Wheat and barley genera represent a wide range of genotypes from Triticeae group grown around the globe. The broad plasticity of Triticeae phenotypes mirrors the robustness of their genomes revealing a high level of gene homeology. Publication and annotation of the reference genome sequences for spring barley Morex and Chinese Spring wheat represents an important milestone enabling the researchers to precisely identify and annotate nearly all proteins. Due to the broad range of environments used for wheat and barley cultivation and their economical importance, proteomic studies focused on their responses to environmental stresses including combined stress treatments. Most of the Triticeae stress proteomics studies are comparative ones aimed at determination of differentially abundant proteins (DAPs) between two or more genotypes with contrasting stress tolerance. Studies focused on subcellular fractions and protein posttranslational modifications (PTMs) are still relatively rare although PTMs play a crucial role in modulation of protein biological function. Functional and interactomics studies are needed although gene homeology and the resulting protein functional redundancy practically excludes the utilization of knock-out mutants. The alternatives could represent either gene overexpression in a heterologous system such as A. thaliana or transient posttranscriptional gene silencing using RNAi. Publication of complete reference genome sequences together with novel technological approaches such as pQTL mapping boost the Triticeae proteomics studies not only to provide data but also to contribute to designing novel genotypes with improved adaptations to ever changing environments.

Salivary proteins are essencial in the maintenance of oral homeostasis and can reflect systemic and localized processes, like gingivitis. However, little is known about the relationship between diet and the occurrence of gingivitis in cattle. The present study aimed to characterize the salivary proteomic profile of cattle (n = 12) fed hay (112.19 g/kg of crude protein) cultivated in reformed pastures, and, one group received protein supplement (PS, n = 6); the effect of the protein supplement on the gingival health of the cattle was determined by weekly intraoral examination and periodontal evaluation of the eight (deciduous) incisors. The whole saliva proteome of the two groups was evaluated after 20 and 60 days of confinement. In the periodontal clinical evaluation both groups had episodes of gingivitis; however, the average number of affected sites in the PS group was higher on day 60. The cattle fed exclusively hay, presented a lower average of affected gingival sites on day 60. After 60 days of experimentation, nine biological and 11 immunological processes were altered in bovine saliva. Proteins with multiple functions were detected in the saliva of the cattle; however, differences were observed in their regulation between the two groups. SIGNIFICANCE: In bovine populations, the relationship between diet and increased incidence of gingivitis is theorized. The results of the present pilot study, both diets caused episodes of gingivitis in the primary dentition of cattle and, apparently, diets with protein supplementation stimulate the expression of salivary proteins with a protective role in cattle that can act against infectious-inflammatory processes, such as gingivitis. However, it is plausible that over time, cattle will adapt to these diets and become more vulnerable to gingivitis.

BACKGROUND: Although it is well known that myxomatous mitral valve disease stage B2 (MMVD stage B2) is predominantly characterized by ECM remodeling of the mitral valve, ECM-related proteomics alterations in plasma from dogs with this disease have yet to be elucidated. OBJECTIVE: To determine whether the differentially expressed protein (DEP) associated with ECM are potential biomarkers of MMVD stage B2. METHODS: Tandem mass tag (TMT) quantitative proteomics analysis was performed to determine the DEPs in plasma samples from a discovery cohort (5 dogs with MMVD stage B2 and 3 healthy controls, poodle). Candidate proteins were identified using DEPs and ECM-related protein network analysis and confirmed by enzyme-linked immunosorbent assay (ELISA) and western blotting in a validation cohort (52 dogs with MMVD stage B2 and 56 healthy controls, multi-breed). The diagnostic potential of a candidate biomarker DEP was evaluated using receiver operating characteristic (ROC) curve analysis. RESULTS: A total of 90 DEPs were identified between healthy and MMVD stage B2 dogs, and of these 90 DEPs, 16 were ECM-related proteins. One ECM-related DEP, serpin family H member 1 (SERPINH1), was significantly overabundance at the protein level in MMVD stage B2 dog plasma, and SERPINH1 expression had an area under the ROC curve (AUC) value of 0.885 (95% CI = 0.814-0.956, P < 0.0001) that allowed discrimination of MMVD stage B2 dogs from healthy dogs. CONCLUSION: Plasma SERPINH1 has good predictive and diagnostic value at dog with MMVD stage B2, suggesting that SERPINH1 may be used as a biomarker for early prediction and diagnosis of stage B2 of MMVD. SIGNIFICANCE: MMVD is the most acquired cardiac disease in dogs. MMVD stage B2, is when the heart valve structure begins to change significantly but there are no clinical symptoms; it is a critical time during which to slow progression of the disease, so timely diagnosis is extremely important. This study suggests that plasma SERPINH1 levels might differentiate MMVD progression in dogs during the early stage. It is also the first study to consider SERPINH1 as a diagnostic biomarker in dogs with stage B2 MMVD. Another advantage is that dogs in the validation cohort were recruited from six breeds to reduce the impacts of breed factors and partly reflect the universality of SERPINH1 for diagnosing MMVD stage B2.

Exposure to chronic social isolation (CSIS) and synapse dysfunction have been implicated in the etiology of major depressive disorder (MDD). Fluoxetine (Flx) has been widely used to treat MDD, but its mechanisms of action remain elusive. We employed comparative synaptoproteomics to investigate the changes in the levels of proteins and molecular signaling pathways in prefrontal cortical samples of adult male Wistar rats exposed to CSIS, a rat model of depression, and CSIS rats treated with chronic Flx and controls, using liquid chromatography coupled to tandem mass spectrometry. Flx-treated control rats showed a decreased level of proteins involved in vesicle-mediated transport, and a predominantly increased level of exocytosis-associated proteins. CSIS significantly reduced the level of proteins involved in the ATP metabolic process, clathrin-dependent endocytosis, and proteolysis. Flx treatment in CSIS rats stimulated synaptic vesicle trafficking by increasing the regulation of exo/endocytosis-associated proteins, proteins involved in synaptic plasticity including neurogenesis, Cox5a, mitochondria-associated proteins involved in oxidative phosphorylation, and ion transport proteins (Slc8a2, Atp1b2). Flx treatment resulted in an increased synaptic vesicle dynamic, plasticity and mitochondrial functionality, and a suppression of CSIS-induced impairment of these processes. BIOLOGICAL SIGNIFICANCE: Identifying biomarkers of MDD and treatment response is the goal of many studies. Contemporary studies have shown that many molecular alterations associated with the pathophysiology of MDD reside within the synapse. As part of this research, a growing importance is the use of proteomics, as monitoring the changes in protein levels enables the identification of (possible) biochemical pathways and processes of importance for the development of depressive-like behavior and the efficacy of antidepressant treatments. We profiled proteomic changes representative of the development of CSIS-induced depressive-like behavior and the antidepressant effects of Flx. Our study has identified synaptosomal proteins and altered molecular pathways that may be potential markers of prefrontal cortical synaptic dysfunction associated with depressive-like behavior, and further clarified the mechanisms of depressive-like behavior and mode of action of Flx. Our findings indicate potential PFC synaptic targets for antidepressant treatment.

Color of retail fresh beef is the most important quality influencing the consumers' purchase decisions at the point of sale. Discolored fresh beef cuts are either discarded or converted to low-value products, before the microbial quality is compromised, resulting in huge economic loss to meat industry. The interinfluential interactions between myoglobin, small biomolecules, proteome, and cellular components in postmortem skeletal muscles govern the color stability of fresh beef. This review examines the novel applications of high-throughput tools in mass spectrometry and proteomics to elucidate the fundamental basis of these interactions and to explain the underpinning mechanisms of fresh beef color. Advanced proteomic research indicates that a multitude of factors endogenous to skeletal muscles critically influence the biochemistry of myoglobin and color stability in fresh beef. Additionally, this review highlights the potential of muscle proteome components and myoglobin modifications as novel biomarkers for fresh beef color. SIGNIFICANCE: This review highlights the important role of muscle proteome in fresh beef color, which is the major trait impacting consumers' purchase decisions. In recent years, innovative approaches in proteomics have been exploited for an in-depth understanding of the biochemical mechanisms influencing color development and color stability in fresh beef. The review suggests that a wide range of factors, including endogenous skeletal muscle components, can affect myoglobin biochemistry and color stability in beef. Furthermore, the potential use of muscle proteome components and myoglobin post-translational modifications as biomarkers for fresh beef color is discussed. The currently available body of evidence presented in this review can have important implications in meat industry as it provides novel insights into the factors influencing fresh beef color and an up-to-date list of biomarkers that can be used to predict beef color quality.

Plants as sessile organisms are challenged by numerous biotic and abiotic stresses. Stomatal guard cells on the leaf surface are at the frontline of biotic and abiotic stress responses. Mitogen-activated protein kinase 4 (MPK4) has higher expression levels in guard cells than in mesophyll cells. The specific functions of MPK4 in guard cells are unknown. In this study, when MPK4 was overexpressed in Arabidopsis, bacterial entry of Pseudomonas syringae (Pst) into the plants was significantly decreased. The MPK4 overexpression plants had a similar trend of stomatal movement as wild-type Col-0, but had a smaller stomatal aperture than the Col-0, highlighting MPK4 plays a role in stomatal immune response. This function of the MPK4 requires its kinase activity because the MPK4 kinase-dead mutant did not have a significant difference in stomatal aperture compared to the Col-0. To understand MPK4 functions in guard cells, we investigated MPK4-associated protein complexes in guard cells using affinity purification mass spectrometry. A total of 145 proteins were identified to be in the MPK4-complex. Ten potential MPK4-interacting proteins were cloned and tested for physical interactions with the MPK4 using a yeast two hybrid (Y2H) system. Four proteins were newly identified to interact directly with the MPK4. SIGNIFICANCE: MPK4 is highly abundant in stomatal guard cells, but its specific functions in guard cells are largely unknown. Through a bacterial entry assay of MPK4 overexpression plants, we found that MPK4 may play an important role in stomatal immune response. To understand the molecular mechanisms underlying the MPK4 functions in guard cells, we characterized the MPK4-associated protein complex in guard cells. Many of the 145 identified proteins were involved in plant immunity and development. Four of the proteins were newly identified to interact directly with the MPK4. This work has provided additional evidence for the MPK4 function as a positive regulator for stomatal immunity. The guard cell MPK4 protein complex and the four new interacting proteins were revealed. Whether MPK4 directly phosphorylates these interacting proteins deserves further investigation. These newly discovered proteins have chartered exciting directions toward understanding new functions of the MPK4 kinase.

Identification of proteins which initiate and/or perpetuate adaptive immune responses has potential to greatly impact pre-clinical and clinical work across numerous fields. To date, however, the methodologies available to identify antigens responsible for driving adaptive immune responses have been plagued by numerous issues which have drastically limited their widespread adoption. Therefore, in this study, we sought to optimize a shotgun immunoproteomics approach to alleviate these persistent issues and create a high-throughput, quantitative methodology for antigen identification. Three individual components of a previously published approach, namely the protein extraction, antigen elution, and LC-MS/MS analysis steps, were optimized in a systematic manner. These studies determined that preparation of protein extracts using a one-step tissue disruption method in immunoprecipitation (IP) buffer, eluting antigens from affinity chromatography columns with 1% trifluoroacetic acid (TFA), and TMT-labeling & multiplexing equal volumes of eluted samples for LC-MS/MS analysis, resulted in quantitative longitudinal antigen identification, with reduced variability between replicates and increased total number of antigens identified. This optimized pipeline provides a multiplexed, highly reproducible, and fully quantitative approach to antigen identification which is broadly applicable to determine the role of antigenic proteins in inciting (i.e., primary antigens) and perpetuating (i.e., secondary antigens) a wide range of diseases. SIGNIFICANCE: Using a systematic, hypothesis-driven approach, we identified potential improvements for three individual steps of a previously published approach for antigen-identification. Optimization of each step created a methodology which resolved many of the persistent issues associated with previous antigen identification approaches. The optimized high-throughput shotgun immunoproteomics approach described herein identifies more than five times as many unique antigens as the previously published method, greatly reduces protocol cost and mass spectrometry time per experiment, minimizes both inter- and intra-experimental variability, and ensures each experiment is fully quantitative. Ultimately, this optimized antigen identification approach has the potential to facilitate novel antigen identification studies, allowing evaluation of the adaptive immune response in a longitudinal manner and encourage innovations in a wide array of fields.

Lysine crotonylation (Kcr) is an evolutionarily conserved protein post-translational modifications, which plays an important role in cellular physiology and pathology, such as chromatin remodeling, gene transcription regulation, telomere maintenance, inflammation, and cancer. Tandem mass spectrometry (LC-MS/MS) has been used to identify the global Kcr profiling of human, at the same time, many computing methods have been developed to predict Kcr sites without high experiment cost. Deep learning network solves the problem of manual feature design and selection in traditional machine learning (NLP), especially the algorithms in natural language processing which treated peptides as sentences, thus can extract more in-depth information and obtain higher accuracy. In this work, we establish a Kcr prediction model named ATCLSTM-Kcr which use self-attention mechanism combined with NLP method to highlight the important features and further capture the internal correlation of the features, to realize the feature enhancement and noise reduction modules of the model. Independent tests have proved that ATCLSTM-Kcr has better accuracy and robustness than similar prediction tools. Then, we design pipeline to generate MS-based benchmark dataset to avoid the false negatives caused by MS-detectability and improve the sensitivity of Kcr prediction. Finally, we develop a Human Lysine Crotonylation Database (HLCD) which using ATCLSTM-Kcr and the two representative deep learning models to score all lysine sites of human proteome, and annotate all Kcr sites identified by MS of current published literatures. HLCD provides an integrated platform for human Kcr sites prediction and screening through multiple prediction scores and conditions, and can be accessed on the website:www.urimarker.com/HLCD/. SIGNIFICANCE: Lysine crotonylation (Kcr) plays an important role in cellular physiology and pathology, such as chromatin remodeling, gene transcription regulation and cancer. To better elucidate the molecular mechanisms of crotonylation and reduce the high experimental cost, we establish a deep learning Kcr prediction model and solve the problem of false negatives caused by the detectability of mass spectrometry (MS). Finally, we develop a Human Lysine Crotonylation Database to score all lysine sites of human proteome, and annotate all Kcr sites identified by MS of current published literatures. Our work provides a convenient platform for human Kcr sites prediction and screening through multiple prediction scores and conditions.

Fish skin mucus is a dynamic external mucosal layer that acts as the first line of defense in the innate immune system. Skin mucus' exudation and composition change severely under stress, making it a valuable biofluid to search for minimally invasive stress markers. This study focused on the skin mucus proteome response to repetitive handling, overcrowding, and hypoxia, using Sparus aurata, an important species in the Mediterranean aquaculture, as a model. Biomarker discovery analysis was performed using label-free shotgun proteomics coupled with bioinformatics to unveil the most predictive proteins for the stressed phenotype. A mean of 2166 proteins were identified at a < 0.2% false discovery rate, from which the differentially abundant proteins (DAPs) were mainly involved in the immune system and protein metabolism. A sparse partial least squares regression analysis revealed a high correlation between DAPs and plasma physiological stress indicators. Feature selection, performed by recursive feature elimination followed by logistic regression analysis of the selected proteins, disclosed 28 candidate biomarkers with values of area under the curve >0.75. These minimally invasive biomarkers could be used in forthcoming species-specific stress management protocols to improve fish welfare and promote farmed fish safety, positive societal outcomes, and business sustainability. SIGNIFICANCE: The fish skin mucus holds a great promise into fish welfare, as a valuable source of minimally invasive biomarkers for stress assessment. In this shotgun proteomics discovery study, we have identified 28 candidate biomarkers by combining a comprehensive functional analysis of the stress regulated proteome with predictive modeling, supported by a significant correlation (p < 0.01) with physiological stress indicators (cortisol, lactate and glucose). The candidate biomarkers showed a good predictive value in the testing set (AUC > 0.75), paving the way for the next step in their validation by targeted proteomics. An early and timely assessment of fish stressful events, by using minimally invasive biomarkers, as those that can be found in the fish skin mucus, can contribute to promote fish health/welfare in the aquaculture sector and its sustainability. The adoption of preventive and surveillance measures based on proteomics approaches can therefore help to avoid unnecessary adverse outcomes with a negative impact on this primordial food sector.