Quantitative iTRAQ-based proteomic analysis of rice grains to assess high night temperature stress

TMT-based proteomics analysis of sea urchin (Strongylocentrotus intermedius) under high temperature stress

In the context of global warming and continuous high temperatures in the northern part of China in summer, the mortality rate of Strongylocentrotus intermedius through the summer reaches 70-80 %. The protein regulatory mechanism of S. intermedius in response to high temperature stress is still unclear. In order to investigate the protein expression of S. intermedius under high temperature stress, the study was conducted with the high-temperature resistant strain of S. intermedius and the control group of S. intermedius. Tandem Mass Tag (TMT) tagging technique was applied to resolve the protein expression profile of S. intermedius in response to high temperature stress. The results showed that, compared to 15 °C，136 DEPs were screened in high-temperature resistant strain groups of S. intermedius under high temperature stress and 87 DEPs were screened in the control group of S. intermedius. There were 33 common differential proteins in the two groups, such as APOLP, HSP 70, CDC37 and CALM. Further Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses revealed that the up-regulated proteins CALM and HSP70 are significantly enriched in the "Phosphatidylinositol signaling system" and "Protein processing in endoplasmic reticulum" in heat-tolerant S. intermedius strains under high temperature stress. The control group of S. intermedius DEPs were significantly enriched in protein processing in the endoplasmic reticulum. These results provide a theoretical basis for the molecular mechanism of sea urchin heat tolerance and fundamental data for sea urchin selection and breeding for high temperature tolerance.

Systematic identification and characterization of microRNAs with target genes involved in high night temperature stress at the filling stage of rice

High night temperature stress is one of the main environmental factors affecting rice yield and quality. More and more evidence shows that microRNA (miRNA) plays an important role in various abiotic stresses. However, the molecular network of miRNA regulation on rice tolerance to high night temperatures remains unclear. Here, small RNA, transcriptome and degradome sequencing were integrated to identify differentially expressed miRNAs, genes, and key miRNA-target gene pairs in rice heat-sensitive and heat-tolerant lines at the filling stage suffering from high night temperature stress. It was discovered that there were notable differences in the relative expression of 102 miRNAs between the two rice lines under stress. Meanwhile, 5263 and 5405 mRNAs were differentially expressed in the heat-sensitive line and heat-tolerant line, and functional enrichment analysis revealed that these genes were involved in heat-related processes and pathways. The miRNAs-mRNAs target relationship was further verified by degradome sequencing. Eventually, 49 miRNAs-222 mRNAs target pairs with reverse expression patterns showed significant relative expression changes between the heat-tolerant and the heat-sensitive line, being suggested to be responsible for the heat tolerance difference of these two rice lines. Functional analysis of these 222 mRNA transcripts showed that high night temperature-responsive miRNAs targeted these mRNAs involved in many heat-related biological processes, such as transcription regulation, chloroplast regulation, mitochondrion regulation, protein folding, hormone regulation and redox process. This study identified possible miRNA-mRNA regulation relationships in response to high night temperature stress in rice and potentially contributed to heat resistance breeding of rice in the future.

OsCSN2 orchestrates Oryza sativa L. growth and development through modulation of the GA and BR pathways

The COP9 signalosome (CSN) is a conserved protein complex found in higher eukaryotes, consisting of eight subunits, and it plays a crucial role in regulating various processes of plant growth and development. Among these subunits, CSN2 is one of the most conserved components within the COP9 signalosome complex. Despite its prior identification in other species, its specific function in Oryza sativa L. (Rice) has remained poorly understood. In this study, we investigated the role of CSN2 in rice using gene editing CRISPR/Cas9 technology and overexpression techniques. We created two types of mutants: the oscsn2 mutant and the OsCSN2-OE mutant, both in the background of rice, and also generated point mutants of OsCSN2 (OsCSN2K64E, OsCSN2K67E, OsCSN2K71E and OsCSN2K104E) to further explore the regulatory function of OsCSN2. Phenotypic observation and gene expression analysis were conducted on plants from the generated mutants, tracking their growth from the seedling to the heading stages. The results showed that the loss and modification of OsCSN2 had limited effects on plant growth and development during the early stages of both the wild-type and mutant plants. However, as the plants grew to 60 days, significant differences emerged. The OsCSN2 point mutants exhibited increased tillering compared to the OsCSN2-OE mutant plants, which were already at the tillering stage. On the other hand, the OsCSN2 point mutant had already progressed to the heading and flowering stages, with the shorter plants. These results, along with functional predictions of the OsCSN2 protein, indicated that changes in the 64th, 67th, 71st, and 104th amino acids of OsCSN2 affected its ubiquitination site, influencing the ubiquitination function of CSN and consequently impacting the degradation of the DELLA protein SLR1. Taken together, it can be speculated that OsCSN2 plays a key role in GA and BR pathways by influencing the functional regulation of the transcription factor SLR1 in CSN, thereby affecting the growth and development of rice and the number of tillers.

Involvement of HSP70 in BAG9-mediated thermotolerance in Solanum lycopersicum

Because of a high sensitivity to high temperature, both the yield and quality of tomato (Solanum lycopersicum L.) are severely restricted by heat stress. The Bcl-2-associated athanogene (BAG) proteins, a family of multi-functional co-chaperones, are involved in plant growth, development, and stress tolerance. We have previously demonstrated that BAG9 positively regulates thermotolerance in tomato. However, the BAG9-mediated mechanism of thermotolerance in tomato has remained elusive. In the present study, we report that BAG9 interacts with heat shock protein 70 (HSP70) in vitro and in vivo. Silencing HSP70 decreased thermotolerance of tomato plants, as reflected by the phenotype, relative electrolyte leakage and malondialdehyde. Furthermore, the photosystem activities, activities of antioxidant enzymes and expression of key genes encoding antioxidant enzymes were reduced in HSP70-silenced plants under heat stress. Additionally, silencing HSP70 decreased thermotolerance of overexpressing BAG9 plants, which was related to decreased photosynthetic rate, increased damage to photosystem I and photosystem II, decreased activity of antioxidant enzymes, and decreased expression of key genes encoding antioxidant enzymes. Taken together, the present study identified that HSP70 is involved in BAG9-mediated thermotolerance by protecting the photosystem stability and improving the efficiency of the antioxidant system in tomato. This knowledge can be helpful to breed improved crop cultivars that are better equipped with thermotolerance.

Pan-Omics in Sheep: Unveiling Genetic Landscapes

Multi-omics-integrated analysis, known as panomics, represents an advanced methodology that harnesses various high-throughput technologies encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Sheep, playing a pivotal role in agricultural sectors due to their substantial economic importance, have witnessed remarkable advancements in genetic breeding through the amalgamation of multiomics analyses, particularly with the evolution of high-throughput technologies. This integrative approach has established a robust theoretical foundation, enabling a deeper understanding of sheep genetics and fostering improvements in breeding strategies. The comprehensive insights obtained through this approach shed light on diverse facets of sheep development, including growth, reproduction, disease resistance, and the quality of livestock products. This review primarily focuses on the application of principal omics analysis technologies in sheep, emphasizing correlation studies between multiomics data and specific traits such as meat quality, wool characteristics, and reproductive features. Additionally, this paper anticipates forthcoming trends and potential developments in this field.

Integration of Transcriptomics and Proteomics Analysis Reveals the Molecular Mechanism of Eriocheir sinensis Gills Exposed to Heat Stress

Heat stress is an increasingly concerning topic under global warming. Heat stress can induce organisms to produce excess reactive oxygen species, which will lead to cell damage and destroy the antioxidant defense of aquatic animals. Chinese mitten crab, Eriocheir sinensis, is sensitive to the change in water temperature, and parent crabs are more vulnerable during the breeding stage. In the present study, the multi-omics responses of parent E. sinensis gills to heat stress (24 h) were determined via transcriptome and proteome. The integrative analysis revealed that heat shock protein 70 (HSP70) and glutathione s-transferase (GST) were significantly up-regulated at gene and protein levels after heat stress, indicating that HSP70 and the antioxidant system participated in the regulatory mechanism of heat stress to resist oxidative damage. Moreover, the "Relaxin signaling pathway" was also activated at gene and protein levels under 30 °C stress, which implied that relaxin may be essential and responsible for reducing the oxidative damage of gills caused by extreme heat stress. These findings provided an understanding of the regulation mechanism in E. sinensis under heat stress at gene and protein levels. The mining of key functional genes, proteins, and pathways can also provide a basis for the cultivation of new varieties resistant to oxidative stress.

Proteomic analysis reveals oxidative stress-induced activation of Hippo signaling in thiamethoxam-exposed Drosophila

Thiamethoxam (THIA) is a widely used neonicotinoid insecticide. However, the toxicity and defense mechanisms activated in THIA-exposed insects are unclear. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) proteomics technology to identify changes in protein expression in THIA-exposed Drosophila. We found that the antioxidant proteins Cyp6a23 and Dys were upregulated, whereas vir-1 was downregulated, which may have been detoxification in response to THIA exposure. Prx5 downregulation promoted the generation of reactive oxygen species. Furthermore, the accumulation of reactive oxygen species led to the induction of antioxidant defenses in THIA-exposed Drosophila, thereby enhancing the levels of oxidative stress markers (e.g., superoxide dismutase, glutathione S-transferase, and glutathione) and reducing catalase expression. Furthermore, the Hippo signaling transcription coactivator Yki was inactivated by THIA. Our results suggesting that Hippo signaling may be necessary to promote insect survival in response to neonicotinoid insecticide toxicity.

Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice

Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.

Integration of transcriptome and proteome analyses reveals the regulation mechanisms of Larimichthys polyactis liver exposed to heat stress

Small yellow croaker (Larimichthys polyactis) is one of the most economically important marine fishery species. L. polyactis aquaculture has experienced stress response and the frequent occurrence of diseases, bringing huge losses to the aquaculture industry. Little is known about the regulation mechanism of heat stress response in L. polyactis. In this study, to provide an overview of the heat-tolerance mechanism of L. polyactis, the transcriptome and proteome of the liver of L. polyactis on the 6 h after high temperature (32 °C) treatment were analyzed using Illumina HiSeq 4000 platform and isobaric tag for relative and absolute quantitation (iTRAQ). A total of 3700 upregulated and 1628 downregulated genes (differentially expressed genes, DEGs) were identified after heat stress in L. polyactis. Also, 198 differentially expressed proteins (DEPs), including 117 upregulated and 81 downregulated proteins, were identified. Integrative analysis revealed that 72 genes were significantly differentially expressed at transcriptome and protein levels. Functional analysis showed that arginine biosynthesis, tyrosine metabolism, pentose phosphate pathway, starch and sucrose metabolism, and protein processing in the endoplasmic reticulum were the main pathways responding to heat stress. Among the pathways, protein processing in the endoplasmic reticulum was enriched by most DEGs/DEPs, which suggests that this pathway may play a more important role in the heat stress response. Further insights into the pathway revealed that transcripts and proteins, especially HSPs and PDIs, were differentially expressed in response to heat stress. These findings contribute to existing data describing the fish response to heat stress and provide information about protein levels, which are of great significance to a deeper understanding of the heat stress responding regulation mechanism in L. polyactis and other fish species.

Integrated Proteotranscriptomics of the Hypothalamus Reveals Altered Regulation Associated with the FecB Mutation in the BMPR1B Gene That Affects Prolificacy in Small Tail Han Sheep

The litter size and ovulation rate are different among ewes of different FecB genotypes in Small Tail Han sheep. These variants in reproductive phenotypes may be regulated by hormones released by the hypothalamic-pituitary-ovarian axis. However, there have been few reports on the hypothalamus regarding regulating an increase in ovulation in sheep with FecB mutation at different estrous stages. Thus, we examined the abundance of hypothalamus tissue protein profiles of six FecB mutant homozygous (BB) and six wild-type (WW) ewes at the luteal and follicular phases. We determined this abundance by tandem mass tag-based quantitative analysis and parallel reaction monitoring methods. Furthermore, an integrated proteotranscriptomic analysis was performed by the Data Integration Analysis for Biomarker discovery using the latent variable approaches for Omics studies (DIABLO) framework to examine biological processes and pathway alterations by the FecB mutant. The abundance of 154 proteins was different between the two estrous stages. Growth hormone and prolactin were particularly enriched in the neuroactive ligand-receptor interactions, the prolactin signaling pathway, and the PI3K-Akt signaling pathway which are related to hypothalamic function and reproduction. We combined proteome and transcriptome data from different estrous stages and genotypes. There is a high correlation (Pearson correlation coefficient = 0.99) between the two datasets in the first two components. We applied the traditional single-omic multivariate approach to obtain differentially abundant proteins and differentially expressed genes. The major fertility related biomarkers were selected using the two approaches mentioned above. Several key pathways (GABAergic synapse, neuroactive ligand-receptor interaction, estrogen and MAPK signaling pathways) were enriched, which are central to gonadotrophin-releasing hormone (GnRH) secretion and reproduction. A higher level of gamma-aminobutyric acid type A receptor subunit alpha1 (GABRA1) and gamma-aminobutyric acid type A receptor subunit beta2 (GABRB2) expression was observed in BB ewes as compared to WW ewes. This finding suggested that a greater production of GnRH during follicular development in BB ewes may explain the higher mature follicle number in mutant ewes. FKBP prolyl isomerase 1A (FKBP1A), which was a major feature factor in the proteome selected by DIABLO, was an important switch for activating the transforming growth factor beta (TGFβ) pathway, and its expression was higher in the WW ewes than in the BB ewes. We suggest that BB sheep maintain TGFβ pathway activity by reducing FKBP1A protein abundance. This innovative data integration in the hypothalamus may provide fresh insight into the mechanisms by which the FecB mutation affects sheep fertility, while providing novel biomarkers related to reproductive endocrinology in sheep breeding.

Integrative Proteomics and Transcriptomics Profiles of the Oviduct Reveal the Prolificacy-Related Candidate Biomarkers of Goats (Capra hircus) in Estrous Periods

The oviduct is a dynamic reproductive organ for mammalian reproduction and is required for gamete storage, maturation, fertilization, and early embryonic development, and it directly affects fecundity. However, the molecular regulation of prolificacy occurring in estrous periods remain poorly understood. This study aims to gain a better understanding of the genes involved in regulating goat fecundity in the proteome and transcriptome levels of the oviducts. Twenty female Yunshang black goats (between 2 and 3 years old, weight 52.22 ± 0.43 kg) were divided into high- and low-fecundity groups in the follicular (FH and FL, five individuals per group) and luteal (LH and LL, five individuals per group) phases, respectively. The DIA-based high-resolution mass spectrometry (MS) method was used to quantify proteins in twenty oviducts. A total of 5409 proteins were quantified, and Weighted gene co-expression network analysis (WGCNA) determined that the tan module was highly associated with the high-fecundity trait in the luteal phase, and identified NUP107, ANXA11, COX2, AKP13, and ITF140 as hub proteins. Subsequently, 98 and 167 differentially abundant proteins (DAPs) were identified in the FH vs. FL and LH vs. LL comparison groups, respectively. Parallel reaction monitoring (PRM) was used to validate the results of the proteomics data, and the hub proteins were analyzed with Western blot (WB). In addition, biological adhesion and transporter activity processes were associated with oviductal function, and several proteins that play roles in oviductal communication with gametes or embryos were identified, including CAMSAP3, ITGAM, SYVN1, EMG1, ND5, RING1, CBS, PES1, ELP3, SEC24C, SPP1, and HSPA8. Correlation analysis of proteomics and transcriptomic revealed that the DAPs and differentially expressed genes (DEGs) are commonly involved in the metabolic processes at the follicular phase; they may prepare the oviductal microenvironment for gamete reception; and the MAP kinase activity, estrogen receptor binding, and angiotensin receptor binding terms were enriched in the luteal phase, which may be actively involved in reproductive processes. By generating the proteome data of the oviduct at two critical phases and integrating transcriptome analysis, we uncovered novel aspects of oviductal gene regulation of fecundity and provided a reference for other mammals.

Genome-wide analysis of the CSN genes in land plants and their expression under various abiotic stress and phytohormone conditions in rice

The CONSTITUTIVE PHOTOMORPHOGENIC9 (COP9) signalosome (CSN) is a multi-functional protein complex, which is involved in plant growth and abiotic stress response. However, the evolution and function of the CSN genes in land plants are still largely unclear. Here, we have identified 124 CSN genes and constructed phylogenetic trees of these CSN proteins to elucidate their feature and evolution in twelve land plants. Analysis of gene structure, protein property and protein motif composition shows the evolutional conservation and variation of the CSN proteins in land plants. These CSN genes might evolve through whole genome duplication (WGD)/segmental duplication (SD) and tandem duplication (TD). Analysis of promoter cis-elements shows that the CSN genes are implicated in diverse biological processes and different signaling pathways. RT-qPCR indicates that the transcript abundance of the OsCSN genes is up-regulated or down-regulated in response to abiotic stress and treatment with various hormones in rice. These results provide new insights into the CSN gene evolution and its possible function in land plants.

iTRAQ-based quantitative proteomic analysis in liver of Pomacea canaliculata induced by oleanolic acid stress

BACKGROUND

Triterpene acid is one of the typical active constituents of Eucalyptus bark, which is the main by-product of the Eucalyptus wood industry. Our studies have demonstrated that triterpene acid stress could inhibit climbing and increase mortality in Pomacea canaliculata (Lamarck). However, limited attention has been paid to the proteomic responses of this snail under triterpene acid stress.

RESULT

Using iTRAQ-based quantitative proteomics, we elucidated the regulatory mechanism in the livers of P. canaliculata held in chlorine-free water and exposed to 100 mg L^-1 oleanolic acid (OA) for 24 h. A total of 4308 proteins were identified, of which 274 were differentially expressed proteins (DEPs) including 168 (61.31%) differentially upregulated proteins and 106 (38.69%) differentially downregulated proteins. Bioinformatics analysis revealed that P. canaliculata responses to OA stress are mainly involved in glucose metabolism, energy synthesis, immune response, stress response, protein synthesis, and apoptosis. According to KEGG analysis, the 274 DEPs were mapped to 168 KEGG pathways and 10 KEGG pathways were significantly enriched (P < 0.05). Furthermore, qRT-PCR was performed for histone H4, catalase, isocitrate dehydrogenase, superoxide dismutase, ferritin, lipase, and tropomyosin to validate the iTRAQ results.

CONCLUSION

Proteomic analysis suggested that OA stress led to the disruption of glucose metabolism, energy synthesis, and protein synthesis, and triggered a series of molecular pathways containing many key proteins involved in the immune process, thereby helping P. canaliculata resist OA stress. © 2022 Society of Chemical Industry.

Proteomic Analysis Reveals Salicylic Acid as a Pivotal Signal Molecule in Rice Response to Blast Disease Infection

Rice blast disease caused by a fungus, Magnaporthe grisea, is one of the most destructive diseases in rice production worldwide, and salicylic acid (SA) can efficiently decrease the damage of M. grisea. Here, we combined the 2-Dimensional-Liquid Chromatography and the Matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (2D-LC-MALDI-TOF-TOF MS) techniques to compare and identify differentially expressed labelled proteins by the isobaric tags for relative and absolute quantitation (iTRAQ) between the blast-resistant cultivar Minghui and the susceptible rice cultivar Nipponbare in response to blast fungus infection. The group samples were treated with salicylic acid and compared to control samples. A total of 139 DEPs from the two cultivars showed either more than a two-fold change or alternating regulation patterns. Protein functionality analysis also exhibited that these proteins are involved in a wide range of molecular functions including: energy-related activity (30%), signal transduction (11%), redox homeostasis (15%), amino acid and nitrogen metabolism (4%), carbohydrate metabolism (5%), protein folding and assembly (10%), protein hydrolysis (9%), protein synthesis (12%), and other unknown functions (4%). Specifically, we demonstrated that exogenous treatment with salicylic acid promoted recovery in both rice cultivars from Magnaporthe grisea infection by enhancing: the regulation of signal transduction, increasing energy conversion and production through the regulation of the glycolytic pathway, and other various biochemical processes. These findings may facilitate future studies of the molecular mechanisms of rice blast resistance.

Increase Crop Resilience to Heat Stress Using Omic Strategies

Varieties of various crops with high resilience are urgently needed to feed the increased population in climate change conditions. Human activities and climate change have led to frequent and strong weather fluctuation, which cause various abiotic stresses to crops. The understanding of crops' responses to abiotic stresses in different aspects including genes, RNAs, proteins, metabolites, and phenotypes can facilitate crop breeding. Using multi-omics methods, mainly genomics, transcriptomics, proteomics, metabolomics, and phenomics, to study crops' responses to abiotic stresses will generate a better, deeper, and more comprehensive understanding. More importantly, multi-omics can provide multiple layers of information on biological data to understand plant biology, which will open windows for new opportunities to improve crop resilience and tolerance. However, the opportunities and challenges coexist. Interpretation of the multidimensional data from multi-omics and translation of the data into biological meaningful context remained a challenge. More reasonable experimental designs starting from sowing seed, cultivating the plant, and collecting and extracting samples were necessary for a multi-omics study as the first step. The normalization, transformation, and scaling of single-omics data should consider the integration of multi-omics. This review reports the current study of crops at abiotic stresses in particular heat stress using omics, which will help to accelerate crop improvement to better tolerate and adapt to climate change.

Low-temperature adaptation and preservation revealed by changes in physiological-biochemical characteristics and proteome expression patterns in post-harvest Hami melon during cold storage

The proteome and its time-dependent effects reveal the importance of stress response (including expression regulation of heat-shock proteins) and fatty acid metabolism in cold adaptation and preservation of Hami melon. To better understand the molecular mechanism of how Hami melons respond to low-temperature stress, this study investigated the relevant physiological characteristics, catalytic antibody activity, and quantitative proteomics of Hami melon (Jiashi muskmelon) during low-temperature storage. Jiashi muskmelon was stored inside two refrigerators set at 21 °C (control group) and 3 °C, respectively, for 24 days. Low-temperature storage led to a significantly reduced decay rate, weight loss rate, and loss of relative conductivity. It also maintained fruit firmness, inhibited the production rate of malondialdehyde and H₂O₂, and induced over-expression of antioxidant enzyme and ATPase. A total of 1064 differentially expressed proteins (DEPs) were identified during low-temperature storage. Stimulation response was the main process in response to low-temperature. To further verify the proteome data, we selected four heat-shock proteins (HSP) displaying relatively high expression levels. Real-time fluorescence PCR results confirmed that HmHSP90 I, HmHSP90 II, HmHSP70, and HmsHSP were significantly up-regulated upon low-temperature induction. These proteins may protect the Hami melon from physiological and cellular damage due to the low-temperature stress by acting alone or synergistically. Additionally, the main enrichment term of the fatty acid metabolism-related DEPs was fatty acid beta oxidation at 21 °C in contrast to fatty acid biosynthesis processes at 3 °C. It is speculated that Hami melon enhances low-temperature adaptability by slowing down the oxidative degradation of fatty acids and synthesizing new fatty acids at low temperatures. This study provides new insights into the mechanism of low-temperature adaptation and preservation in post-harvest Hami melon during cold storage.

Regulatory Mechanism of the Constitutive Photomorphogenesis 9 Signalosome Complex in Response to Abiotic Stress in Plants

The constitutive photomorphogenesis 9 (COP9) signalosome (CSN) is a highly conserved protein complex that regulates signaling pathways in plants under abiotic stress. We discuss the potential molecular mechanisms of CSN under abiotic stress, including oxidative stress with reactive oxygen species signaling, salt stress with jasmonic acid, gibberellic acid, and abscisic acid signaling, high-temperature stress with auxin signaling, and optical radiation with DNA damage and repair response. We conclude that CSN likely participates in affecting antioxidant biosynthesis and hormone signaling by targeting receptors, kinases, and transcription factors in response to abiotic stress, which potentially provides valuable information for engineering stress-tolerant crops.

Global identification and integrated analysis of heat-responsive long non-coding RNAs in contrasting rice cultivars

Identified 2743 rice lncRNAs LncRNAs in response to heat stress Function prediction of HRLs Network among HRLs, genes and miRNAs co-localization of HRLs with QTLs Significant motifs in HRL sequences Long non-coding RNAs (lncRNAs) play vital roles in plant responses to environmental challenges. A better understanding of the gene regulation mediated by lncRNAs and their systematic identification would provide great benefits for modern agriculture. In this study, we performed strand-specific RNA sequencing for two rice varieties, heat-tolerant ZS97B and heat-susceptible SYD2 under heat stress. In total, 2743 putative lncRNAs were identified, and their expression profiles in response to heat treatments were established. We identified 231 differentially expressed lncRNAs (DELs) under heat stress, including 31 DELs common to both varieties and 103 and 97 specific to ZS97B and SYD2, respectively, all defined as heat-responsive lncRNAs (HRLs). The target-coding genes of HRLs were predicted, and GO and KEGG annotations of HRL targets revealed functions in which HRLs might be involved. The interaction network between HRLs, target genes and relevant miRNAs was constructed. The HRLs and their targets were compared with publicly available QTLs for rice seedling growth under heat stimulus. Ten HRLs and twelve target genes were linked with five heat stress-relevant QTLs. Sequence analysis revealed several motifs significantly enriched within the 231 HRL sequences. Our findings provide a valuable resource for further characterization of lncRNAs in terms of heat response and plant heat tolerance improvement.

Comparative Phosphoproteomic Analysis Reveals the Response of Starch Metabolism to High-Temperature Stress in Rice Endosperm

High-temperature stress severely affects rice grain quality. While extensive research has been conducted at the physiological, transcriptional, and protein levels, it is still unknown how protein phosphorylation regulates seed development in high-temperature environments. Here, we explore the impact of high-temperature stress on the phosphoproteome of developing grains from two indica rice varieties, 9311 and Guangluai4 (GLA4), with different starch qualities. A total of 9994 phosphosites from 3216 phosphoproteins were identified in all endosperm samples. We identified several consensus phosphorylation motifs ([sP], [LxRxxs], [Rxxs], [tP]) induced by high-temperature treatment and revealed a core set of protein kinases, splicing factors, and regulatory factors in response to high-temperature stress, especially those involved in starch metabolism. A detailed phosphorylation scenario in the regulation of starch biosynthesis (AGPase, GBSSI, SSIIa, SSIIIa, BEI, BEIIb, ISA1, PUL, PHO1, PTST) in rice endosperm was proposed. Furthermore, the dynamic changes in phosphorylated enzymes related to starch synthesis (SSIIIa-Ser94, BEI-Ser562, BEI-Ser620, BEI-Ser821, BEIIb-Ser685, BEIIb-Ser715) were confirmed by Western blot analysis, which revealed that phosphorylation might play specific roles in amylopectin biosynthesis in response to high-temperature stress. The link between phosphorylation-mediated regulation and starch metabolism will provide new insights into the mechanism underlying grain quality development in response to high-temperature stress.

Proteome characterization of two contrasting soybean genotypes in response to different phosphorus treatments

Phosphorus (P) is an essential element for the growth and development of plants. Soybean (Glycine max) is an important food crop that is grown worldwide. Soybean yield is significantly affected by P deficiency in the soil. To investigate the molecular factors that determine the response and tolerance at low-P in soybean, we conducted a comparative proteomics study of a genotype with low-P tolerance (Liaodou 13, L13) and a genotype with low-P sensitivity (Tiefeng 3, T3) in a paper culture experiment with three P treatments, i.e. P-free (0 mmol·L-1), low-P (0.05 mmol·L-1) and normal-P (0.5 mmol·L-1). A total of 4126 proteins were identified in roots of the two genotypes. Increased numbers of differentially expressed proteins (DEPs) were obtained from low-P to P-free conditions compared to the normal-P treatment. All DEPs obtained in L13 (660) were upregulated in response to P deficiency, while most DEPs detected in T3 (133) were downregulated under P deficiency. Important metabolic pathways such as oxidative phosphorylation, glutathione metabolism and carbon metabolism were suppressed in T3, which could have affected the survival of the plants in P-limited soil. In contrast, L13 increased the metabolic activity in the 2-oxocarboxylic acid metabolism, carbon metabolism, glycolysis, biosynthesis of amino acids, pentose phosphatase, oxidative phosphorylation, other types of O-glycan biosynthesis and riboflavin metabolic pathways in order to maintain normal plant growth under P deficiency. Three key proteins I1KW20 (prohibitins), I1K3U8 (alpha-amylase inhibitors) and C6SZ93 (alpha-amylase inhibitors) were suggested as potential biomarkers for screening soybean genotypes with low-P tolerance. Overall, this study provides new insights into the response and tolerance to P deficiency in soybean.

iTRAQ-based quantitative glutelin proteomic analysis reveals differentially expressed proteins in the physiological metabolism process during endosperm development and their impacts on yield and quality in autotetraploid rice

Autotetraploid rice, which is developed through chromosome set doubling using diploid rice, produces high-quality kernels that are rich in storage proteins. However, little information is available about the content of different proteins in autotetraploid rice and their proteomic analysis. The dynamic changes in four storage proteins, namely, albumin, globulin, prolamin, and glutelin, were analyzed in the endosperm of autotetraploid rice (AJNT-4x) and in that of its diploid counterpart (AJNT-2x) for comparison. The contents of the four proteins were all higher during endosperm development in AJNT-4x than in AJNT-2x, but their change and composition were almost the same in the two materials. Then, iTRAQ was employed to analyze the glutelin profiles of AJNT-4x and AJNT-2x at 10 DAF, 15 DAF, and 20 DAF. A total of 1326 proteins were identified in AJNT-4x and AJNT-2x using high-throughput LC-MS/MS. Among the 1326 identified proteins, there were 362 DEPs in AJNT-4x compared with AJNT-2x and 372 DEPs between different developmental stages in AJNT-4x. Eight important upregulated proteins were identified by qRT-PCR, including B8AM24, B8ARJ0, B8AQM6, A2ZCE6, and P37833. Among them, B8AM24 and B8ARJ0 were related to the lysine biosynthesis process. GO enrichment analysis revealed that the critical functions of DEPs exhibited little overlap between the 10, 15, and 20 DAF groups. Endosperm glutelin accumulation was regulated mainly by different DEPs during the early stage, and 15 DAF was a critical regulating point for glutelin accumulation. KEGG pathway analysis showed that ribosomal proteins were significantly higher in AJNT-4x than in AJNT-2x at 10 DAF, and protein processing, biosynthesis, and metabolism of amino acids were higher and more active in AJNT-4x at 15 DAF, while the peroxisome was richer in AJNT-4x at 20 DAF. The PPI network showed that ribosomal proteins gradually decreased with increasing endosperm development. These results provide new insights into dynamic glutelin expression differences during endosperm development in autotetraploid rice, which will aid in the development of rice cultivars with increased yield and improved grain nutritional quality.

Constitutive expression of Ribosomal Protein L6 modulates salt tolerance in rice transgenic plants

We have functionally characterized the RPL6, a Ribosomal Protein Large subunit gene for salt stress tolerance in rice. The overexpression of RPL6 resulted in tolerance to moderate (150 mM) to high (200 mM) levels of salt (NaCl). The transgenic rice plants expressing RPL6 constitutively showed better phenotypic and physiological responses with high quantum efficiency, accumulation of higher chlorophyll and proline contents, and an overall increase in seed yield compared with the wild type in salt stress treatments. An iTRAQ-based comparative proteomic analysis revealed the high expression of about 333 proteins among the 4378 DAPs in a selected overexpression line of RPL6 treated with 200 mM of NaCl. The functional analysis showed that these highly accumulated proteins (HAPs) are involved in photosynthesis, ribosome and chloroplast biogenesis, ion transportation, transcription and translation regulation, phytohormone and secondary metabolite signal transduction. An in silico network analysis of HAPs predicted that RPL6 binds with translation-related proteins and helicases, which coordinately affect the activities of a comprehensive signaling network, thereby inducing tolerance and promoting growth and productivity in response to salt stress. Our overall findings identified a novel candidate, RPL6, whose characterization contributed to the existing knowledge on the complexity of salt tolerance mechanism in plants.

Physiological and Biochemical Characteristics of Two Soybean Cultivars with Different Seed Vigor During Seed Physiological Maturity

Background:

The soybean seed’s physiological maturity (R7) period is an extraordinary period for the formation of seed vigor. However, how proteins and their related metabolic pathways in seed and leaf change during seed physiological maturity is still not fully understood.

Methods:

In the present study, using a pair of pre-harvest seed deterioration-sensitive and -resistant soybean cultivars Ningzhen No. 1 and Xiangdou No. 3, the changes were investigated through analyzing leaf, cotyledon and embryo at the levels of protein, ultrastructure, and physiology and biochemistry.

Results:

Soybean cultivars with stronger photosynthetic capacity in leaf, higher nutrients accumulation and protein biosynthesis in cotyledon, as well as stronger resistant-pathogen ability and cell stability in embryo during seed physiological maturity, would produce higher vitality seeds.

Conclusion:

Such a study allows us to further understand the changes at protein, ultrastructure, and physiology and biochemistry levels in developing seeds during the physiological maturity and provide a theoretical basis for cultivating soybean cultivars with higher seed vigor.

iTRAQ and PRM-based comparative proteomic profiling in gills of white shrimp Litopenaeus vannamei under copper stress

Crustaceans are particularly sensitive to heavy metal pollution. Copper (Cu) is one of typical heavy metal pollutants in aquatic ecosystems. However, limited attention has been paid on the proteomic responses of shrimp under Cu stress. White shrimp Litopenaeus vannamei held in 5‰ seawater were exposed to 5 mg L^-1 Cu for 3 h, and the regulatory mechanism in the gills was elucidated using iTRAQ-based quantitative proteomics. The results showed that a total of 5034 proteins were identified, 385 differentially expressed proteins (DEPs), including 147 differentially up-regulated proteins (DUPs) and 238 differentially down-regulated proteins (DDPs) were found. Bioinformatics analysis indicated the DEPs responding to Cu stress mainly involved in cytoskeleton, immune response, stress response, protein synthesis, detoxification, ion homeostasis and apoptosis. Furthermore, we still performed PRM analysis on sarcoplasmic calcium binding protein (SCP), serine proteinase inhibitor B3 (SPIB3), C-type lectin 4 (CTL4), cathepsin L (CATHL), JHE-like carboxylesterase 1 (CXE1) and paramyosin (PMY), and biochemical analysis on Cu/Zn-superoxide dismutase (Cu/Zn-SOD) to validate the iTRAQ results, respectively. The present proteome analysis revealed that Cu stress disrupted the ion homeostasis and protein synthesis, and L.vannamei mainly regulates a series of molecular pathways which contained many key proteins involved in the immune process to protect the organism from Cu stress. Our data provides more insight about the underlying mechanisms that related to the stress response of Cu exposure in crustacean.

Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles

Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest ubiquitinome dataset in rice to date, identifying 1638 lysine ubiquitination sites on 916 unique proteins. We detected three conserved ubiquitination motifs, noting that acidic glutamic acid (E) and aspartic acid (D) were most frequently present around ubiquitinated lysine. Enrichment analysis of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles. Interestingly, enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptor-like kinases and cytoplasmic tyrosine and serine-threonine kinases. Furthermore, we analyzed the crosstalk between ubiquitination, acetylation, and succinylation, and constructed a potential protein interaction network within our rice ubiquitinome. Moreover, we identified ubiquitinated proteins related to pollen and grain development, indicating that ubiquitination may play a critical role in the physiological functions in young panicles. Taken together, we reported the most comprehensive lysine ubiquitinome in rice so far, and used it to reveal the functional role of lysine ubiquitination in rice young panicles.

Identification and Characterization of Contrasting Genotypes/Cultivars for Developing Heat Tolerance in Agricultural Crops: Current Status and Prospects

Rising global temperatures due to climate change are affecting crop performance in several regions of the world. High temperatures affect plants at various organizational levels, primarily accelerating phenology to limit biomass production and shortening reproductive phase to curtail flower and fruit numbers, thus resulting in severe yield losses. Besides, heat stress also disrupts normal growth, development, cellular metabolism, and gene expression, which alters shoot and root structures, branching patterns, leaf surface and orientation, and anatomical, structural, and functional aspects of leaves and flowers. The reproductive growth stage is crucial in plants' life cycle, and susceptible to high temperatures, as reproductive processes are negatively impacted thus reducing crop yield. Genetic variation exists among genotypes of various crops to resist impacts of heat stress. Several screening studies have successfully phenotyped large populations of various crops to distinguish heat-tolerant and heat-sensitive genotypes using various traits, related to shoots (including leaves), flowers, fruits (pods, spikes, spikelets), and seeds (or grains), which have led to direct release of heat-tolerant cultivars in some cases (such as chickpea). In the present review, we discuss examples of contrasting genotypes for heat tolerance in different crops, involving many traits related to thermotolerance in leaves (membrane thermostability, photosynthetic efficiency, chlorophyll content, chlorophyll fluorescence, stomatal activity), flowers (pollen viability, pollen germination, fertilization, ovule viability), roots (architecture), biomolecules (antioxidants, osmolytes, phytohormones, heat-shock proteins, other stress proteins), and "omics" (phenomics, transcriptomics, genomics) approaches. The traits linked to heat tolerance can be introgressed into high yielding but heat-sensitive genotypes of crops to enhance their thermotolerance. Involving these traits will be useful for screening contrasting genotypes and would pave the way for characterizing the underlying molecular mechanisms, which could be valuable for engineering plants with enhanced thermotolerance. Wherever possible, we discussed breeding and biotechnological approaches for using these traits to develop heat-tolerant genotypes of various food crops.

iTRAQ-based quantitative proteomic analysis reveals the metabolic pathways of grain chalkiness in response to nitrogen topdressing in rice

Grain chalkiness is a highly undesirable trait that adversely affects rice quality. This chalkiness is easily influenced by the application of chemical nitrogen (N) fertilizer at the late growth stage. However, on the molecular mechanism underlying grain chalkiness caused by late N fertilization is not fully clear. In this study, proteomic differences in expression were determined in developing grains exposed to N topdressing (108 kg N ha^-1, N+) and a control (0 kg N ha^-1, N0), using the rice variety OM052, which has a high level of chalkiness. A total of 198 differentially expressed proteins (DEPs) were detected between the N+ and N0 treatments, including 9 up-regulated proteins and 189 down-regulated proteins. Of these DEPs, approximately half were associated with carbohydrate metabolism (glycolysis, tricarboxylic acid cycle, pentose phosphate pathway, fermentation and starch metabolism) and N metabolism (protein synthesis, folding, degradation and storage, amino acid synthesis and catabolism). A detailed pathway dissection revealed that multiple metabolic pathways during the grain filling stage were involved in the N-induced grain chalkiness. Reduced abundances of proteins associated with respiratory metabolism and energy metabolism drastically impaired the biosynthesis and deposition of starch in the developmental endosperms, which might be a crucial trigger for the increase in grain chalkiness. The disturbed N metabolism and differential expression of storage proteins up-regulated during the grain filling stage are able to partially explain the occurrence of grain chalkiness in rice.

Analysis of leaf morphology, secondary metabolites and proteins related to the resistance to Tetranychus cinnabarinus in cassava (Manihot esculenta Crantz)

Constitutive resistance of plant can be divided into physical and chemical barriers. Cassava (Manihot esculenta Crantz) is susceptible to mites, especially Tetranychus cinnabarinus. Although significant differences in the resistance to T. cinnabarinus are observed in different cassava cultivars, limited research has been done on the mechanism accounting for the resistance. The aim of this study was to explore the mechanism of resistance to T. cinnabarinus by comparing morphology, secondary metabolites and proteins in different cassava cultivars. The anatomical structure of leaves showed that the cassava cultivar Xinxuan 048 (XX048), which showed a stronger resistance to T. cinnabarinus in both greenhouse testing and three years field evaluation tests (2016–2018), had thicker palisade tissue, spongy tissue, lower epidermis and leaf midrib tissue compared to cultivar Guire 4 (GR4). Greenhouse evaluation demonstrated that originally these cultivars were different, leading to differences in constitutive levels of metabolites. The proteomic analysis of protected leaves in XX048 and GR4 revealed that up-regulated differentially expressed proteins (DEPs) were highly enriched in secondary metabolic pathways, especially in the biosynthesis of flavonoids. This study not only provides a comprehensive data set for overall proteomic changes of leaves in resistant and susceptible cassava, but also sheds light on the morphological characteristics of cassava-mite interaction, secondary metabolite defense responses, and molecular breeding of mite-resistant cassava for effective pest control.

Cytosine methylations in the promoter regions of genes involved in the cellular oxidation equilibrium pathways affect rice heat tolerance

Background

High temperatures, particularly at night, decrease rice yield and quality. As high nighttime temperatures (HNTs) become increasingly frequent due to climate change, it is imperative to develop rice crops that tolerate HNTs. DNA methylation may represent a potential avenue for HNT-tolerant rice strain development, as this mechanism regulates gene activity and cellular phenotype in response to adverse environmental conditions without changing the nucleotide sequence.

Results

After HNT exposure, the methylation patterns of cytosines in the CHH context differed noticeably between two coisogenic rice strains with significantly different levels in heat tolerance. Methylation differences between strains were primarily observed on successive cytosines in the promoter or downstream regions of transcription factors and transposon elements. In contrast to the heat-sensitive rice strain, the regions 358–359 bp and 2–60 bp downstream of two basal transcriptional factors (TFIID subunit 11 and mediator of RNA polymerase II transcription subunit 31, respectively) were fully demethylated in the heat-tolerant strain after HNT exposure. In the heat-tolerant strain, HNTs reversed the methylation patterns of successive cytosines in the promoter regions of various genes involved in abscisic acid (ABA)-related reactive oxygen species (ROS) equilibrium pathways, including the pentatricopeptide repeat domain gene PPR (LOC_Os07g28900) and the homeobox domain gene homeobox (LOC_Os01g19694). Indeed, PRR expression was inhibited in heat-sensitive rice strains, and the methylation rates of the cytosines in the promoter region of PRR were greater in heat-sensitive strains as compared to heat-tolerant strains.

Conclusions

After HNT exposure, cytosines in the CHH context were more likely than cytosines in other contexts to be methylated differently between the heat-sensitive and heat-tolerant rice strains. Methylation in the promoter regions of the genes associated with ABA-related oxidation and ROS scavenging improved heat tolerance in rice. Our results help to clarify the molecular mechanisms underlying rice heat tolerance.

iTRAQ-based quantitative proteomics analysis of cantaloupe (Cucumis melo var. saccharinus) after cold storage

Background

Cantaloupe is susceptible to cold stress when it is stored at low temperatures, resulting in the loss of edible and commercial quality. To ascertain the molecular mechanisms of low temperatures resistance in cantaloupe, a cold-sensitive cultivar, Golden Empress-308 (GE) and a cold-tolerant cultivar, Jia Shi-310 (JS), were selected in parallel for iTRAQ quantitative proteomic analysis.

Results

The two kinds of commercial cultivars were exposed to a temperature of 0.5 °C for 0, 12 and 24 days. We found that the cold-sensitive cultivar (GE) suffered more severe damage as the length of the cold treatment increased. Proteomic analysis of both cultivars indicated that the number of differentially expressed proteins (DEPs) changed remarkably during the chilly treatment. JS expressed cold-responsive proteins more rapidly and mobilized more groups of proteins than GE. Furthermore, metabolic analysis revealed that more amino acids were up-regulated in JS during the early phases of low temperatures stress. The DEPs we found were mainly related to carbohydrate and energy metabolism, structural proteins, reactive oxygen species scavenging, amino acids metabolism and signal transduction. The consequences of phenotype assays, metabolic analysis and q-PCR validation confirm the findings of the iTRAQ analysis.

Conclusion

We found that the prompt response and mobilization of proteins in JS allowed it to maintain a higher level of cold tolerance than GE, and that the slower cold responses in GE may be a vital reason for the severe chilling injury commonly found in this cultivar. The candidate proteins we identified will form the basis of future studies and may improve our understanding of the mechanisms of cold tolerance in cantaloupe.

iTRAQ proteomics reveals the regulatory response to Magnaporthe oryzae in durable resistant vs. susceptible rice genotypes

Rice blast disease caused by Magnaporthe oryzae (M. oryzae) is one of the most serious diseases. Although previous research using two-dimensional gel-based proteomics to assess the proteins related to the rice blast resistance had been done, few proteins were identified. Here, we used the iTRAQ method to detect the differentially expressed proteins (DEPs) in the durable resistant rice variety Gangyuan8 (GY8) and the susceptible rice variety Lijiangxintuanheigu (LTH) in response to M. oryzae invasion, and then transcriptome sequencing was used to assist analysis A total of 193 and 672 DEPs were specifically identified in GY8 and LTH, respectively, with only 46 similarly expressed DEPs being shared by GY8 and LTH.39 DEPs involved in plant-pathogen interaction, plant hormone signal transduction, fatty acid metabolism and peroxisome biosynthesis were significantly different between compatible interaction (LTH) and incompatible interaction (GY8). Some proteins participated in peroxide signal transduction and biosynthesis was down-regulated in GY8 but up-regulated in LTH. A lot of genes encoding pathogenesis-related gene (PR), such as chitinase and glucanase, were significantly up-regulated at both the transcriptome and proteome levels at 24 hours post-inoculation in GY8, but up-regulated at the transcriptome level and down-regulated at the proteome level in LTH. Our study reveals that the pathogen-associated molecular pattern (PAMP)-triggered immunity defense system may be activated at the transcriptome level but was inhibited at the protein level in susceptible rice varieties after inoculation. The results may facilitate future studies of the molecular mechanisms of rice blast resistance.

COP9 signalosome: Discovery, conservation, activity, and function

The COP9 signalosome (CSN) is a conserved protein complex, typically composed of eight subunits (designated as CSN1 to CSN8) in higher eukaryotes such as plants and animals, but of fewer subunits in some lower eukaryotes such as yeasts. The CSN complex is originally identified in plants from a genetic screen for mutants that mimic light-induced photomorphogenic development when grown in the dark. The CSN complex regulates the activity of cullin-RING ligase (CRL) families of E3 ubiquitin ligase complexes, and play critical roles in regulating gene expression, cell proliferation, and cell cycle. This review aims to summarize the discovery, composition, structure, and function of CSN in the regulation of plant development in response to external (light and temperature) and internal cues (phytohormones).

Proteomic analysis of sheep uterus reveals its role in prolificacy

Small Tail Han sheep have attracted attention for their high fecundity and year-round estrus. However, the molecular mechanisms of this fecundity are unknown. Polymorphism of the FecB gene has been shown to be associated with the ovulation rate and litter size in sheep. In this study, we used tandem mass tag quantitative proteomic techniques to identify the differentially abundant proteins in polytocous and monotocous Small Tail Han sheep (FecB++) uterine tissues in the follicular and luteal phases. In total, 41 and 43 differentially abundant proteins were identified in the follicular and luteal phases, respectively. Correlation analysis between the transcriptome and proteome revealed a positive correlation at the two omics levels of prolificacy. GO and KEGG pathway analyses indicated that the mRNAs and proteins upregulated in the polytocous group relative to the monotocous group are involved in sphingolipid metabolism and amino acid metabolism, and may be important in maintaining uterine functions and increasing the embryo survival rate during the estrus cycle of polytocous sheep. In conclusion, our work provides a prospective understanding of the molecular mechanism underlying the high prolificacy of Small Tail Han sheep. SIGNIFICANCE: Fecundity critically affects the profitability of sheep production, but the genetic mechanism of high-prolificacy is still unclear in sheep. We identified potential signaling pathways and differentially abundant proteins associated with reproductive performance through a combination of sheep uterus tissues proteome and transcriptome analyses. These findings will facilitate a better revealing the mechanism and provide possible targets for molecular design breeding for the formation of polytocous traits in sheep.

Polysaccharide Fraction Extracted from Endophytic Fungus Trichoderma atroviride D16 Has an Influence on the Proteomics Profile of the Salvia miltiorrhiza Hairy Roots

Trichoderma atroviride develops a symbiont relationship with Salvia miltiorrhiza and this association involves a number of signaling pathways and proteomic responses between both partners. In our previous study, we have reported that polysaccharide fraction (PSF) of T. atroviride could promote tanshinones accumulation in S.miltiorrhiza hairy roots. Consequently, the present data elucidates the broad proteomics changes under treatment of PSF. Furthermore, we reported several previously undescribed and unexpected responses, containing gene expression patterns consistent with biochemical stresses and metabolic patterns inside the host. In summary, the PSF-induced tanshinones accumulation in S.miltiorrhiza hairy roots may be closely related to Ca2+ triggering, peroxide reaction, protein phosphorylation, and jasmonic acid (JA) signal transduction, leading to an increase in leucine-rich repeat (LRR) protein synthesis. This results in the changes in basic metabolic flux of sugars, amino acids, and protein synthesis, along with signal defense reactions. The results reported here increase our understanding of the interaction between T.atroviride and S.miltiorrhiza and specifically confirm the proteomic responses underlying the activities of PSF.

Role of Cop9 Signalosome Subunits in the Environmental and Hormonal Balance of Plant

The COP9 (Constitutive photomorphogenesis 9) signalosome (CSN) is a highly conserved protein complex that influences several signaling and developmental processes. The COP9 signalosome consists of eight subunits, among which two subunits, CSN5 and CSN6, contain an Mpr1/Pad1 N-terminal (MPN) domain and the remaining six subunits contain a proteasome, COP9 signalosome, and initiation factor 3 (PCI) domain. In plants, each MPN subunit is encoded by two genes, which is not the case in other organisms. This review aims to provide in-depth knowledge of each COP9 signalosome subunit, concentrating on genetic analysis of both partial and complete loss-of-function mutants. At the beginning of this review, the role of COP9 signalosome in the hormonal signaling and defense is discussed, whereas later sections deal in detail with the available partial loss-of-function, hypomorphic mutants of each subunit. All available hypomorphic mutants are compared based on their growth response and deneddylation activity.

Comparative proteomic analysis of two sesame genotypes with contrasting salinity tolerance in response to salt stress

Sesame is one of the most important oilseed crops and has high nutritional value. The yield and quality of sesame are severely affected by high salinity in coastal and semi-arid/arid regions. In this study, the phenotypic, physiological, and proteomic changes induced by salt treatment were analyzed in salt-tolerant (G441) and salt-sensitive (G358) seedlings. Phenotypic and physiological results indicated that G441 had an enhanced capacity to withstand salinity stress compared to G358. Proteomic analysis revealed a strong induction of salt-responsive protein species in sesame, mainly related to catalytic, hydrolase, oxidoreductase, and binding activities. Pathway enrichment analysis showed that more salt-responsive proteins in G441 were involved in tyrosine metabolism, carbon fixation in photosynthetic organisms, carbon metabolism, alpha-linolenic acid metabolism, biosynthesis of amino acids, photosynthesis, and glutathione metabolism. Furthermore, G441 displayed unique differentially accumulated proteins in seedlings functioning as heat shock proteins, abscisic acid receptor PYL2-like, calcium-dependent protein kinases, serine/threonine-protein phosphatases, nucleoredoxin, and antioxidant enzymes. Quantitative real-time PCR analysis revealed that some of the proteins were also regulated by salinity stress at the transcript level. Our findings provide important information on salinity responses in plants and may constitute useful resources for enhancing salinity tolerance in sesame. SIGNIFICANCE: Our study identified potential biological pathways and salt-responsive protein species related to transducing stress signals and scavenging reactive oxygen species under salt stress. These findings will provide possible participants/pathways/proteins that contribute to salt tolerance and may serve as the basis for improving salinity tolerance in sesame and other plants.

iTRAQ-based quantitative proteomic analysis of Takifugu fasciatus liver in response to low-temperature stress

Low temperatures profoundly influence the physiological and behavioural processes of ectotherms, especially teleosts, which have made them the subjects of strong interest over time. However, the characteristics of fish cold-tolerance at the protein level remain unclear. Therefore, to shed further light on the molecular mechanisms of low temperature adaptation in fish, we conducted quantitative proteomics on the T. fasciatus liver using iTRAQ. Comparing the proteomic profiles of the T. fasciatus liver at 12 °C and 26 °C, a total of 3741 proteins were identified, and 160 were differentially abundant proteins (DAPs). Among the DAPs, the most significant changes were noted in proteins involved in oxidative stress (nine proteins), mitochondrial enzymes (eleven proteins) and signal transduction (thirteen proteins). The KEGG enrichment analysis indicated significant enhancement of D-arginine and D-ornithine metabolism, MAPK signalling, Wnt signalling and Gap junction pathway. Subsequently, three significantly up-regulated proteins (CIRB, HSP90 and GST) and two significantly down-regulated proteins (FLNB and A2ML1) were validated with parallel reaction monitoring (PRM) assays. Furthermore, the changes in abundance of proteins that are involved in oxidative stress, mitochondrial enzymes and signal transduction were validated at the transcriptional level with qPCR. These verification results show that the experimental data of iTRAQ are reliable. Our results not only deepen the understanding of the mechanisms underlying low-temperature tolerance in fish, but they also may contribute to the enhancement of cold tolerance during its breeding process. SIGNIFICANCE OF THE STUDY: The study focused on a comparative quantitative proteomics analysis of the T. fasciatus liver in response to low temperatures using iTRAQ, which has not yet been reported in the literatures. The results showed that the effect of low temperature on T. fasciatus is significant, including a detoxification of metabolic by-products and oxidative stress, an activation of the mitochondrial enzyme to strengthen energy metabolism, and a negative effect on signal transduction, which result in dysfunction or suboptimal performance. These low-temperature-related changes in the liver proteome of T. fasciatus can facilitate the understanding of the low temperature-related response that takes place in similar conditions in the liver and may contribute to the breeding of cold-resistant strains.

iTRAQ analysis of liver immune-related proteins from darkbarbel catfish (Pelteobagrus vachelli) infected with Edwardsiella ictaluri

Edwardsiella ictaluri causes enteric septicemia of catfish (ESC), a major disease occurring in these siluriform fish. As the liver is an important organ for defending against bacterial pathogens in fish, this study aimed to determine the liver immune response at the protein level. The differential proteomes of the darkbarbel catfish liver in response to E. ictaluri infection were identified with isobaric tags for relative and absolute quantitation (iTRAQ) labeling followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Using a 1.2-fold change in expression as a physiologically significant benchmark, a total of 819 differentially expressed proteins were reliably quantified using iTRAQ analysis, including 6 up-regulated proteins and 813 down-regulated proteins. GO enrichment analysis indicated that the "complement activation, alternative pathway" and "complement activation, classical pathway" were significantly enriched. KEGG enrichment analysis indicated the "antigen processing and presentation" and "bacterial secretion system" were significantly enriched. We selected the 6 up-regulated proteins and 10 immune-related down-regulated proteins for validation using real-time PCR. The 10 immune-related proteins included complement component C1r, C3, C5, C7, and C9 and plasma protease C1 inhibitor (C1-INH), signal recognition particle 54 kDa protein (SRP54), SRP receptor, proteasome activator complex subunit 1 (PSME1) and major histocompatibility complex class I (MHC class I) were selected from the GO clusters and KEGG pathways. The variations in mRNA expression for these genes were similar to the results of iTRAQ. This is the first report detailing the proteome response in the darkbarbel catfish liver during E. ictaluri infection and markedly contributes to our understanding of the defense mechanisms in the livers of darkbarbel catfish.

Proteomic dissection of the rice-Fusarium fujikuroi interaction and the correlation between the proteome and transcriptome under disease stress

Background

Bakanae disease, caused by the fungus Fusarium fujikuroi, occurs widely throughout Asia and Europe and sporadically in other rice production areas. Recent changes in climate and cropping patterns have aggravated this disease. To gain a better understanding of the molecular mechanisms of rice bakanae disease resistance, we employed a 6-plex tandem mass tag approach for relative quantitative proteomic comparison of infected and uninfected rice seedlings 7 days post-inoculation with two genotypes: the resistant genotype 93–11 and the susceptible genotype Nipponbare.

Results

In total, 123 (77.2% up-regulated, 22.8% down-regulated) and 91 (94.5% up-regulated, 5.5% down-regulated) differentially expressed proteins (DEPs) accumulated in 93–11 and Nipponbare, respectively. Only 11 DEPs were both shared by the two genotypes. Clustering results showed that the protein regulation trends for the two genotypes were highly contrasting, which suggested obviously different interaction mechanisms of the host and the pathogen between 93 and 11 and Nipponbare. Further analysis showed that a noticeable aquaporin, PIP2–2, was sharply upregulated with a fold change (FC) of 109.2 in 93–11, which might be related to pathogen defense and the execution of bakanae disease resistance. Certain antifungal proteins were regulated in both 93–11 and Nipponbare with moderate FCs. These proteins might participate in protecting the cellular integrity required for basic growth of the susceptible genotype. Correlation analysis between the transcriptome and proteome revealed that Pearson correlation coefficients of R = 0.677 (P = 0.0005) and R = − 0.097 (P = 0.702) were obtained for 93–11 and Nipponbare, respectively. Our findings raised an intriguing result that a significant positive correlation only in the resistant genotype, while no correlation was found in the susceptible genotype. The differences in codon usage was hypothesized for the cause of the result.

Conclusions

Quantitative proteomic analysis of the rice genotypes 93-11and Nipponbare after F. fujikuroi infection revealed that the aquaporin protein PIP2–2 might execute bakanae disease resistance. The difference in the correlation between the transcriptome and proteome might be due to the differences in codon usage between 93-11and Nipponbare. Overall, the protein regulation trends observed under bakanae disease stress are highly contrasting, and the molecular mechanisms of disease defense are obviously different between 93 and 11 and Nipponbare. In summary, these findings deepen our understanding of the functions of proteins induced by bakanae disease and the mechanisms of rice bakanae disease resistance.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5435-5) contains supplementary material, which is available to authorized users.

High Nighttime Temperature Induces Antioxidant Molecule Perturbations in Heat-Sensitive and Heat-Tolerant Coisogenic Rice ( Oryza sativa) Strains

Global warming-associated increases in temperature, particularly at nighttime, are detrimental to rice yield and quality. Metabolomic profiling was used to examine and compare the short-term extreme high nighttime temperature-induced molecular perturbations in rice ( Oryza sativa) coisogenic strains with contrasting heat-tolerances at the first stage of seed ripening. Compared to the heat-sensitive strain, antioxidant molecules were higher in abundance in the heat-tolerant strain, whereas the abundances of molecules involved in photosynthesis, nucleotide catabolism, and the S-adenosylmethionine (SAM) cycle varied only slightly. Thus, we proposed that the high abundance of antioxidant molecules in the heat-tolerant strain alleviated cellular oxidative stress, which protected photosynthesis, nucleotide catabolism, and the SAM cycle, leading to good grain filling.

Combinatorial Interactions of Biotic and Abiotic Stresses in Plants and Their Molecular Mechanisms: Systems Biology Approach

Plants are continually facing biotic and abiotic stresses, and hence, they need to respond and adapt to survive. Plant response during multiple and combined biotic and abiotic stresses is highly complex and varied than the individual stress. These stresses resulted alteration of plant behavior through regulating the levels of microRNA, heat shock proteins, epigenetic variations. These variations can cause many adverse effects on the growth and development of the plant. Further, in natural conditions, several abiotic stresses causing factors make the plant more susceptible to pathogens infections and vice-versa. A very intricate and multifaceted interactions of various biomolecules are involved in metabolic pathways that can direct towards a cross-tolerance and improvement of plant's defence system. Systems biology approach plays a significant role in the investigation of these molecular interactions. The valuable information obtained by systems biology will help to develop stress-resistant plant varieties against multiple stresses. Thus, this review aims to decipher various multilevel interactions at the molecular level under combinatorial biotic and abiotic stresses and the role of systems biology to understand these molecular interactions.

Andrographolide Sulfonate Attenuates Acute Lung Injury by Reducing Expression of Myeloperoxidase and Neutrophil-Derived Proteases in Mice

Andrographolide sulfonate (Andro-S), a sulfonation derivative of andrographolide, is known to be effective in treating inflammation-related diseases, while the underlying mechanisms and global protein alterations in response to Andro-S remain unknown. This study aimed to investigate the pharmacological effects and potential targets of Andro-S in a murine model of acute lung injury (ALI). ALI was induced by aerosolized lipopolysaccharide (LPS) exposure before treatment with Andro-S. Inflammatory state of each treatment group was determined by histological analysis and quantification of inflammatory markers. Differentially expressed proteins in lung tissues were identified by an iTRAQ-based quantitative proteomic approach and further confirmed by immunohistochemistry analysis. Administration of Andro-S alleviated LPS-induced histological changes in the lung and reduced the expression of inflammatory markers in serum, bronchoalveolar fluid and lung tissues. Proteomic analysis identified 31 differentially expressed proteins from a total of 2,234 quantified proteins in the lung. According to bioinformatics analysis, neutrophil elastase (ELANE), cathepsin G (CTSG) and myeloperoxidase (MPO), three neutrophil-derived proteases related to immune system process and defense responses to fungi were chosen as potential targets of Andro-S. Further immunohistochemistry analysis confirmed the inhibitory effects of Andro-S on LPS-induced ELANE, CTSG and MPO up-regulation. These results indicate that Andro-S suppressed the severity of LPS-induced ALI, possibly by attenuating the expression of and neutrophil-derived proteases.

Comparative proteomic analysis of QTL CTS-12 derived from wild rice (Oryza rufipogon Griff.), in the regulation of cold acclimation and de-acclimation of rice (Oryza sativa L.) in response to severe chilling stress

BACKGROUND

Rice (Oryza sativa L.) is a thermophilic crop vulnerable to chilling stress. However, common wild rice (Oryza rufipogon Griff.) in Guangxi (China) has the ability to tolerate chilling stress. To better understand the molecular mechanisms underlying chilling tolerance in wild rice, iTRAQ-based proteomic analysis was performed to examine CTS-12, a major chilling tolerance QTL derived from common wild rice, mediated chilling and recovery-induced differentially expressed proteins (DEPs) between the chilling-tolerant rice line DC90 and the chilling-sensitive 9311.

RESULTS

Comparative analysis identified 206 and 155 DEPs in 9311 and DC90, respectively, in response to the whole period of chilling and recovery. These DEPs were clustered into 6 functional groups in 9311 and 4 in DC90. The majority were enriched in the 'structural constituent of ribosome', 'protein-chromophore linkage', and 'photosynthesis and light harvesting' categories. Short Time-series Expression Miner (STEM) analysis revealed distinct dynamic responses of both chloroplast photosynthetic and ribosomal proteins between 9311 and DC90.

CONCLUSION

CTS-12 might mediate the dynamic response of chloroplast photosynthetic and ribosomal proteins in DC90 under chilling (cold acclimation) and recovery (de-acclimation) and thereby enhancing the chilling stress tolerance of this rice line. The identified DEPs and the involvement of CTS-12 in mediating the dynamic response of DC90 at the proteomic level illuminate and deepen the understanding of the mechanisms that underlie chilling stress tolerance in wild rice.

Low night temperature at veraison enhances the accumulation of anthocyanins in Corvina grapes (Vitis Vinifera L.)

Climate change is a major concern in grape production worldwide. Nights have been warming much faster than the days, raising attention on the effect of night temperatures on grape and wine composition. In this study we evaluated the effect of night temperatures on grape coloration in the cv. Corvina (Vitis vinifera L.). In 2015 and 2016 potted plants were cooled overnight (10-11 °C) during two berry ripening phases, veraison (TV) or post-veraison (TPV), and compared to control vines (C) grown at ambient night temperature (15-20 °C on average). Cooling treatment around veraison (TV) hastened berry anthocyanin accumulation, while the same treatment applied after veraison (TPV) was ineffective. Molecular analysis revealed an increased transcription of four key genes in anthocyanin biosynthesis (CHS3, F3H1, MYBA1 and UFGT) in TV treatment. These results suggest that the anthocyanin biosynthesis capacity was enhanced by cool nights during veraison. However, since the gene expression was not always temporally correlated to the increase in anthocyanin concentration, we speculate on the presence of mechanisms, such as enzymatic regulation or anthocyanin transport, which may contribute in determining the anthocyanin accumulation under low night temperatures.

Differential proteomic analysis reveals sequential heat stress-responsive regulatory network in radish (Raphanus sativus L.) taproot

Differential abundance protein species (DAPS) involved in reducing damage and enhancing thermotolerance in radish were firstly identified. Proteomic analysis and omics association analysis revealed a HS-responsive regulatory network in radish. Heat stress (HS) is a major destructive factor influencing radish production and supply in summer, for radish is a cool season vegetable crop being susceptible to high temperature. In this study, the proteome changes of radish taproots under 40 °C treatment at 0 h (Control), 12 h (Heat12) and 24 h (Heat24) were analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification) approach. In total, 2258 DAPS representing 1542 differentially accumulated uniprotein species which respond to HS were identified. A total of 604, 910 and 744 DAPS was detected in comparison of Control vs. Heat12, Control vs. Heat24, and Heat12 vs. Heat24, respectively. Gene ontology and pathway analysis showed that annexin, ubiquitin-conjugating enzyme, ATP synthase, heat shock protein (HSP) and other stress-related proteins were predominately enriched in signal transduction, stress and defense pathways, photosynthesis and energy metabolic pathways, working cooperatively to reduce stress-induced damage in radish. Based on iTRAQ combined with the transcriptomics analysis, a schematic model of a sequential HS-responsive regulatory network was proposed. The initial sensing of HS occurred at the plasma membrane, and then key components of stress signal transduction triggered heat-responsive genes in the plant protective metabolism to re-establish homeostasis and enhance thermotolerance. These results provide new insights into characteristics of HS-responsive DAPS and facilitate dissecting the molecular mechanisms underlying heat tolerance in radish and other root crops.

Quantitative iTRAQ-based proteomic analysis of rice grains to assess high night temperature stress

Rice yield and quality are adversely affected by increasing global surface temperature, and are strongly attributed to high night temperature (HNT) than high daytime temperature. However, the molecular mechanism underlying the heat‐tolerant characteristics of rice remains unclear. In the present study, we compared the proteomes of heat‐tolerant and ‐sensitive lines of rice at early milky stage using an iTRAQ method. We have identified 38 differentially expressed proteins between the two lines, of which 32 proteins have been functionally annotated in NCBI and/or the UniProt database. These proteins were then classified into seven functional subgroups, which include signal transduction, transcript regulation, oxidation, defense response, transport, energy metabolism, and biosynthesis. Further analysis indicated that HNT stress could disrupt the redox equilibrium of plant cells, which in turn triggers the calcium‐dependent protein kinase and COP9 signalosome, thereby regulating downstream genes/proteins that are involved in the HNT response. The candidate proteins may provide genetic resources for the improvement of heat‐tolerant characteristics in rice, and the proposed model for signal transduction and transcriptional regulation may facilitate in the elucidation of the molecular mechanism underlying the response to HNT stress in rice.