Significant Changes In Protein Abundance Research Articles

Sex differences in proteomics of cardiovascular disease: results from the Yale-CMD registry

Abstract Background Cardiovascular disease is the leading cause of death globally, with notable sex differences in its presentation, mechanisms, and outcomes. Purpose We investigated the serum proteomic profiles of coronary artery disease (CAD) and coronary microvascular dysfunction (CMD) patients to uncover sex-specific biological pathways and their roles in disease development. Methods Using the Yale-CMD registry's biobank, we performed a secondary analysis on adults with ischemic symptoms who underwent cardiac PET/CT and were not experiencing myocardial infarction, hemodynamic instability, acute heart failure, febrile illness, dialysis, or consent incapacity. Using PET/CT, we classified participants as controls (normal coronary flow reserve [CFR], no perfusion defect or coronary calcification), CAD (if new perfusion defect or known revascularization), or CMD (CFR <2 without defect or calcification). Using proximity extension assays (Olink® Explore 3072) in high-throughput proteomic analysis, we examined 2944 plasma proteins. Differential protein abundance analysis was performed using linear regression models adjusting for age, race, body mass index, history of diabetes, dyslipidemia, hypertension, and smoking to detect significant changes in protein abundance, with false discovery rate (FDR) control. Functional pathway analyses were conducted to identify the biological functions of the sex-differentially expressed proteins. Results Between 2014-2020, 91 patients of 190 in the registry provided blood samples for this analysis. Participants had median age 56.0 (50.0 - 62.0) years with 66% females. Among these, 48% were controls, 24% had CAD and 27% had CMD. Using linear regression adjusting for confounders, we identified significant sex differences in protein levels related to reproductive functions across all 3 cohorts (Fig. 1). In the CAD cohort, FSHB was upregulated in females, while INSL3 and EDDM3B were upregulated in males (FDR < 0.05). In the CMD cohorts, 6 proteins were differentially expressed (FDR < 0.05), with SCGB3A1 and HGFAC higher in females, and INSL3, SPINT3, EDDM3B, and KLK3 higher in males. Pathway analysis revealed that among patients with CAD, females had upregulation in immune system processes (Fig. 2A), while males showed upregulation of proteins related to endothelial regulation of blood flow (Fig. 2B). Among patients with CMD, females showed upregulation of lipid and glucose metabolism (Fig. 2C), while males showed upregulation of angiogenesis-related proteins (Fig. 2D). Conclusion We demonstrated significant sex differences in proteomic profiles among patients with CAD and CMD, underscoring the potential importance of sex-specific pathways in the pathophysiology of CVD. Our finding supports a need for large-scale validation studies to develop sex-tailored therapeutic strategies and advance precision medicine in cardiovascular health.Differential protein expression by sexPathway overrepresentation

Integrating Physiological Features and Proteomic Analyses Provides New Insights in Blue/Red Light-Treated Moso Bamboo (Phyllostachys edulis).

Bamboo is one of the most important nontimber forestry products in the world. Light is not only the most critical source of energy for plant photosynthesis but also involved in regulating the biological processes of plants. However, there are few reports on how blue/red light affects Moso bamboo. This study investigated the growth status and physiological responses of Moso bamboo (Phyllostachys edulis) to blue/red light treatments. The growth status of the bamboo plants was evaluated, revealing that both blue- and red-light treatments promoted plant height and overall growth. Gas exchange parameters, chlorophyll fluorescence, and enzyme activity were measured to assess the photosystem response of Moso bamboo to light treatments. Additionally, the blue light treatment led to a higher chlorophyll content and enzyme activities compared to the red light treatment. A tandem mass tag quantitative proteomics approach identified significant changes in protein abundance under different light conditions with specific response proteins associated with distinct pathways, such as photosynthesis and starch metabolism. Overall, this study provides valuable insights into the physiological and proteomic responses of Moso bamboo to blue/red light treatments, highlighting their potential impact on growth and development.

Quantitative proteomics analysis of bacteriocin-like substance producing Lactococcus spp. in simulated vegetable and fruit media

Lactic acid bacteria (LAB) and their metabolites such as bacteriocins have gained considerable interest in terms of their bio-preservative properties to improve food safety and quality. In this study, a quantitative proteomic investigation employing stable isotope labeling by peptide demethylation was carried out to investigate changes in intracellular proteins of bacteriocin-like substance (BLS) producing Lactococcus spp. 7.17 grown in vegetable or fruit juice culture media at 10 °C for 0, 3 or 7 days. In total, 1053 proteins in vegetable medium and 1113 in fruit medium were identified and quantified. Proteins that changed more than two- fold were identified as increased or decreased ones and grouped into four clusters. Those increased proteins were involved in the events of low temperature and ROS stress responses, DNA processing, transcription and translation, central carbon metabolism, fatty acid and phospholipid metabolism, amino acid and cell wall biosynthesis. Key proteins in relation to BLS producing property were also identified suggesting that at least one bacteriocin IIa production system exists in Lactococcus spp. 7.17. These findings provide insights into protein changes of L. lactis at low temperature and lay foundations for further investigations on BLS producing LAB using targeted quantitative proteomic approaches. Significance of the researchThe inhibitory effects of Lactococcus spp. 7.17 on Listeria innocua in fruit and vegetable juice culture media were confirmed.Using a quantitative proteomic approach employing stable isotope labeling by peptide demethylation, 99 or 113 significantly changed proteins of Lactococcus spp. 7.17 grown in vegetable or fruit juice medium were determined, respectively.The significant change in protein abundance suggested an adaptive mechanism of Lactococcus spp. to culture condition at low temperatures.This research provides insights on protein changes of Lactococcus spp. which has potential application in fresh and fresh-cut fruit and vegetables at low temperature.

Quantitative Proteomics Reveals the Protein Regulatory Network of Anabaena sp. PCC 7120 under Nitrogen Deficiency.

Anabaena sp. PCC 7120 (Anabaena 7120) is a photoautotrophic filamentous cyanobacterium capable of fixing atmospheric nitrogen. It is a model organism used for studying cell differentiation and nitrogen fixation. Under nitrogen deficiency, Anabaena 7120 forms specialized heterocysts capable of nitrogen fixation. However, the molecular mechanisms involved in the cyanobacterial adaptation to nitrogen deficiency are not well understood. Here, we employed a label-free quantitative proteomic strategy to systematically investigate the nitrogen deficiency response of Anabaena 7120 at different time points. In total, 363, 603, and 669 proteins showed significant changes in protein abundance under nitrogen deficiency for 3, 12, and 24 h, respectively. With mapping onto metabolic pathways, we revealed proteomic perturbation and regulation of carbon and nitrogen metabolism in response to nitrogen deficiency. Functional analysis confirmed the involvement of nitrogen stress-responsive proteins in biological processes, including nitrogen fixation, photosynthesis, energy and carbon metabolism, and heterocyst development. The expression of 10 proteins at different time points was further validated by using multiple reaction monitoring assays. In particular, many dysregulated proteins were found to be time-specific and involved in heterocyst development, providing new candidates for future functional studies in this model cyanobacterium. These results provide novel insights into the molecular mechanisms of nitrogen stress responses and heterocyst development in Anabaena 7120.

Cysteine Proteome Reveals Response to Endogenous Oxidative Stress in Bacillus cereus.

At the end of exponential growth, aerobic bacteria have to cope with the accumulation of endogenous reactive oxygen species (ROS). One of the main targets of these ROS is cysteine residues in proteins. This study uses liquid chromatography coupled to high-resolution tandem mass spectrometry to detect significant changes in protein abundance and thiol status for cysteine-containing proteins from Bacillus cereus during aerobic exponential growth. The proteomic profiles of cultures at early-, middle-, and late-exponential growth phases reveals that (i) enrichment in proteins dedicated to fighting ROS as growth progressed, (ii) a decrease in both overall proteome cysteine content and thiol proteome redox status, and (iii) changes to the reduced thiol status of some key proteins, such as the transition state transcriptional regulator AbrB. Taken together, our data indicate that growth under oxic conditions requires increased allocation of protein resources to attenuate the negative effects of ROS. Our data also provide a strong basis to understand the response mechanisms used by B. cereus to deal with endogenous oxidative stress.

Proteomics analysis of Cyclobalanopsis gilva provides new insights of low seed germination

A valuable plant, Cyclobalanopsis gilva, (C. gilva) has a low germination rate (below 50%) under its natural habitations. In order to examine the reasons for the low germination rate, the seeds of C. gilva (germinated and non-germinated) were evaluated using comparative proteomics analysis. A total of 3078 differentially abundant proteins (DAPs) were identified through a label-free method; most DAPs up-accumulated in germinated seeds were related to carbohydrates metabolism. Furthermore the proteins related to the signals, stress, and protein metabolism showed up-accumulation in germinated and no abundance or down-accumulation in non-germinated seeds. Enzyme activity of HK, PGK, PFK, and PK from glycolysis in SG-Control samples were 1.7-, 1.1-, 1.4-, and 1.3-times higher compared with those in control ones while CS, NAD-MDH, α-KGDH, and ICDH from the TCA cycle in SG-Control samples were 3, 1.1, 1.2, and 1.2 times higher than those in NG-Control ones. The β-amylase activity was 4-fold higher in successfully germinated seeds compared to non-germinated seeds. Interestingly, α-amylase did not show significant changes in protein abundance and enzyme activity among the three samples. The present findings reveal that unsuccessful germination of C. gilva seeds is due to lack of energy.

Changes in glycolytic and mitochondrial protein profiles regulates postmortem muscle acidification and oxygen consumption in dark-cutting beef

Dark-cutting beef is a condition in which beef fails to have a characteristic bright-red color when the cut surface is exposed to oxygen. However, the mechanistic basis for this occurrence is not clear. Protein expression profiles were compared between dark-cutting and normal-pH beef using LC-MS/MS-based proteomics. Mass spectrometry analysis identified 1162 proteins in the proteomes of dark-cutting and normal-pH beef. Of these, 92 proteins had significant changes in protein abundance between dark-cutting versus normal-pH beef. In dark-cutting beef, 25 proteins were down-regulated, including enzymes related to glycogen metabolism, glucose homeostasis, denovo synthesis of adenosine monophosphate (AMP), and glycogen phosphorylase activity. In comparison, 27 proteins were up-regulated in dark-cutting beef related to oxidation-reduction processes, muscle contraction, and oxidative phosphorylation. Down-regulation of glycogenolytic proteins suggests decreased glycogen mobilization and utilization, while the up-regulation of mitochondrial transport chain proteins indicates a greater capacity to support mitochondrial respiration in dark-cutting beef. These results showed that changes in proteins involved in glycogenolysis and mitochondrial electron transport would promote the development of high-pH and greater oxygen consumption, respectively; thus limiting myoglobin oxygenation in dark-cutting beef. SignificanceThe current understanding indicates that defective glycolysis causes less carbon flow, leading to less postmortem lactic acid formation and elevated muscle pH in dark-cutting beef. However, to the best of our knowledge, limited research has evaluated how changes in glycolytic and mitochondrial protein abundance regulate postmortem muscle acidification and oxygen consumption in dark-cutting beef. We utilized a shotgun proteomics approach to elucidate potential differences in protein profiles between dark-cutting versus normal-pH beef that may influence differences in postmortem metabolism and muscle surface color characteristics. Our study shows that down-regulation of glycolgenolytic and IMP/AMP biosynthetic proteins results in elevated postmortem muscle pH in dark-cutting beef. In addition, the up-regulation of mitochondrial protein content coupled with the higher muscle pH are conducive factors for enhanced oxygen consumption and less myoglobin oxygenation, contributing to a dark meat color typically associated with dark-cutting beef.

Comprehensive Proteomic Profiling of Pressure Ulcers in Patients with Spinal Cord Injury Identifies a Specific Protein Pattern of Pathology.

Objective: Severe pressure ulcers (PUs) do not respond to conservative wound therapy and need surgical repair. To better understand the pathogenesis and to advance on new therapeutic options, we focused on the proteomic analysis of PU, which offers substantial opportunities to identify significant changes in protein abundance during the course of PU formation in an unbiased manner.Approach: To better define the protein pattern of this pathology, we performed a proteomic approach in which we compare severe PU tissue from spinal cord injury (SCI) patients with control tissue from the same patients.Results: We found 76 proteins with difference in abundance. Of these, 10 proteins were verified as proteins that define the pathology: antithrombin-III, alpha-1-antitrypsin, kininogen-1, alpha-2-macroglobulin, fibronectin, apolipoprotein A-I, collagen alpha-1 (XII) chain, haptoglobin, apolipoprotein B-100, and complement factor B.Innovation: This is the first study to analyze differential abundance protein of PU tissue from SCI patients using high-throughput protein identification and quantification by tandem mass tags followed by liquid chromatography tandem mass spectrometry.Conclusion: Differential abundance proteins are mainly involved in tissue regeneration. These proteins might be considered as future therapeutic options to enhance the physiological response and permit cellular repair of damaged tissue.

Proteomic analysis in cells treated with pristine carbon nano-onions and its subcellular localization

Nanoparticles toxicity and cellular uptake are substantial factors that regulate the utility of nanoparticles for biomedical applications in diagnostic imaging and therapy. In this work, the cellular uptake of pristine carbon nano-onions (CNOs) produced by submerged arc discharge was confirmed by transmission electron microscopy (TEM) analysis. Carbon nano-onions were localized within early and late endosomes of human keratinocyte cells. TEM images suggest the possible degradation of these structures, in late endosomes of keratinocyte cells after 24 h. Proteomic shotgun analysis revealed that carbon nano-onions cause statistically significant protein abundance changes in a total of 168 proteins. Most of the differentially expressed proteins are involved in biological processes such as metabolic, cellular and immune system processes. Treated cells showed increased expression of clathrin heavy chain 1, calnexin and isoforms β/α, ε and σ 14-3-3 protein, which are related to clathrin-mediated endocytosis. Thus changes in protein abundance concerning clathrin-mediated endocytosis may suggest this as a plausible way by which the carbon nano-onions intracellular traffic occurs.

296 - Reversal of age related post-translational modifications improves mitochondrial and skeletal muscle function through redox dependent mechanisms

Muscle redox status and post-translational modifications (PTMs) regulate diverse aspects of skeletal muscle function, including mitochondrial energetics and contractile performance. In aging skeletal muscle mitochondrial oxidative stress contributes to altered redox homeostasis. We have previously demonstrated that reducing mitochondrial oxidant production with acute (1 hr) and chronic (8 week) treatment with the peptide elamipretide (SS-31) can reverse skeletal muscle and mitochondrial dysfunction and reduce redox stress in aging mice. These improvements were also associated with increased exercise tolerance and greater fatigue resistance. However, the mechanisms by which improving mitochondrial function with SS-31 reverses age-related decline in skeletal muscle function remain unknown. To investigate the effect of SS-31 on the skeletal muscle proteome we assessed global changes in protein abundance, and phosphorylation and S-glutathionylation PTMs in young vs. aged and aged+SS-31 vs. aged mice. Osmotically regulated pumps were surgically implanted into 26-month old female C57Bl/6 mice to deliver saline or SS-31 (3mg/kg/day) for 8 weeks. At the end of 8-week treatment, animals were dissected and gastrocnemius muscle was separated and flash-frozen for analysis via mass spectrometry. Seven-month old female C57Bl/mice were sacrificed as healthy young controls. Relatively few significant protein abundance changes occur with age in skeletal muscle (43) using a false discovery rate of

Effect of the Surgical Intervention of Laparoscopic Donor Nephrectomy on Proteomic Changes in Living Kidney Donors using either Propofol or Sevoflurane Anaesthesia

Introduction Surgical intervention i.e. ‘trauma’ induces perioperative stress impacting on systemic inflammatory and humoral responses that are associated with postoperative comorbidity. Different types of anaesthesia and anaesthetic agents are shown to have differential effects on the innate and adaptive immunity. In this study, the biological effect of the surgical intervention combined with propofol or sevoflurane anaesthesia in the healthy cohort of living kidney donors undergoing laparoscopic surgery was assessed by proteome profiling of blood plasma samples. Materials and Methods Plasma samples of healthy living donors (LD) participating in the VAPOR-1 trial were used. Sample points were: before surgery (T0), immediately after surgery (T1), and 24 hours after surgery (T2). LDs were anaesthetised with either propofol (n=19) or sevoflurane (n=17) and matched by age, gender, BMI, comorbidity and medication. Anaesthetic and hemodynamic management was strictly protocolised. Samples were subjected to proteome profiling by mass spectrometry followed by data analysis with MaxQuant software. Student’s T-Test and multiple testing correction were applied to detect significant changes in protein abundance between comparisons. Results Quantitative protein identification resulted in detection of 633 plasma proteins. A subset of 28 proteins showed statistically significant (P<0.05) expression level changes between time points. Proteins with over two-fold change comprised a smaller group of nine upregulated targets that are known to be involved in acute phase inflammatory response (CRP, SAA1, SAA2, LBP, SERPINA1, SERPINA3) and tissue regeneration (FGL1, LRG1, MAN1A1). These targets were common in all LDs, except MAN1A1 that was upregulated only in propofol anaesthesia. Discussion In this study, we have evaluated the effect of a major surgical intervention in a unique cohort of healthy subjects selected to donate a kidney, using systems biology by analysing individual sequential proteomic profiles. The predominant changes in profiles before and after surgery involved pathways of acute phase response and tissue remodelling. The highest detected changes in protein levels were found to be independent of anaesthesia type, while proteome profiles also displayed a number of moderate level anaesthesia-specific changes. More proteins with statistically significant level changes were detected one day after surgery (T2) when compared to immediately after surgery (T1), in both anaesthesia groups. Conclusion This study is a first attempt to gain better insight in molecular effects of surgical intervention in a selected healthy ‘control’ group using systems biology. Quantitative proteome analysis identified upregulated proteins in response to laparoscopic intervention independent of anaesthetic type, which known to be involved in acute phase inflammatory response, immunogenicity and tissue remodelling.

Abstract IA16: The global proteome and phospho-proteome of K-Ras mutant tissues

Abstract K-Ras is the most commonly mutated oncogene in cancer, and it plays a predominant role in the pathogenesis of cancers of the pancreas, colon, and lung. Mutationally activated K-Ras influences cellular behaviors through broad and complex effects on downstream signal transduction pathways. In an effort to understand the molecular mechanisms underlying the oncogenic properties of mutant forms of K-Ras, we have used multiplexed mass spectroscopy (MS) to quantify proteome-wide changes in protein phosphorylation in primary mouse tissues that are engineered to express mutant K-Ras, either alone or in combination with mutations in other cancer genes. This multidimensional dataset highlights the context dependence of K-Ras signaling because the significant changes in protein abundance and/or phosphorylation due to activation of K-Ras are highly dependent upon both tissue context and cooperating mutations. The dataset also paints a complex picture of signaling downstream of K-Ras within a given tissue, as phosphorylation of many proteins in known Ras effector pathways (i.e., MAPK and PI3K) are unaffected or downregulated by mutationally activated K-Ras. Overall, this study provides an unprecedented view of K-Ras signaling on a global scale and reveals a variety of novel insights into the signal transduction properties of mutant K-Ras alleles. Citation Format: Kevin Haigis. The global proteome and phospho-proteome of K-Ras mutant tissues [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr IA16.

An Aptamer‐Based Approach to Assess the Human Plasma Proteome for Pre‐Analytical Variability

The quality of clinical samples is of utmost importance when conducting biomedical research with OMICS‐based assays as the variability introduced before sample analysis is a potential confounder in the results. In this study, we used the aptamer‐based SOMAscan® proteomic technology to characterize pre‐analytical variability in human EDTA plasma. The goal of the study was to investigate how variation in the pre‐analytical steps during processing of whole blood to plasma impacts the plasma proteome. Whole blood was obtained from apparently healthy individuals and was collected in a randomized sequence of six EDTA tubes. The pre‐analytical variables included prolongation of the processing start time, storage temperature of whole blood or plasmaprior to and after processing, and variation in applied centrifugal force. The SOMAscan® assay was performed to measure the relative abundance of 1305 proteins. To determine the effects of variations inpre‐analytical processing, the data was statistically analyzed and the results were used to identify significant changes in protein abundance under each study condition relative to the control condition (samples processed without delay and immediately stored at −80°C). Both low centrifugation force(1300 × g compared to 2500 × g) and blood storage at 0°C for 6 hours resulted in the most significant changes in protein abundance (200 and 148 proteins, respectively, fold change ≥ 1.2, P &lt; 0.05, and FDR &lt; 0.05), while storing immediately processed plasma for 24 hours at 4°C yielded the least changes (28 proteins). The results indicate that blood samples should be immediately processed to plasma and frozen in −80°C without delay in order to preserve sample integrity and to minimize any proteome abundance alterations. The results also provide important information on the discovery of protein abundance changes due to pre‐analytical variability that can be useful in performing effective quality control assessments.Support or Funding InformationThis study was supported with funds from the National Center for Toxicological Research, Food &amp; Drug Administration, Jefferson, Arkansas.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Robust determination of differential abundance in shotgun proteomics using nonparametric statistics.

Label-free shotgun mass spectrometry enables the detection of significant changes in protein abundance between different conditions. Due to often limited cohort sizes or replication, large ratios of potential protein markers to number of samples, as well as multiple null measurements pose important technical challenges to conventional parametric models. From a statistical perspective, a scenario similar to that of unlabeled proteomics is encountered in genomics when looking for differentially expressed genes. Still, the difficulty of detecting a large fraction of the true positives without a high false discovery rate is arguably greater in proteomics due to even smaller sample sizes and peptide-to-peptide variability in detectability. These constraints argue for nonparametric (or distribution-free) tests on normalized peptide values, thus minimizing the number of free parameters, as well as for measuring significance with permutation testing. We propose such a procedure with a class-based statistic, no parametric assumptions, and no parameters to select other than a nominal false discovery rate. Our method was tested on a new dataset which is available via ProteomeXchange with identifier PXD006447. The dataset was prepared using a standard proteolytic digest of a human protein mixture at 1.5-fold to 3-fold protein concentration changes and diluted into a constant background of yeast proteins. We demonstrate its superiority relative to other approaches in terms of the realized sensitivity and realized false discovery rates determined by ground truth, and recommend it for detecting differentially abundant proteins from MS data.

Profiling invasive Plasmodium falciparum merozoites using an integrated omics approach

The symptoms of malaria are brought about by blood-stage parasites, which are established when merozoites invade human erythrocytes. Our understanding of the molecular events that underpin erythrocyte invasion remains hampered by the short-period of time that merozoites are invasive. To address this challenge, a Plasmodium falciparum gamma-irradiated long-lived merozoite (LLM) line was developed and investigated. Purified LLMs invaded erythrocytes by an increase of 10–300 fold compared to wild-type (WT) merozoites. Using an integrated omics approach, we investigated the basis for the phenotypic difference. Only a few single nucleotide polymorphisms within the P. falciparum genome were identified and only marginal differences were observed in the merozoite transcriptomes. By contrast, using label-free quantitative mass-spectrometry, a significant change in protein abundance was noted, of which 200 were proteins of unknown function. We determined the relative molar abundance of over 1100 proteins in LLMs and further characterized the major merozoite surface protein complex. A unique processed MSP1 intermediate was identified in LLM but not observed in WT suggesting that delayed processing may be important for the observed phenotype. This integrated approach has demonstrated the significant role of the merozoite proteome during erythrocyte invasion, while identifying numerous unknown proteins likely to be involved in invasion.

In-depth proteomic analysis of Glycine max seeds during controlled deterioration treatment reveals a shift in seed metabolism

Seed aging is one of the major events, affecting the overall quality of agricultural seeds. To analyze the effect of seed aging, soybean seeds were exposed to controlled deterioration treatment (CDT) for 3 and 7days, followed by their physiological, biochemical, and proteomic analyses. Seed proteins were subjected to protamine sulfate precipitation for the enrichment of low-abundance proteins and utilized for proteome analysis. A total of 14 differential proteins were identified on 2-DE, whereas label-free quantification resulted in the identification of 1626 non-redundant proteins. Of these identified proteins, 146 showed significant changes in protein abundance, where 5 and 141 had increased and decreased abundances, respectively while 352 proteins were completely degraded during CDT. Gene ontology and KEGG analyses suggested the association of differential proteins with primary metabolism, ROS detoxification, translation elongation and initiation, protein folding, and proteolysis, where most, if not all, had decreased abundance during CDT. Western blotting confirmed reduced level of antioxidant enzymes (DHAR, APx1, MDAR, and SOD) upon CDT. This in-depth integrated study reveals a major downshift in seed metabolism upon CDT. Reported data here serve as a resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality. Biological significanceControlled deterioration treatment (CDT) is one of the major events that negatively affects the quality and nutrient composition of agricultural seeds. However, the molecular mechanism of CDT is largely unknown. A combination of gel-based and gel-free proteomic approach was utilized to investigate the effects of CDT in soybean seeds. Moreover, we utilized protamine sulfate precipitation method for enrichment of low-abundance proteins, which are generally masked due to the presence of high-abundance seed storage proteins. Reported data here serve as resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality.

Biocompatibility of iron carbide and detection of metals ions signaling proteomic analysis via HPLC/ESI-Orbitrap

Recently, magnetic nanoparticles (NPs) have been extensively used in food industry and biomedical treatments. However, the biocompatibility mechanism on expression proteomics, before consideration of magnetic NPs for clinical application, has not yet been fully elucidated. Therefore, this study was undertaken to identify potential biomarkers of metal ion signaling proteins in human cervical cancer cell line (HeLa) cells. Here, we report the in vitro investigations of the cell cycle response and significant changes in protein abundance of HeLa cells when exposed to self-tailored hydrophilic Fe2C NPs. The comparative proteomic approach based on 18O labeling coupled with high performance liquid chromatography/electrospray ionization with ion trap mass analyzer (HPLC/ESI-Orbitrap) was applied, and 394 proteins were identified. There were 46 significantly differentiated proteins based on the specific metal ion signaling response. Among them, 60S ribosomal protein L37a, serine/arginine-rich splicing factor 7, calmodulin, and calumenin were downregulated, whereas transketolase was overexpressed. Functional interaction network of Fe2C-regulated proteins was successfully created by the STRING algorithm to show the strong interactions between proteins. This work will not only help to understand the molecular mechanism of metal ion signaling proteins that can potentially be used to develop therapeutic protocols for diagnosis of diseases but also give direction for tailoring biocompatible magnetic NPs.

Comparative proteomic analysis of the response to silver ions and yeast extract in Salvia miltiorrhiza hairy root cultures

Biotic and abiotic stresses can inhibit plant growth, resulting in losses of crop productivity. However, moderate adverse stress can promote the accumulation of valuable natural products in medicinal plants. Elucidating the underlying molecular mechanisms thus might help optimize the variety of available plant medicinal materials and improve their quality. In this study, Salvia miltiorrhiza hairy root cultures were employed as an in vitro model of the Chinese herb Danshen. A comparative proteomic analysis using 2-dimensional gel electrophoresis and MALDI-TOF-MS was performed. By comparing the gel images of groups exposed to the stress of yeast extract (YE) combined with Ag+ and controls, 64 proteins were identified that showed significant changes in protein abundance for at least one time point after treatment. According to analysis based on the KEGG and related physiological experimental verification, it was found that YE and Ag+ stress induced a burst of reactive oxygen species and activated the Ca2+/calmodulin signaling pathway. Expression of immune-suppressive proteins increased. Epidermal cells underwent programmed cell death. Energy metabolism was enhanced and carbon metabolism shifted to favor the production of secondary metabolites such as lignin, tanshinone and salvianolic acids. The tanshinone and salvianolic acids were deposited on the collapsed epidermal cells forming a physicochemical barrier. The defense proteins and these natural products together enhanced the stress resistance of the plants. Since higher levels of natural products represent good quality in medicinal materials, this study sheds new light on quality formation mechanisms of medicinal plants and will hopefully encourage further research on how the planting environment affects the efficacy of herbal medicines.

Protein Abundance Control by Non-coding Antisense Transcription.

SummaryStable unannotated transcripts (SUTs), some of which overlap protein-coding genes in antisense direction, are a class of non-coding RNAs. While case studies have reported important regulatory roles for several of such RNAs, their general impact on protein abundance regulation of the overlapping gene is not known. To test this, we employed seamless gene manipulation to repress antisense SUTs of 162 yeast genes by using a unidirectional transcriptional terminator and a GFP tag. We found that the mere presence of antisense SUTs was not sufficient to influence protein abundance, that observed effects of antisense SUTs correlated with sense transcript start site overlap, and that the effects were generally weak and led to reduced protein levels. Antisense regulated genes showed increased H3K4 di- and trimethylation and had slightly lower than expected noise levels. Our results suggest that the functionality of antisense RNAs has gene and condition-specific components.

Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways.

Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch, and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs) generated from the wild-type strains N2 (Bristol) and CB4856 (Hawaii) to enable quantitative trait locus (QTL) mapping. About half of the cases from the 44 genes tested showed a statistically significant change in protein abundance between various strains, most of these were however very weak (below 1.3-fold change). We detected a distant QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance) and phenotypic levels.