Thermobifida fusca, a thermophilic bacterium belonging to Actinobacteria, is a major degrader of plant cell walls. The protein profiles of the secretome produced by T. fusca grown in cellulose, lignin, and mixture of cellulose and lignin containing culture media, promoting production of respective substrate hydrolyzing enzymes, was explored using a proteomics approach with high throughput isobaric tag for relative and absolute quantification (iTRAQ) technique using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The iTRAQ quantification of the secretome revealed unique extracellular enzyme system, including discrete multienzyme complexes of cellulases, hemicellulases, glycoside hydrolases, proteases, peroxidases, and protein translocating transporter proteins. When the strain was grown in these substrate conditions, proteins corresponding to cellulases, hemicellulases and transport proteins were highly up-regulated, while lignin degrading DyP-type peroxidase, novel nonheme peroxidases, catalase, cytochrome-c oxidase, and superoxide dismutase were also identified. Numerous proteins presumed to be involved in lignocellulose hydrolysis were expressed in response to these different culture conditions, and among these were several secreted hypothetical proteins that were not previously observed.

Neutrophil extracellular traps (NETs) consist of a decondensed DNA scaffold decorated with neutrophil-derived proteins. The proteome of NETs, or “NETome,” has been largely elucidated in vitro. However, components such as plasma and extracellular matrix proteins may affect the NETome under physiological conditions. Here, using a reductionistic approach, we explored the effects of two proteases active during injury and wounding, human thrombin and plasmin, on the NETome. Using high-resolution mass spectrometry, we identified a total of 164 proteins, including those previously not described in NETs. The serine proteases, particularly thrombin, were also found to interact with DNA and bound to NETs in vitro. Among the most abundant proteins were those identified previously, including histones, neutrophil elastase, and antimicrobial proteins. We observed reduced histone (H2B, H3, and H4) and neutrophil elastase levels upon the addition of the two proteases. Analyses of NET-derived tryptic peptides identified subtle changes upon protease treatments. Our results provide evidence that exogenous proteases, present during wounding and inflammation, influence the NETome. Taken together, regulation of NETs and their proteins under different physiological conditions may affect their roles in infection, inflammation, and the host response.

Despite decades of intensive research, there is still no effective treatment for ischemia/reperfusion (I/R) injury, an important corollary in the treatment of ischemic disease. I/R injury is initiated when the altered biochemistry of cells after ischemia is no longer compatible with oxygenated microenvironment (or reperfusion). To better understand the molecular basis of this alteration and subsequent incompatibility, we assessed the temporal and quantitative alterations in the cardiac proteome of a mouse cardiac I/R model by an iTRAQ approach at 30 min of ischemia, and at 60 or 120 min reperfusion after the ischemia using sham-operated mouse heart as the baseline control. Of the 509 quantified proteins identified, 121 proteins exhibited significant changes (p-value<0.05) over time and were mostly clustered in eight functional groups: Fatty acid oxidation, Glycolysis, TCA cycle, ETC (electron transport chain), Redox Homeostasis, Glutathione S-transferase, Apoptosis related, and Heat Shock proteins. The first four groups are intimately involved in ATP production and the last four groups are known to be important in cellular antioxidant activity. During ischemia and reperfusion, the short supply of oxygen precipitates a pivotal metabolic switch from aerobic metabolism involving fatty acid oxidation, TCA, and phosphorylation to anaerobic metabolism for ATP production and this, in turn, increases reactive oxygen species (ROS) formation. Therefore the implication of these 8 functional groups suggested that ischemia-reperfusion injury is underpinned in part by proteomic alterations. Reversion of these alterations to preischemia levels took at least 60 min, suggesting a refractory period in which the ischemic cells cannot adjust to the presence of oxygen. Therefore, therapeutics that could compensate for these proteomic alterations during this interim refractory period could alleviate ischemia-reperfusion injury to enhance cellular recovery from an ischemic to a normoxic microenvironment. Among the perturbed proteins, Park7 and Ppia were selected for further investigation of their functions under hypoxia. The results show that Park7 plays a key role in regulating antioxidative stress and cell survival, and Ppia may function in coping with the unfolded protein stress in the I/R condition.

Altered AH proteome in human PACG indicated oxidative stress in the neuronal damage that preceded vision loss. Identifying key mediators of PACG pathology will yield new prognostic biomarkers and novel targets for future therapeutic interventions.

Aging is an inevitable time-dependent decline of various physiological functions that finally leads to death. Progressive protein damage and aggregation have been proposed as the root cause of imbalance in regulatory processes and risk factors for aging and neurodegenerative diseases. Oxygen is a modulator of aging. The oxygen-deprived conditions (hypoxia) leads to oxidative stress, cellular damage and protein modifications. Despite unambiguous evidence of the critical role of spontaneous non-enzymatic Degenerative Protein Modifications (DPMs) such as oxidation, glycation, carbonylation, carbamylation, and deamidation, that impart deleterious structural and functional protein alterations during aging and age-associated disorders, the mechanism that mediates these modifications is poorly understood. This review summarizes up-to-date information and recent developments that correlate DPMs, aging, hypoxia, and age-associated neurodegenerative diseases. Despite numerous advances in the study of the molecular hallmark of aging, hypoxia, and degenerative protein modifications during aging and age-associated pathologies, a major challenge remains there to dissect the relative contribution of different DPMs in aging (either natural or hypoxia-induced) and age-associated neurodegeneration.

Metabolomics is the latest state-of-the-art omics technology that provides a comprehensive quantitative profile of metabolites. The metabolites are the cellular end products of metabolic reactions that explain the ultimate response to genomic, transcriptomic, proteomic, or environmental changes. Aging is a natural inevitable process characterized by a time-dependent decline of various physiological and metabolic functions and are dominated collectively by genetics, proteomics, metabolomics, environmental factors, diet, and lifestyle. The precise mechanism of the aging process is unclear, but the metabolomics has the potential to add significant insight by providing a detailed metabolite profile and altered metabolomic functions with age. Although the application of metabolomics to aging research is still relatively new, extensive attempts have been made to understand the biology of aging through a quantitative metabolite profile. This review summarises recent developments and upto-date information on metabolomics studies in aging research with a major emphasis on aging biomarkers in less invasive biofluids. The importance of an integrative approach that combines multi-omics data to understand the complex aging process is discussed. Despite various innovations in metabolomics and metabolite associated with redox homeostasis, central energy pathways, lipid metabolism, and amino acid, a major challenge remains to provide conclusive aging biomarkers.

Metabolic disorders in T2DM generate multiple sources of free radicals and oxidative stress that accelerate nonenzymatic degenerative protein modifications (DPMs) such as protein oxidation, disrupt redox signaling and physiological function, and remain a major risk factor for clinical diabetic vascular complications. in order to identify potential oxidative biomarkers in the blood plasma of patients with T2DM, we used LC-MS/MS-based proteomics to profile plasma samples from patients with T2DM and healthy controls. The results showed that human serum albumin (HSA) is damaged by irreversible cysteine trioxidation, which can be a potential oxidative stress biomarker for the early diagnosis of T2DM. The quantitative detection of site-specific thiol trioxidation is technically challenging; thus, we developed a sensitive and selective LC-MS/MS workflow that has been used to discover and quantify three unique thiol-trioxidized HSA peptides, ALVLIAFAQYLQQC (SO3H) PFEDHVK (m/z 1241.13), YIC (SO3H) ENQDSISSK (m/z 717.80) and RPC (SO3H) FSALEVDETYVPK (m/z 951.45), in 16 individual samples of healthy controls (n = 8) and individuals with diabetes (n = 8). Targeted quantitative analysis using multiple reaction monitoring mass spectrometry revealed impairment of the peptides with m/z 1241.13, m/z 717.80 and m/z 951.45, with significance (P < 0.02, P < 0.002 and P < 0.03), in individuals with diabetes. the results demonstrated that a set of three HSA thiol-trioxidized peptides, which are irreversibly oxidatively damaged in HSA in the plasma of patients with T2DM, can be important indicators and potential biomarkers of oxidative stress in T2DM.open Scientific RepoRtS | (2020) 10:6475 | https://doi.org/10.1038/s41598-020-62341-zwww.nature.com/scientificreports www.nature.com/scientificreports/ neuropathy and retinopathy 5 . However, measuring oxidative stress is challenging since reactive oxygen species (ROS) or other metabolic products are extremely unstable; hence, the gold standard to measure oxidative stress has not yet been established. As oxidative stress is a potential indicator to predict diabetes progression and is also beneficial for longitudinal follow-up to evaluate the response to treatment, there remains an unmet need to develop a reliable biomarker that can be used to estimate oxidative stress quantitatively.Modified proteins are prospective biomarkers for both diagnoses and assessment of disease treatment; hence, the American Diabetes Association 6 and the World Health Organization 7 approved the use of glycated hemoglobin A1c (HbA1c) in diagnosing DM. Modified proteins such as plasma glycoproteins including human epidermal growth factor receptor 2 (HER2) in breast cancer, prostate-specific antigen (PSA) in prostate cancer, carcinoembryonic antigen (CEA) in colorectal cancer, cancer antigen 125 (CA-125) in ovarian cancer, alpha-fetoprotein in hepatocellular carcinoma have been approved by the Food and Drug Administration (FDA) as a potential diagnostic biomarker of various cancers 8 . Further, the role of DPMs, su...

Tissue‐resident macrophages in white adipose tissue (WAT) dynamically adapt to the metabolic changes of their microenvironment that are often induced by excess energy intake. Currently, the exact contribution of these macrophages in obesity‐driven WAT remodeling remains controversial. Here, using a transgenic CD169‐DTR mouse strain, we provide new insights into the interplay between CD169+ adipose tissue macrophages (ATMs) and their surrounding WAT microenvironment. Using targeted in vivo ATM ablation followed by transcriptional and metabolic WAT profiling, we found that ATMs protect WAT from the excessive pathological remodeling that occurs during obesity. As obesity progresses, ATMs control not only vascular integrity, adipocyte function, and lipid and metabolic derangements but also extracellular matrix accumulation and resultant fibrosis in the WAT. The protective role of ATMs during obesity‐driven WAT dysfunction supports the notion that ATMs represent friends, rather than foes, as has previously assumed.