. Additionally, AS pattern change of arginine/serine-rich splicing factor 31(RS31) via TOR pathway, which was previously described in response to light and sucrose signaling, was also induced in a similar manner by both glucose stress and reactive oxygen species (ROS). Here we conclude that (i) glucose stress suppresses photosynthesis and activates the glycolysis-mitochondria energy relay and ROS scavenging system; (ii) glucose stress triggers transcriptome-wide AS pattern changes including a large set of splicing factors, such as GRPs and RS31; (iii) high sugars regulate AS pattern change of both GRPs and RS31 via TOR-ROS pathway. The results from this study will deepen our understanding of the AS regulation mechanism in sugar signaling.

Genome-Wide Association Mapping of Crown and Brown Rust Resistance in Perennial Ryegrass

A population of 239 perennial ryegrass (Lolium perenne L.) genotypes was analyzed to identify marker-trait associations for crown rust (Puccinia coronata f. sp. lolii) and brown rust (Puccinia graminis f. sp. loliina) resistance. Phenotypic data from field trials showed a low correlation (r = 0.17) between the two traits. Genotypes were resequenced, and a total of 14,538,978 SNPs were used to analyze population structure, linkage disequilibrium (LD), and for genome-wide association study. The SNP heritability (h²_SNP) was 0.4 and 0.8 for crown and brown rust resistance, respectively. The high-density SNP dataset allowed us to estimate LD decay with the highest possible precision to date for perennial ryegrass. Results showed a low LD extension with a rapid decay of r² value below 0.2 after 520 bp on average. Additionally, QTL regions for both traits were detected, as well as candidate genes by applying Genome Complex Trait Analysis and Multi-marker Analysis of GenoMic Annotation. Moreover, two significant genes, LpPc6 and LpPl6, were identified for crown and brown rust resistance, respectively, when SNPs were aggregated to the gene level. The two candidate genes encode proteins with phosphatase activity, which putatively can be induced by the host to perceive, amplify and transfer signals to downstream components, thus activating a plant defense response.

Proteins, Small Peptides and Other Signaling Molecules Identified as Inconspicuous but Possibly Important Players in Microspores Reprogramming Toward Embryogenesis

In this review, we describe and integrate the latest knowledge on the signaling role of proteins and peptides in the stress-induced microspore embryogenesis (ME) in some crop plants with agricultural importance (i.e., oilseed rape, tobacco, barley, wheat, rice, triticale, rye). Based on the results received from the most advanced omix analyses, we have selected some inconspicuous but possibly important players in microspores reprogramming toward embryogenic development. We provide an overview of the roles and downstream effect of stress-related proteins (e.g., β-1,3-glucanases, chitinases) and small signaling peptides, especially cysteine—(e.g., glutathione, γ-thionins, rapid alkalinization factor, lipid transfer, phytosulfokine) and glycine-rich peptides and other proteins (e.g., fasciclin-like arabinogalactan protein) on acclimation ability of microspores and the cell wall reconstruction in a context of ME induction and haploids/doubled haploids (DHs) production. Application of these molecules, stimulating the induction and proper development of embryo-like structures and green plant regeneration, brings significant improvement of the effectiveness of DHs procedures and could result in its wider incorporation on a commercial scale. Recent advances in the design and construction of synthetic peptides–mainly cysteine-rich peptides and their derivatives–have accelerated the development of new DNA-free genome-editing techniques. These new systems are evolving incredibly fast and soon will find application in many areas of plant science and breeding.

Changes in the expression level of genes encoding transcription factors and cell wall-related proteins during Meloidogyne arenaria infection of maize (Zea mays)

BACKGROUND

Meloidogyne arenaria is an economically important root-knot nematode (RKN) species whose hosts include maize (Zea mays). The plant response to RKN infection activates many cellular mechanisms, among others, changes in the expression level of genes encoding transcription and elongation factors as well as proteins related to cell wall organization.

METHODS AND RESULTS

This study is aimed at characterization of expression of selected transcription and elongation factors encoding the genes WRKY53, EF1a, and EF1b as well as the ones encoding two proteins associated with cell wall functioning (glycine-rich RNA-binding protein, GRP and polygalacturonase, PG) during the maize response to M. arenaria infection. The changes in the relative level of expression of genes encoding these proteins were assessed using the reverse transcription-quantitative real-time PCR. The material studied were leaves and root samples collected from four maize varieties showing different susceptibilities toward M. arenaria infection, harvested at three different time points. Significant changes in the expression level of GRP between susceptible and tolerant varieties were observed.

CONCLUSIONS

Results obtained in the study suggest pronounced involvement of glycine-rich RNA-binding protein and EF1b in the maize response and resistance to RKN.