Differentially Abundant Proteins Research Articles

Effects of resveratrol on DLD and NDUFB9 decrease in frozen semen of Mongolian sheep

Mongolian sheep are a breed of sheep in China known for their excellent cold and drought resistance. Sperm from Mongolian sheep are often cryopreserved to improve breeding outcomes. However, cryopreservation of sperm often results in issues such as reduced vitality and altered morphology. Therefore, the objective of this study was to investigate the impact of the cryoprotectant resveratrol on frozen sperm from Mongolian sheep, specifically examining its effects on key proteins during cryopreservation. In this study, sperm samples were obtained from three adult Mongolian rams and processed through semen centrifugation. The sperm motility parameters of Fresh Sperm Group (FR), Resveratrol added before freezing group (FF-Res), Resveratrol-free frozen sperm group (FT), and Resveratrol added after freeze-thawing group (FA-Res) were determined. The tandem mass tags (TMT) peptide labeling combined with LC-MS/MS was used for proteomic analysis of the total proteins in FR and FT groups. A total of 2651 proteins were identified, among which 41 proteins were upregulated and 48 proteins were downregulated after freezing. In-depth bioinformatics analysis of differentially abundant proteins (DAPs) revealed their close association with the tricarboxylic acid cycle (TCA) and oxidative phosphorylation pathway. The energy-related protein dihydrolipoamide dehydrogenase (DLD) and the reactive oxygen species (ROS)-related protein NADH dehydrogenase 1 beta subcomplex subunit 9 (NDUFB9) exhibited significant decreases, indicating their potential role as key proteins contributing to reduced sperm vitality. The study demonstrated that the addition of resveratrol (RES) to semen could elevate the expression levels of DLD and NDUFB9 proteins. This study represents the pioneering proteomic analysis of Mongolian ram sperm before and after cryopreservation, establishing the significance of DLD and NDUFB9 as key proteins influencing the decline in vitality following cryopreservation of Mongolian ram sperm. These findings clarify that resveratrol can enhance the levels of DLD and NDUFB9 proteins in cryopreserved Mongolian ram sperm, consequently enhancing their vitality.

Quality changes in gazami crab (Portunus trituberculatus) during refrigeration

Gazami crab (Portunus trituberculatus) is prone to spoilage during storage and transportation. More research is needed to determine how to reliably show its freshness and explain the mechanism of quality deterioration. We hypothesized that proteins extracted from crabs can be biomarkers to detect crab muscle quality changes. This work used physicochemical and proteomic approaches to investigate protein biomarkers and molecular mechanisms driving changes in gazami crab muscle quality after long-term refrigeration. It was shown that 66 differentially abundant proteins (DAPs) were closely associated with pH and texture and can be used as biomarkers to assess crab muscle freshness. According to bioinformatics studies, ribosomes and autophagy were significant mechanisms in crab rotting. These findings provided new concepts and a theoretical foundation for evaluating the freshness of refrigerated gazami crab and help uncover the molecular mechanism of its quality deterioration.

Protein biomarkers for root length and root dry mass on chromosomes 4A and 7A in wheat

Improving the wheat (Triticum aestivum L.) root system is important for enhancing grain yield and climate resilience. Total root length (RL) and root dry mass (RM) significantly contribute to water and nutrient acquisition directly impacting grain yield and stress tolerance. This study used label-free quantitative proteomics to identify proteins associated with RL and RM in wheat near-isogenic lines (NILs). NIL pair 6 had 113 and NIL pair 9 had 30 differentially abundant proteins (DAPs). Three of identified DAPs located within the targeted genomic regions (GRs) of NIL pairs 6 (qDT.4A.1) and 9 (QHtscc.ksu-7A), showed consistent gene expressions at the protein and mRNA transcription (qRT-PCR) levels for asparagine synthetase (TraesCS4A02G109900), signal recognition particle 19 kDa protein (TraesCS7A02G333600) and 3,4-dihydroxy-2-butanone 4-phosphate synthase (TraesCS7A02G415600). This study discovered, for the first time, the involvement of these proteins as candidate biomarkers for increased RL and RM in wheat. However, further functional validation is required to ascertain their practical applicability in wheat root breeding. Significance of the studyClimate change has impacted global demand for wheat (Triticum aestivum L.). Root traits such as total root length (RL) and root dry mass (RM) are crucial for water and nutrient uptake and tolerance to abiotic stresses such as drought, salinity, and nutrient imbalance in wheat. Improving RL and RM could significantly enhance wheat grain yield and climate resilience. However, breeding for these traits has been limited by lack of appropriate root phenotyping methods, advanced genotypes, and the complex nature of the wheat genome. In this study, we used a semi-hydroponic root phenotyping system to collect accurate root data, near-isogenic lines (NILs; isolines with similar genetic backgrounds but contrasting target genomic regions (GRs)) and label-free quantitative proteomics to explore the molecular mechanisms underlying high RL and RM in wheat. We identified differentially abundant proteins (DAPs) and their molecular pathways in NIL pairs 6 (GR: qDT.4A.1) and 9 (GR: QHtscc.ksu-7A), providing a foundation for further molecular investigations. Furthermore, we identified three DAPs within the target GRs of the NIL pairs with differential expression at the transcript level, as confirmed by qRT-PCR analysis which could serve as candidate protein biomarkers for RL and RM improvement.

Quantitative proteomics analysis on the meat quality of processed pale, soft, and exudative (PSE)-like broiler pectoralis major by different heating methods.

This study aims to assess and compare the influences of different heating methods on the quality characteristics of pale, soft, and exudative (PSE)-like and normal (NOR) pectoralis major through quantitative proteomic analysis. A total of 632 proteins were identified, and there were 84, 89, 50, and 43 differentially abundant proteins (DAPs) between processed PSE and NOR samples after four thermal treatments, including boiling (BO), steaming (ST), roasting (RO), and microwaving (MV), respectively, where moist heating conditions led to more different protein abundance. Processed PSE muscles resulted in significant changes in structural proteins related to myofibrillar and connective tissue, which could be associated with their structural instability and degraded quality. Collagen, tropomyosin, myoglobin, and hemoglobin could be potential indicators of PSE muscles color stability and variation during thermal processing. The quantitative proteomic analysis will help correlate molecular changes with processed meat quality towards future optimization of PSE poultry meat processing.

ITRAQ-based proteomics identifies proteins associated with betaine accumulation in Lycium barbarum L

In order to better understand the mechanism of betaine accumulation in Lycium barbarum L. (LBL), we used iTRAQ (Isotope relative and absolute quantitative labeling) proteomics to screen and identify differentially abundant proteins (DAPs) at five stages (S1-young fruit stage, S2-green fruit stage, S3-early yellowing stage, S4-late yellowing stage, S5-ripening stage). A total of 1799 DAPs and 171 betaine-related DAPs were identified, and phosphatidylethanolamine N-methyltransferase (NMT), choline monooxygenase (CMO), and betaine aldehyde dehydrogenase (BADH) were found to be the key enzymes related to betaine metabolism. These proteins are mainly involved in carbohydrates, amino acids and their derivatives, fatty acids, carboxylic acids, photosynthesis and photoprotection, isoquinoline alkaloid biosynthesis, peroxisomes, and glycine, serine, and threonine metabolism. Three of the key enzymes were also up- and down-regulated to different degrees at the mRNA level. The study provide new insights into the of mechanism of betaine accumulation in LBL. SignificanceBetaine, a class of naturally occurring, water-soluble alkaloids, has been found to be widespread in animals, higher plants, and microbes. In addition to being an osmotic agent, betaine has biological functions such as hepatoprotection, neuroprotection, and antioxidant activity. Betaine metabolism (synthesis and catabolism) is complexly regulated by developmental and environmental signals throughout the life cycle of plant fruit maturation. As a betaine-accumulating plant, little has been reported about the regulatory mechanisms of betaine metabolism during the growth and development of Lycium barbarum L. (LBL) fruit. Therefore, this study used iTRAQ quantitative proteomics technology to investigate the abundance changes of betaine-related proteins in LBL fruit, screen and analyze the differential abundance proteins related to betaine metabolism, and provide theoretical references for the in-depth study of the mechanism of betaine metabolism in LBL fruit.

Candidate regulators of drought stress in tomato revealed by comparative transcriptomic and proteomic analyses.

Drought is among the most common abiotic constraints of crop growth, development, and productivity. Integrating different omics approaches offers a possibility for deciphering the metabolic pathways and fundamental mechanisms involved in abiotic stress tolerance. Here, we explored the transcriptional and post-transcriptional changes in drought-stressed tomato plants using transcriptomic and proteomic profiles to determine the molecular dynamics of tomato drought stress responses. We identified 22467 genes and 5507 proteins, among which the expression of 3765 genes and 294 proteins was significantly changed under drought stress. Furthermore, the differentially expressed genes (DEGs) and differentially abundant proteins (DAPs) showed a good correlation (0.743). The results indicated that integrating different omics approaches is promising in exploring the multilayered regulatory mechanisms of plant drought resistance. Gene ontology (GO) and pathway analysis identified several GO terms and pathways related to stress resistance, including response to stress, abiotic stimulus, and oxidative stress. The plant hormone abscisic acid (ABA) plays pivotal roles in response to drought stress, ABA-response element binding factor (AREB) is a key positive regulator of ABA signaling. Moreover, our analysis indicated that drought stress increased the abscisic acid (ABA) content, which activated AREB1 expression to regulate the expression of TAS14, GSH-Px-1, and Hsp, ultimately improving tomato drought resistance. In addition, the yeast one-hybrid assay demonstrated that the AREB1 could bind the Hsp promoter to activate Hsp expression. Thus, this study involved a full-scale analysis of gene and protein expression in drought-stressed tomato, deepening the understanding of the regulatory mechanisms of the essential drought-tolerance genes in tomato.

An iTRAQ-based quantitative proteomic analysis reveals the role of mitochondrial complex I subunits in S-type cytoplasmic male sterility of maize

Maize S-type cytoplasmic male sterility (CMS-S) arises from the activity of the mitochondrial gene orf355. This sterility can be counteracted by the nuclear fertility-restoring allele, Rf3. CMS-S occurs when bicellular pollen collapses following microspore mitosis. Despite this knowledge, the precise protein alterations in CMS-S mitochondria preceding pollen collapse are not well-understood. Our study compared the mitochondrial proteomic profiles between CMS-S and maintainer lines. We found that oxidative phosphorylation (OXPHOS) and glycolysis were significantly associated with CMS-S. A detailed analysis of the differentially abundant proteins (DAPs) associated with the OXPHOS pathway revealed that complex I (CI) subunits play a vital role in the degenerative process of maize CMS-S. Among these, the CI-B8 subunit exhibited abundant presence in CMS-S and displayed earlier transcriptional changes compared to other DAP genes. A yeast two-hybrid assay revealed a physical interaction between another DAP, the CI-13kDa subunit, and orf355 in yeast. These findings highlight the pivotal role played by complex I in the sterility mechanism of CMS-S in maize microspores.

Multi-omics analysis reveals new insights into the bicolor flower phenotype of Paeonia suffruticosa ‘Erqiao’

The bicolor phenotype is conducive to revealing the changes in plant flower color and an important scientific model for studying the regulatory mechanism of flower color. The flowers of Paeonia suffruticosa ‘Erqiao’ have two colors, pink-white and purple-red, and bicolor flowers are rare, possessing unique ornamental value. The distribution of the two colors in a bicolor ‘Erqiao’ flower is similar to a pie chart and can be divided into two distinct parts, with the percentages of the two parts varying. We analyzed the mechanism of flower color formation in ‘Erqiao’ using transcriptomics, proteomics, and metabolomics. The results showed that the differentially abundant metabolites (DAMs), differentially abundant proteins (DAPs), and differentially expressed genes (DEGs) in the two petal types were primarily enriched in phenylpropanoid and flavonoid biosynthesis. Compared with purple-red petals, the PsF3′H protein content in pink-white petals was lower than that in purple-red petals. The content of PsF3′H’s downstream metabolites decreased, while that of some metabolites in the collateral branch of phenylpropanoid biosynthesis increased. The PsF3′H sequence analysis of different P. suffruticosa cultivars and ‘Erqiao’ tissues revealed that the 6 bp insertion mutation of PsF3′H existed only in ‘Erqiao’ and was stably expressed in the pink-white petals. Using virus-induced gene silencing to silence PsF3′H in ‘Erqiao’ petals, the color of the petals faded significantly. Therefore, through multi-omics analysis, we found that the insertion mutation of PsF3′H reduced the synthesis of the PsF3′H protein and led to the obstruction of anthocyanin synthesis; furthermore, other branches and metabolic pathways of the upstream pathway were more active, thus changing the synthesis direction of the entire metabolic pathway. The 6-bp insertion mutation of PsF3′H may be a reason for the rare appearance of bicolor flowers and the unstable ratio of two-colored petals in ‘Erqiao’. This study provides new insights into the formation of the bicolor flower phenotype in ‘Erqiao’.

TMT-Based Proteomics Reveal the Mechanism of Action of Amygdalin against Rheumatoid Arthritis in a Rat Model through Regulation of Complement and Coagulation Cascades.

The limitations of current medications for treating rheumatoid arthritis (RA) emphasize the urgent need for the development of new drugs. This study aimed to investigate the potential anti-RA mechanism of amygdalin using tandem mass tag (TMT)-based quantitative proteomics technology. First, the anti-RA activity of amygdalin was evaluated in a Complete Freund's adjuvant (CFA)-induced rat model. Then, the roles and importance of proteins in the extracted rat joint tissue were evaluated using TMT-based quantitative proteomics technology. A bioinformatics analysis was used to analyze differentially abundant proteins (DAPs). A proteomics analysis identified 297 DAPs in the amygdalin group compared with the model group, of which 53 upregulated proteins and 51 downregulated proteins showed opposite regulatory trends to the DAPs produced after modeling. According to enrichment analyses of the DAPs, the signaling pathways with a high correlation degree were determined to be the complement and coagulation cascades. Furthermore, western blotting and molecular docking were used to further validate the key node proteins, e.g., complement C1s subcomponent (C1s), component C3 (C3) and kininogen 1 (Kng1). These results suggest that amygdalin may be a promising agent for treating RA by regulating the complement and coagulation cascades.

Liver proteomics analysis reveals the differentiation of lipid mechanism and antioxidant enzyme activity during chicken embryonic development

Chicken embryo development is a dynamic process. However, no detailed information is available about the protein abundance changes associated with the lipid mechanism and antioxidant enzyme activity during the egg embryo development. Thus, in the present study, an TMT-based proteomic approach was used to quantify protein abundance changes at different stages of chicken embryonic development. A total of 289 significantly differentially abundant hepatic proteins were quantified, of which 180 were upregulated and 109 were downregulated in the comparison of Day 20 with Day 12 in chicken embryos. Pathway analysis showed that metabolic pathways were the most highly enriched pathways, followed by arachidonic acid metabolism and steroid biosynthesis. Integration of proteomic-based studies profiling of three incubation stages revealed that the two compare groups (Day 12 vs Day 20 and Day 16 vs Day 20) shared some key differentially abundant proteins (DAPs), including LBFABP, FABP5, CYP4V2, PDCD4, LAL, APOA1, APOA4, SAA, FABP2, ACBSG2, FABP2, CYP51A1, and FBXO9. The STRING database and GO analysis results showed that there was close connectivity between APOA4, LBFABP, SERPINC1, APOA1, FGB, FGA, ANGPTL3 and these proteins were involved in the oxidation-reduction process, lipid transport, iron ion, heme, and lipid binding. Importantly, APOA4, FABP2, and CYP51A1 might be key factors to control fat deposition and antioxidant enzyme activity during chicken embryonic development. These findings will facilitate a better understanding of antioxidant and lipid mechanisms in chicken embryo and these DAPs can be further investigated as candidate markers to predict lipid deposition and the activity of antioxidant enzymes.

Proteomic Analysis of the Cold Stress Response of Ammopiptanthus mongolicus Reveals the Role of AmCHIA in Its Cold Tolerance

Ammopiptanthus mongolicus, a traditional ethnic medicinal herb, is a rare broad-leaved evergreen shrub in the arid region of central Asia that can survive under extremely low temperatures during winter. In this study, we investigated the cold stress response of A. mongolicus leaves using physiological and proteomic approaches. Cold stress treatment increased the relative electrolyte leakage, proline, and soluble sugar levels and decreased the chlorophyll content in A. mongolicus leaves. Moreover, 93 differentially abundant proteins (DAPs) were identified using two-dimensional electrophoresis, of which 79 were further confirmed via tandem mass spectrometric analysis. The predicted functions of DAPs were mainly associated with photosynthesis in chloroplasts, reactive oxygen species scavenging, defense, and protein synthesis, folding, and degradation. A. mongolicus chitinase A (AmCHIA) is a cold-induced apoplast protein whose transcription is upregulated under cold, osmotic, high-salinity, and mechanical stresses. Recombinant AmCHIA expressed in Escherichia coli exhibits chitinase activity. Here, AmCHIA expression enhanced the cold tolerance of E. coli cells, suggesting that it may contribute to the cold adaptation of A. mongolicus after cold treatment. The present study not only provides important data for understanding the cold stress responses in plants but also serves as a basis for further exploration of the biological functions of cold-induced proteins in A. mongolicus using genetic approaches.

Integrated Transcriptomic and Proteomic Analyses of Low-Nitrogen-Stress Tolerance and Function Analysis of ZmGST42 Gene in Maize.

Maize (Zea mays L.) is one of the major staple crops providing human food, animal feed, and raw material support for biofuel production. For its growth and development, maize requires essential macronutrients. In particular, nitrogen (N) plays an important role in determining the final yield and quality of a maize crop. However, the excessive application of N fertilizer is causing serious pollution of land area and water bodies. Therefore, cultivating high-yield and low-N-tolerant maize varieties is crucial for minimizing the nitrate pollution of land and water bodies. Here, based on the analysis of the maize leaf transcriptome and proteome at the grain filling stage, we identified 3957 differentially expressed genes (DEGs) and 329 differentially abundant proteins (DAPs) from the two maize hybrids contrasting in N stress tolerance (low-N-tolerant XY335 and low-N-sensitive HN138) and screened four sets of low-N-responsive genes and proteins through Venn diagram analysis. We identified 761 DEGs (253 up- and 508 down-regulated) specific to XY335, whereas 259 DEGs (198 up- and 61 down-regulated) were specific to HN138, and 59 DEGs (41 up- and 18 down-regulated) were shared between the two cultivars under low-N-stress conditions. Meanwhile, among the low-N-responsive DAPs, thirty were unique to XY335, thirty were specific to HN138, and three DAPs were shared between the two cultivars under low-N treatment. Key among those genes/proteins were leucine-rich repeat protein, DEAD-box ATP-dependent RNA helicase family proteins, copper transport protein, and photosynthesis-related proteins. These genes/proteins were involved in the MAPK signaling pathway, regulating membrane lipid peroxidation, and photosynthesis. Our results may suggest that XY335 better tolerates low-N stress than HN138, possibly through robust low-N-stress sensing and signaling, amplified protein phosphorylation and stress response, and increased photosynthesis efficiency, as well as the down-regulation of 'lavish' or redundant proteins to minimize N demand. Additionally, we screened glutathione transferase 42 (ZmGST42) and performed physiological and biochemical characterizations of the wild-type (B73) and gst42 mutant at the seedling stage. Resultantly, the wild-type exhibited stronger tolerance to low N than the mutant line. Our findings provide a better understanding of the molecular mechanisms underlying low-N tolerance during the maize grain filling stage and reveal key candidate genes for low-N-tolerance breeding in maize.

Bull Sperm SWATH-MS-Based Proteomics Reveals Link between High Fertility and Energy Production, Motility Structures, and Sperm-Oocyte Interaction.

The prediction of male or semen fertility potential remains a persistent challenge that has yet to be fully resolved. This work analyzed several in vitro parameters and proteome of spermatozoa in bulls cataloged as high- (HF; n = 5) and low-field (LF; n = 5) fertility after more than a thousand artificial inseminations. Sperm motility was evaluated by computer-assisted sperm analysis. Sperm viability, mitochondrial membrane potential (MMP) and reactive oxygen species (mROS) of spermatozoa were assessed by flow cytometry. Proteome was evaluated by the SWATH-MS procedure. Spermatozoa of HF bulls showed significantly higher total motility than the LF group (41.4% vs 29.7%). Rates of healthy sperm (live, high MMP, and low mROS) for HF and LF bull groups were 49% and 43%, respectively (p > 0.05). Spermatozoa of HF bulls showed a higher presence of differentially abundant proteins (DAPs) related to both energy production (COX7C), mainly the OXPHOS pathway, and the development of structures linked with the motility process (TPPP2, SSMEM1, and SPAG16). Furthermore, we observed that equatorin (EQTN), together with other DAPs related to the interaction with the oocyte, was overrepresented in HF bull spermatozoa. The biological processes related to protein processing, catabolism, and protein folding were found to be overrepresented in LF bull sperm in which the HSP90AA1 chaperone was identified as the most DAP. Data are available via ProteomeXchange with identifier PXD042286.

Unraveling proteome changes of Sunit lamb meat in different feeding regimes and its relationship to flavor analyzed by TMT-labeled quantitative proteomic

In order to explore the molecular mechanism of the effect of feeding regimes on lamb flavor, biceps femoris muscle samples from pasture-fed groups (PF) and concentrate-fed groups (CF) were chosen, and tandem mass tag (TMT) labeling combined with mass spectrometry (MS) was performed to find associations between flavor indicators and proteome profiles. The content and composition of amino acids and volatile flavor substances were better in the PF compared to the CF, with higher levels of some beneficial flavor components such as Arg, Pro Pentanal, Heptanal, Octanal, 1-octen-3-ol and 2,3-Octanedione. About 82 differentially abundant proteins (DAPs) were identified. The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that the pathways that may be associated with lamb flavor are focused on amino acid anabolism. These results provide a basis for further understanding of the molecular mechanisms of proteins in meat flavor regulation.

Subgroups of children with Kawasaki disease: a data-driven cluster analysis.

Although Kawasaki disease is commonly regarded as a single disease entity, variability in clinical manifestations and disease outcome has been recognised. We aimed to use a data-driven approach to identify clinical subgroups. We analysed clinical data from patients with Kawasaki disease diagnosed at Rady Children's Hospital (San Diego, CA, USA) between Jan 1, 2002, and June 30, 2022. Patients were grouped by hierarchical clustering on principal components with k-means parcellation based on 14 variables, including age at onset, ten laboratory test results, day of illness at the first intravenous immunoglobulin infusion, and normalised echocardiographic measures of coronary artery diameters at diagnosis. We also analysed the seasonality and Kawasaki disease incidence from 2002 to 2019 by subgroup. To explore the biological underpinnings of identified subgroups, we did differential abundance analysis on proteomic data of 6481 proteins from 32 patients with Kawasaki disease and 24 healthy children, using linear regression models that controlled for age and sex. Among 1016 patients with complete data in the final analysis, four subgroups were identified with distinct clinical features: (1) hepatobiliary involvement with elevated alanine transaminase, gamma-glutamyl transferase, and total bilirubin levels, lowest coronary artery aneurysm but highest intravenous immunoglobulin resistance rates (n=157); (2) highest band neutrophil count and Kawasaki disease shock rate (n=231); (3) cervical lymphadenopathy with high markers of inflammation (erythrocyte sedimentation rate, C-reactive protein, white blood cell, and platelet counts) and lowest age-adjusted haemoglobin Z scores (n=315); and (4) young age at onset with highest coronary artery aneurysm but lowest intravenous immunoglobulin resistance rates (n=313). The subgroups had distinct seasonal and incidence trajectories. In addition, the subgroups shared 211 differential abundance proteins while many proteins were unique to a subgroup. Our data-driven analysis provides insight into the heterogeneity of Kawasaki disease, and supports the existence of distinct subgroups with important implications for clinical management and research design and interpretation. US National Institutes of Health and the Irving and Francine Suknow Foundation.

Exogenous methyl jasmonate promotes the biosynthesis of endogenous melatonin in mustard sprouts

The present study investigated the effects regulating melatonin (MT) biosynthesis under methyl jasmonate (MeJA) treatment in mustard sprouts. The results revealed that MeJA significantly increased the MT content in the sprouts to 11.43 times that of the control. However, MeJA treatment had an inhibitory effect on growth. Tryptophan decarboxylase and tryptamine 5-hydroxylase gene expression were significantly induced by MeJA. Moreover, 156 differential abundance proteins (DAPs) were detected in 4-day-old sprouts using quantitative proteomic methods. These DAPs were divided into 13 functional groups, and the vast majority of DAPs involved in defense/stress, energy, signal transduction, and secondary metabolism increased. MeJA treatment significantly enriched 15 pathways, including glutathione metabolism, biosynthesis of secondary metabolites, and tryptophan metabolism. In particular, the abundance of three DAPs (myrosinase 1, cytosolic sulfotransferase 16, and glutamate-glyoxylate aminotransferase 2) in the tryptophan metabolism pathway, a substrate for MT biosynthesis, increased significantly. In summary, MeJA induces endogenous MT biosynthesis in mustard sprouts by promoting the genes expression of MT synthetase and increasing the abundance of tryptophan-related proteins.

Comparative transcriptomic and proteomic analyses provide insights into the key genes involved in muscle growth in the large Diqing Tibetan pig

Pig growth involves multiple genes and coordinated regulatory mechanisms. The large Diqing Tibetan pigs (TPs) are a unique plateau pig breed in China. Data on the mechanisms of muscle growth and development in TPs are limited, and its transcriptional regulation mechanism remains unclear. This study identifies important genes and proteins involved in muscle growth in TPs. We obtained transcriptomic and proteomic data from the longissimus dorsi muscle tissues of TPs and Duroc pigs (DPs) via RNA-seq and isobaric tags for relative and absolute quantitation analyses, respectively. Comparative analyses of TPs and DPs yielded 557 differentially expressed genes (DEGs) and 56 differentially abundant proteins (DAPs). Functional annotation of these DEGs and DAPs was enriched in metabolic processes, metabolic pathways, cytoskeletal protein binding, AMPK signaling pathway, insulin signaling pathway, PPAR signaling pathway, and other related pathways. Ten genes were identified as key candidate regulators ( FASN, PPARG, PCK1, ACTA2, TXN, SNU13, APOA1, ATP8, ALDH2, and IGFN1) that may play important roles in the muscle growth traits of TPs. This study provides a reference for analyzing the genetic regulation mechanism underlying muscle growth in pigs and improving the meat yield of TPs via molecular marker-assisted selection.

Proteomic profile of epidermal mucus from Labeo rohita reveals differentially abundant proteins after Aeromonas hydrophila infection

We report the proteomic profile of Epidermal Mucus (EM) from Labeo rohita and identified the differentially abundant proteins (DAPs) against Aeromonas hydrophila infection through label-free liquid chromatography-mass spectrometry (LC-MS/MS). Using discovery-based proteomics, a total of 2039 proteins were quantified in nontreated group and 1,328 proteins in the treated group, of which 114 were identified as DAPs in both the groups. Of the 114 DAPs, 68 proteins were upregulated and 46 proteins were downregulated in the treated group compared to nontreated group. Functional annotations of these DAPs shows their association with metabolism, cellular process, molecular process, cytoskeletal, stress, and particularly immune system. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and Fisher's exact test between the two groups shows that most of the proteins were immune-related, which were significantly associated with the proteasome, phagosome, and Salmonella infection pathways. Overall, this study shows a basic and primary way for further functional research of the involvement of vitellogenin 2, alpha-2-macroglobulin-like protein, toll-like receptors (TLR-13), calpain, keratin-like proteins, and heat shock proteins against bacterial infection. Nonetheless, this first-ever comprehensive report of a proteomic sketch of EM from L. rohita after A. hydrophila infection provides systematic protein information to broadly understand the biological role of fish EM against bacterial infection.

Insight into Ionic Strength-Induced Solubilization of Myofibrillar Proteins from Silver Carp (Hypophthalmichthys molitrix): Structural Changes and 4D Label-Free Proteomics Analysis.

In this study, changes in the physical, structural, and assembly characteristics of silver carp myofibrillar proteins (MPs) at different ionic strength (I) values were investigated. Moreover, the differential proteomic profile of soluble MPs was analyzed using 4D proteomics based on timsTOF Pro mass spectrometry. Solubility of MPs significantly increased at high I (>0.3), and the increase in I enhanced the apparent viscosity, fluorescence intensity, surface hydrophobicity, and α-helix content of MPs solution. Particle size and sodium dodecyl sulfate-polyacrylamide gel electrophoresis patterns also supported the solubility profiles. Transmission electron microscopy and atomic force microscopy observations revealed the morphological assembly and disassembly of MPs under different I conditions. Finally, proteomic analysis revealed the evolution law of salt-induced solubilization of MPs and the critical molecular characteristics in different I environments. The number of differentially abundant proteins (DAPs) decreased with the increase of I, and most DAPs related to the muscle filament sliding, contraction and assembly, actinin binding, and actin filament binding. The soluble abundance of myosin and some structural proteins was dependent on I, and structural proteins in the Z-disk and M-band might contribute to the solubilization of myosin. Our findings provide insightful information about the impact of common I on the solubility pattern of MPs from freshwater fish.

Proteomic Analysis Reveals Salt-Tolerant Mechanism in Soybean Applied with Plant-Derived Smoke Solution.

Salt stress of soybean is a serious problem because it reduces plant growth and seed yield. To investigate the salt-tolerant mechanism of soybean, a plant-derived smoke (PDS) solution was used. Three-day-old soybeans were subjected to PDS solution under 100 mM NaCl for 2 days, resulting in PDS solution improving soybean root growth, even under salt stress. Under the same condition, proteins were analyzed using the proteomic technique. Differential abundance proteins were associated with transport/formaldehyde catabolic process/sucrose metabolism/glutathione metabolism/cell wall organization in the biological process and membrane/Golgi in the cellular component with or without PDS solution under salt stress. Immuno-blot analysis confirmed that osmotin, alcohol dehydrogenase, and sucrose synthase increased with salt stress and decreased with additional PDS solution; however, H+ATPase showed opposite effects. Cellulose synthase and xyloglucan endotransglucosylase/hydrolase increased with salt and decreased with additional PDS solution. Furthermore, glycoproteins decreased with salt stress and recovered with additional treatment. As mitochondrion-related events, the contents of ATP and gamma-aminobutyric acid increased with salt stress and recovered with additional treatment. These results suggest that PDS solution improves the soybean growth by alleviating salt stress. Additionally, the regulation of energy metabolism, protein glycosylation, and cell wall construction might be an important factor for the acquisition of salt tolerance in soybean.