Clostridium cellulovorans metabolism of cellulose as studied by comparative proteomic approach.
Abstract Clostridium cellulovorans is among the most promising candidates for consolidated bioprocessing (CBP) of cellulosic biomass to liquid biofuels (ethanol, butanol). C. cellulovorans metabolizes all the main plant polysaccharides and mainly produces butyrate. Since most butyrate and butanol biosynthetic reactions from acetyl-CoA are common, introduction of single heterologous alcohol/aldehyde dehydrogenase can divert the branching-point intermediate (butyryl-CoA) towards butanol production in this strain. However, engineering C. cellulovorans metabolic pathways towards industrial utilization requires better ...
Source: Journal of Proteomics - January 23, 2020 Category: Biochemistry Authors: Usai G, Cirrincione S, Re A, Manfredi M, Pagnani A, Pessione E, Mazzoli R Tags: J Proteomics Source Type: research

Chilling stress reduced protein translation by the ubiquitination of ribosomal proteins in Volvariella volvacea.
This study significantly contributes to our understanding of ubiquitination-mediated autolysis associated with a decrease in protein translation in V. volvacea. Our data highlight the mechanistic role of UBEV2 in facilitating the cryogenic autolysis of V. volvacea. We provided a new idea for the preservation of V. volvacea by inhibiting UBEV2 to increase its marketability. PMID: 31982547 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - January 23, 2020 Category: Biochemistry Authors: Gong M, Li Z, Wan J, Chen M, Wang H, Shang J, Zhou S, Tan Q, Wang Y, Bao D Tags: J Proteomics Source Type: research

Proteomic investigation into the action mechanism of berberine against Streptococcus pyogenes.
Abstract Berberine is an isoquinoline alkaloid found in many plants. Although berberine is known to possess the antibacterial activity against Streptococcus pyogenes, the mechanism underlying it is not fully understood. In the current study, to investigate the molecular mechanism how berberine exerts its antibacterial effects, quantitative proteomics was conducted to investigate differential expressed proteins in S. pyogenes in response to berberine treatment. KEGG pathways analysis revealed that berberine regulated proteins were mainly involved in carbohydrate metabolism, fatty acid biosynthesis, pyrimidine metab...
Source: Journal of Proteomics - January 22, 2020 Category: Biochemistry Authors: Du GF, Le YJ, Sun X, Yang XY, He QY Tags: J Proteomics Source Type: research

Identification of glycan branching patterns using multistage mass spectrometry with spectra tree analysis.
In this study, we present an approach called glyBranch (glycan Branching pattern identification based on spectra tree) to exploit the information contained in MSn spectra tree for glycan identification. This approach will greatly facilitate the automated identification of glycan structures and related biological studies. PMID: 31978548 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - January 21, 2020 Category: Biochemistry Authors: Wang H, Zhang J, Dong J, Hou M, Pan W, Bu D, Zhou J, Zhang Q, Wang Y, Zhao K, Li Y, Huang C, Sun S Tags: J Proteomics Source Type: research

The golden mussel proteome and its response to niclosamide: Uncovering rational targets for control or elimination.
ges W Abstract The Asian invasive species Limnoperna fortunei (Dunker, 1857), known as the golden mussel, causes great economic and environmental damage due to its fixative capacity and accelerated proliferation. Molecular studies for the control of larval and adult forms are of great economic, scientific and technological interest. Here, we first report on the compositional analysis of the L. fortunei proteome obtained through shotgun analysis using LC-MS/MS. Among those 2790 proteins identified, many of them related to secretory processes and membrane receptors. Our second approach consisted in exposing the moll...
Source: Journal of Proteomics - January 20, 2020 Category: Biochemistry Authors: Sanson AL, Cosenza-Contreras M, DeMarco R, Neves LX, Mattei B, Silva GG, Magalhães PHV, de Andrade MHG, Castro-Borges W Tags: J Proteomics Source Type: research

Human sperm phosphoproteome reveals differential phosphoprotein signatures that regulate human sperm motility.
Abstract Human sperm motility is essential for fertilization and among pathologies underlying male infertility is asthenozoospermia. Nevertheless, mechanisms regulating sperm motility are not completely unraveled. This work investigates phosphoproteins underlying human sperm motility by using differential phosphoproteomic in two human sperm subpopulations: high (HM) and low (LM) motility, obtained by centrifugation in a density gradient. Phosphoproteomics (HPLC-MS/MS triple TOF), comparing human LM and HM phosphoproteomes, identified 210 phosphopeptides with different abundance that correspond with 119 sperm prote...
Source: Journal of Proteomics - January 20, 2020 Category: Biochemistry Authors: Martin-Hidalgo D, Serrano R, Zaragoza C, Garcia-Marin LJ, Bragado MJ Tags: J Proteomics Source Type: research

In-depth proteomics and natural peptidomics analyses reveal antibacterial peptides in human endometrial fluid.
, Matorras R, Elortza F Abstract The composition of endometrial fluid reflects the status of the endometrium; it is a good atraumatic source of information on embryo implantation processes and possible pathological conditions. Although some attempts have been made to characterise its proteome, the catalogue of its proteins remains incomplete and little has been done to analyse the natural peptides it contains. Here, we present a comprehensive analysis of the proteins and natural peptides of the endometrial fluid. The protein content of samples from 11 individuals was analysed using the novel timsTOF Pro mass spect...
Source: Journal of Proteomics - January 17, 2020 Category: Biochemistry Authors: Azkargorta M, Bregón-Villahoz M, Escobes I, Ibáñez-Pérez J, Iloro I, Iglesias M, Zapirain MD, Rabanal A, Prieto B, Moragues MD, Matorras R, Elortza F Tags: J Proteomics Source Type: research

BoMiProt: A database of bovine milk proteins.
Abstract Bovine milk has become an important biological fluid for proteomic research due to its nutritional and immunological benefits. To date, over 300 publications have reported changes in bovine milk protein composition based on seasons, lactation stages, breeds, health status and milk fractions while there are no reports on consolidation or overlap of data between studies. Thus, we have developed a literature-based, manually curated open online database of bovine milk proteome, BoMiProt (http://bomiprot.org), with over 3100 proteins from whey, fat globule membranes and exosomes. Each entry in the database is ...
Source: Journal of Proteomics - January 17, 2020 Category: Biochemistry Authors: Maity S, Bhat AH, Giri K, Ambatipudi K Tags: J Proteomics Source Type: research

Global discovery the PstP interactions using Mtb proteome microarray and revealing novel connections with EthR.
In this study, we performed an Mtb proteome microarray to globally identify the PstP bindings. In this way, we discovered 78 interactors between PstP and Mtb proteins, and found a novel connections with EthR. The interaction between PstP and EthR has been validated by Bio-Layer interferometry and Yeast-two-hybrid. And functional studies showed that PstP significantly enhances the binding between EthR and related DNA domain through its interaction with EthR. Phenotypically, overexpression of PstP promoted the resistance of Mycobacterium smegmatis with the antibiotic of ethionamide. Overall, we hopefully wish that the PstP i...
Source: Journal of Proteomics - January 17, 2020 Category: Biochemistry Authors: Li KK, Qu DH, Zhang HN, Chen FY, Xu L, Wang MY, Su HY, Tao SC, Wu FL Tags: J Proteomics Source Type: research

Hepatic proteomic analysis of selenoprotein F knockout mice by iTRAQ: An implication for the roles of selenoprotein F in metabolism and diseases.
Abstract Selenoprotein F (Selenof) is an endoplasmic reticulum (ER)-resident protein. It may be functionally linked to glycoprotein folding in the ER but the detail function is not fully understood. To study the function of Selenof, we used CRISPR/Cas9 to generate Selenof knockout mice and performed proteomic analysis of hepatic proteins by iTRAQ. Collectively, 83 differently expressed proteins (DEPs) were identified in the liver of Selenof knockout mice. The changes of mRNA and protein levels of 6 selected DEPs, Fatty acid synthase, ATP-citrate synthase, Glutathione S-transferase P 1, Transformer-2 protein homolo...
Source: Journal of Proteomics - January 17, 2020 Category: Biochemistry Authors: Zheng X, Ren B, Wang H, Huang R, Zhou J, Liu H, Tian J, Huang K Tags: J Proteomics Source Type: research

Intermittent fasting from dawn to sunset for 30 consecutive days is associated with anticancer proteomic signature and upregulates key regulatory proteins of glucose and lipid metabolism, circadian clock, DNA repair, cytoskeleton remodeling, immune system and cognitive function in healthy subjects.
Abstract Murine studies showed that disruption of circadian clock rhythmicity could lead to cancer and metabolic syndrome. Time-restricted feeding can reset the disrupted clock rhythm, protect against cancer and metabolic syndrome. Based on these observations, we hypothesized that intermittent fasting for several consecutive days without calorie restriction in humans would induce an anticarcinogenic proteome and the key regulatory proteins of glucose and lipid metabolism. Fourteen healthy subjects fasted from dawn to sunset for over 14 h daily. Fasting duration was 30 consecutive days. Serum samples were collect...
Source: Journal of Proteomics - January 9, 2020 Category: Biochemistry Authors: Mindikoglu AL, Abdulsada MM, Jain A, Choi JM, Jalal PK, Devaraj S, Mezzari MP, Petrosino JF, Opekun AR, Jung SY Tags: J Proteomics Source Type: research

A multi-approach peptidomic analysis of hen egg white reveals novel putative bioactive molecules and food markers of storage.
This study provided the largest inventory of peptides described in chicken egg while so far. In addition, it identified a number of protein fragments associated with hypothetical antihypertensive, antioxidant, antiinflammatory, antimicrobial, anticancer, antiviral, antibiofilm, calcium-binding, antidiabetic, antithrombotic, adipogenic differentiating, stimulating/immunostimulating, hormonal, lipid-binding and cell adhesion-affecting activities. These results confirmed previous observations regarding functional characteristics of egg white unfractionated preparations or purified molecules, emphasizing the useful application...
Source: Journal of Proteomics - January 9, 2020 Category: Biochemistry Authors: Arena S, Renzone G, Scaloni A Tags: J Proteomics Source Type: research

Spatially resolved proteomics in osteoarthritis: State of the art and new perspectives.
tor B Abstract Osteoarthritis (OA) is one of the most common diseases worldwide caused by chronic degeneration of the joints. Its high prevalence and the involvement of several tissues define OA as a highly heterogeneous disease. New biological markers to evaluate the progression of the pathology and improve its prognosis are needed. Among all the different -omic strategies applied to OA, solution phase bottom-up proteomics has made an extensive contribution to the field of biomarker research. However, new technologies for protein analyses should be considered for a better understanding of the disease. This review...
Source: Journal of Proteomics - January 8, 2020 Category: Biochemistry Authors: Eveque-Mourroux MR, Rocha B, Barré FPY, Heeren RMA, Cillero-Pastor B Tags: J Proteomics Source Type: research

Defining the TLT-1 interactome from resting and activated human platelets.
This study defines the TLT-1 interactome in resting and active human platelets, identifying several novel TLT-1 interactors, as well as TLT-1 phosphorylation sites, all with likely signaling implications in platelet aggregation dynamics. PMID: 31923473 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - January 7, 2020 Category: Biochemistry Authors: Schmoker AM, Perez Pearson LM, Cruz C, Colon Flores LG, Branfeild S, Pagán Torres FD, Fonseca K, Cantres YM, Salgado Ramirez CA, Melendez LM, Ballif BA, Washington AV Tags: J Proteomics Source Type: research

Identification of tumor-associated antigens with diagnostic ability of colorectal cancer by in-depth immunomic and seroproteomic analysis.
ute;nguez G, de Los Ríos V, Peláez-García A, Guzmán-Aránguez A, Barderas R Abstract Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer related death worldwide. Its diagnosis at early stages would significantly improve the survival of CRC patients. The humoral immune response has been demonstrated useful for cancer diagnosis, predating clinical symptoms up to 3 years. Here, we employed an in-depth seroproteomic approach to identify proteins that elicit a humoral immune response in CRC patients. The seroproteomic approach relied on the ...
Source: Journal of Proteomics - January 6, 2020 Category: Biochemistry Authors: Garranzo-Asensio M, Segundo-Acosta PS, Povés C, Fernández-Aceñero MJ, Martínez-Useros J, Montero-Calle A, Solís-Fernández G, Sanchez-Martinez M, Rodríguez N, Cerón MÁ, Fernandez-Diez S, Domínguez G, de Los Ríos V, Peláez-García A, Guzmán-Ar Tags: J Proteomics Source Type: research

Perusal of food allergens analysis by mass spectrometry-based proteomics.
Abstract Food allergy is the disease where the immune system is elicited by antigens in food. Although innocuous for immune-tolerant individuals, an ever-growing number of food allergenic people are being registered worldwide. To date, no treatment to cure food allergy is available and the disease management relies on the careful exclusion of the allergenic food from the diet of the allergic individuals. Great efforts are ongoing to clarify the allergenic mechanisms of the diverse allergenic proteins of food origin, aimed to both designing suitable therapies and for a timely and precise diagnosis of the allergic c...
Source: Journal of Proteomics - January 6, 2020 Category: Biochemistry Authors: Marzano V, Tilocca B, Fiocchi AG, Vernocchi P, Mortera SL, Urbani A, Roncada P, Putignani L Tags: J Proteomics Source Type: research

Analysis of ubiquitin signaling and chain topology cross-talk.
Abstract Protein ubiquitination is a powerful post-translational modification implicated in many cellular processes. Although ubiquitination is associated with protein degradation, depending on the topology of polyubiquitin chains, protein ubiquitination is connected to non-degradative events in DNA damage response, cell cycle control, immune response, trafficking, intracellular localization, and vesicle fusion events. Recently it has been shown that ubiquitin can be conjugated to two or more different chains at the same time. These branched chains add another level of complexity to ubiquitin signaling, increasing...
Source: Journal of Proteomics - January 6, 2020 Category: Biochemistry Authors: Mendes ML, Fougeras MR, Dittmar G Tags: J Proteomics Source Type: research

Hypothalamic proteome changes in response to nicotine and its withdrawal are potentially associated with alteration in body weight.
Abstract Nicotine, a major addictive component in tobacco, plays an important role in the changes of body weight upon smoking and its cessation. Here we showed that nicotine-treated mice exhibited weight loss and nicotine withdrawal led to weight gain. Using TMT-based proteomic analysis, we obtained the different hypothalamic protein profiles in response to nicotine and its withdrawal. A total of ~5000 proteins were identified from the hypothalamus with 50 altered proteins upon 28-day nicotine treatment and 28 altered proteins upon 15-day nicotine withdrawal. Of the altered proteins, CASP3, LCMT2, GRIN2D, CCNT2, F...
Source: Journal of Proteomics - January 3, 2020 Category: Biochemistry Authors: Gao MM, Hu F, Zeng XD, Tang HL, Zhang H, Jiang W, Yan HJ, Shi H, Shu Y, Long YS Tags: J Proteomics Source Type: research

Association of proteome and metabolome signatures with severity in patients with community-acquired pneumonia.
;lker U Abstract A combined OMICS screening approach of human plasma and serum was used to characterize protein and metabolome signatures displaying association to severity of Community-acquired pneumonia (CAP). 240 serum and BD P100 EDTA plasma samples from patients diagnosed with CAP, collected during the day of enrolment to the hospital, were analyzed by a metabolomic and proteomic approach, respectively. Disease severity of CAP patients was stratified using the Sequential Organ Failure Assessment (SOFA) score. Quantitative proteome and metabolome data, derived by LC-MS/MS, were associated to SOFA and specific ...
Source: Journal of Proteomics - December 30, 2019 Category: Biochemistry Authors: Salazar MG, Neugebauer S, Kacprowski T, Michalik S, Ahnert P, Creutz P, Rosolowski M, PROGRESS Study Group, Löffler M, Bauer M, Suttorp N, Kiehntopf M, Völker U Tags: J Proteomics Source Type: research

Plasma metabonomics and proteomics studies on the anti-thrombosis mechanism of aspirin eugenol ester in rat tail thrombosis model.
This study established the foundation to further evaluate the druggability of AEE on thrombosis treatment. PMID: 31891783 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - December 28, 2019 Category: Biochemistry Authors: Ma N, Yang Y, Liu X, Li S, Qin Z, Li J Tags: J Proteomics Source Type: research

Characterizing fruit ripening in plantain and Cavendish bananas: A proteomics approach.
We present data from the green to the fully mature stage. By analyzing the protein abundances during ripening we provide some new insights into the ripening process and how plantains fruits are different. Multivariate analysis of the proteins was performed correlated to the starch dynamics. A drop in sucrose synthase and a rise of acid invertase during ripening indicated a change in the balance of the sucrose fate. During ripening, sugars may no longer be available for respiration since they are stored in the vacuoles, making citrate the preferred respiratory substrate. We found significant cultivar specific differences in...
Source: Journal of Proteomics - December 28, 2019 Category: Biochemistry Authors: Bhuiyan F, Campos NA, Swennen R, Carpentier S Tags: J Proteomics Source Type: research

Proteomic analysis and antibacterial resistance mechanisms of Salmonella Enteritidis submitted to the inhibitory effect of Origanum vulgare essential oil, thymol and carvacrol.
Abstract Biological properties of natural products are an important research target and essential oils (EO) from aromatic plants with antimicrobial properties are well documented. However, their uses are limited, and the mechanisms underlying their antibacterial activity are still not well known. Therefore, our objective was to evaluate the antibacterial activities of Origanum vulgare EO, thymol and carvacrol against Salmonella Enteritidis ATCC 13076 strain, particularly regarding the bacterial proteic profile, enzymatic activities and DNA synthesis. Bacterial expressed proteins were evaluated using an untreated a...
Source: Journal of Proteomics - December 24, 2019 Category: Biochemistry Authors: Barbosa LN, Alves FCB, Andrade BFMT, Albano M, Rall VLM, Fernandes AAH, Buzalaff MAR, de Lima Leite A, de Pontes LG, Dos Santos LD, Junior AF Tags: J Proteomics Source Type: research

TMT-labeled quantitative proteomic analyses on the longissimus dorsi to identify the proteins underlying intramuscular fat content in pigs.
In this study, we performed an integrated transcriptome-assisted TMT-labeled quantitative proteomic analysis of the longissimus dorsi (LD) muscle in Laiwu pigs at the fastest IMF deposition stage and identified 5074 unique proteins and 52 differentially abundant proteins (DAPs) (>1.5-fold cutoff, p 
Source: Journal of Proteomics - December 24, 2019 Category: Biochemistry Authors: Ma C, Wang W, Wang Y, Sun Y, Kang L, Zhang Q, Jiang Y Tags: J Proteomics Source Type: research

Cucumber mosaic virus resistance: Comparative proteomics of contrasting Cucumis sativus cultivars after long-term infection.
We report original findings of comparative analysis of plant genotypes exposed to CMV. Deep discovery proteomics of resistant and susceptible cucumber cultivars, inoculated with widespread phytovirus, allowed to suggest several novel molecular targets for functional testing in plant protection strategies. PMID: 31881349 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - December 24, 2019 Category: Biochemistry Authors: Nováková S, Šubr Z, Kováč A, Fialová I, Beke G, Danchenko M Tags: J Proteomics Source Type: research

Differences on salivary proteome at rest and in response to an acute exercise in men and women: A pilot study.
In conclusion, these results indicate sex-related differences in the salivary proteome at rest and after an acute exercise, pointing out possible candidate biomarkers for sports performance and allowing further knowledge of the physiological processes occurring during ELF. SIGNIFICANCE: The present study describes for the first time the changes that occur in salivary proteome detected by TMT-based proteomics in response to an acute exercise and the differences in these changes depending on sex. Of the 274 protein identified, the 87 differentially expressed proteins and their related pathways were discussed, focusing on the...
Source: Journal of Proteomics - December 24, 2019 Category: Biochemistry Authors: Franco-Martínez L, Hernández JMG, Horvatić A, Guillemin N, Cerón J, Martínez-Subiela S, Sentandreu MÁ, Brkljačić M, Mrljak V, Tvarijonaviciute A, Reyes PJ Tags: J Proteomics Source Type: research

Identification of genes related to skeletal muscle growth and development by integrated analysis of transcriptome and proteome in myostatin-edited Meishan pigs.
Abstract Embryonic development of skeletal muscle is a complex process that is important to the growth of skeletal muscle after birth. However, the mechanisms by which skeletal muscle growth and development in embryonic phase remain unclear. We have previously produced myostatin-knockout (MKO) Meishan pigs with double-muscle (DM) phenotype via zinc finger nucleases (ZFN) technology. To further investigate the molecular mechanisms involved in skeletal muscle growth and development, in this study, we performed an integrated analysis of transcriptome and proteome in longissimus dorsi muscle from myostatin wild type (...
Source: Journal of Proteomics - December 24, 2019 Category: Biochemistry Authors: Li X, Xie S, Qian L, Cai C, Bi H, Cui W Tags: J Proteomics Source Type: research

Improved integrative analysis of the thiol redox proteome using filter-aided sample preparation.
rcena JA, Peral B, Vázquez J Abstract Changes in the oxidation state of protein Cys residues are involved in cell signalling and play a key role in a variety of pathophysiological states. We had previously developed GELSILOX, an in-gel method that enables the large-scale, parallel analysis of dynamic alterations to the redox state of Cys sites and protein abundance changes. Here we present FASILOX, a further development of the GELSILOX approach featuring: i) significantly increased peptide recovery, ii) enhanced sensitivity for the detection of Cys oxidative alterations, and iii) streamlined workflow that r...
Source: Journal of Proteomics - December 21, 2019 Category: Biochemistry Authors: Bonzon-Kulichenko E, Camafeita E, López JA, Gómez-Serrano M, Jorge I, Calvo E, Núñez E, Trevisan-Herraz M, Bagwan N, Bárcena JA, Peral B, Vázquez J Tags: J Proteomics Source Type: research

The total microbiome functions in bacteria and fungi.
Abstract Unveiling the relationship between phylogeny and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial phylogenetic diversity, our understanding of its relationship to functional diversity is still scarce. Here we predicted the total microbiome functions of bacteria and fungi on Earth using the total known functions from level 3 of KEGG Orthology by modelling the increase of functions with increasing diversity of bacteria or fungi. For bacteria and fungi, the unsaturated model described the da...
Source: Journal of Proteomics - December 18, 2019 Category: Biochemistry Authors: Starke R, Capek P, Morais D, Callister SJ, Jehmlich N Tags: J Proteomics Source Type: research

Proteomic-components provide insights into the defensive secretion in termite workers of the soldierless genus Ruptitermes.
Abstract Termite soldiers constitute the defensive frontline of the colonies, despite workers also perform such tasks, especially within the Neotropical Apicotermitinae, in which all species are soldierless. Workers of the genus Ruptitermes display an extreme form of defense, characterized by body rupture and release of a sticky secretion. Previous observations suggested that such behavior may be advantageous against enemies, but the chemical composition of this secretion has been neglected. Here we firstly provide the proteomic profile of the defensive secretion of Ruptitermes reconditus and Ruptitermes pitan wor...
Source: Journal of Proteomics - December 18, 2019 Category: Biochemistry Authors: Costa-Leonardo AM, da Silva IB, Poiani SB, Santos-Pinto JRAD, Esteves FG, da Silva LHB, Palma MS Tags: J Proteomics Source Type: research

Phenotype and TMT-based quantitative proteomics analysis of Brassica napus reveals new insight into chlorophyll synthesis and chloroplast structure.
Abstract The conversion of light energy into chemical energy in leaves is very important for plant growth and development. During this process, chlorophylls and their derivatives are indispensable as their fundamental role in the energy absorption and transduction activities. Chlorophyll variation mutants are important materials for studying chlorophyll metabolism, chloroplast biogenesis, photosynthesis and related physiological processes. Here, a chlorophyll-reduced mutant (crm1) was isolated from ethyl methanesulfonate (EMS) mutagenized Brassica napus. Compared to wild type, crm1 showed yellow leaves, reduced ch...
Source: Journal of Proteomics - December 18, 2019 Category: Biochemistry Authors: Yang P, Li Y, He C, Yan J, Zhang W, Li X, Xiang F, Zuo Z, Li X, Zhu Y, Liu X, Zhao X Tags: J Proteomics Source Type: research

LC-MS/MS based comparative proteomics of floral nectars reveal different mechanisms involved in floral defense of Nicotiana spp., Petunia hybrida and Datura stramonium.
This study represents a comparative proteomic analysis of floral nectars of the Nicotiana spp. with two correlated Solanaceous species. Significant differences were identified between the proteome of taxonomic sections providing relevant insights into the group of proteins related to defense/stress associated with Nectar Redox Cycle, antimicrobial proteins and signaling pathways. The activity of FNs proteins is suggested impact the microbial growth. The knowledge about these proteomes provides significant insights into the diversity of proteins secreted in the nectars and the array of mechanisms used by Nicotiana spp. in i...
Source: Journal of Proteomics - December 14, 2019 Category: Biochemistry Authors: Silva F, Guirgis A, von Aderkas P, Borchers CH, Thornburg R Tags: J Proteomics Source Type: research

Global characterization of proteome and lysine methylome features in EZH2 wild-type and mutant lymphoma cell lines.
In this study, we presented a deep exploration of lysine mono-, di- and trimethylomes in EZH2 wild-type and Y641 mutant lymphoma cell lines. Our results showed that several substrates were modified in different methylation levels. Moreover, these methylated lysine residues could also undergo other types of PTMs. Combined with the differences proved in protein expression, lysine acetylation, lysine ubiquitylation and protein N-termianl acetylation level, our study underlined the substrate specificity of lysine methylation and its crosstalk with other types of PTMs. Totally, our study raised new insights into the global cell...
Source: Journal of Proteomics - December 14, 2019 Category: Biochemistry Authors: Hao B, Sun M, Zhang M, Zhao X, Zhao L, Li B, Zhai L, Liu P, Hu H, Xu JY, Tan M Tags: J Proteomics Source Type: research

Serum metabolic fingerprinting of pre-lameness dairy cows by GC-MS reveals typical profiles that can identify susceptible cows.
The objectives of this study were to identify metabolite fingerprints in the serum related to amino acid (AA), carbohydrate, and lipid metabolism in transition dairy cows at -8 and -4 wks prior to parturition, at +2 wks postpartum during lameness diagnosis as well as at +4 and +8 wks after parturition. All cases of lameness occurred at around +2 wks after parturition. Out of 100 dairy cows included in this nested case-control study only 6 pregnant multiparous (parity: 3.0 ± 0.6, Mean ± SEM) Holstein dairy cows with lameness only and 20 healthy control cows (CON) were selected for serum GC-MS metabolom...
Source: Journal of Proteomics - December 14, 2019 Category: Biochemistry Authors: Dervishi E, Zhang G, Zwierzchowski G, Mandal R, Wishart DS, Ametaj BN Tags: J Proteomics Source Type: research

The developmental phosphoproteome of Haemonchus contortus.
Abstract Protein phosphorylation plays essential roles in many cellular processes. Despite recent progress in the genomics, transcriptomics and proteomics of socioeconomically important parasitic nematodes, there is scant phosphoproteomic data to underpin molecular biological discovery. Here, using the phosphopeptide enrichment-based LC-MS/MS and DIA quantitation, we characterised the first developmental phosphoproteome of the parasitic nematode Haemonchus contortus - one of the most pathogenic parasites of ruminant livestock. Totally, 1804 phosphorylated proteins with 4406 phosphorylation sites ('phosphosites') f...
Source: Journal of Proteomics - December 14, 2019 Category: Biochemistry Authors: Wang T, Ma G, Ang CS, Korhonen PK, Stroehlein AJ, Young ND, Hofmann A, Chang BCH, Williamson NA, Gasser RB Tags: J Proteomics Source Type: research

MALDI TOF MS-profiling: Applications for bacterial and plant sample differentiation and biological variability assessment.
In this study, we evaluated the potential use of MALDI-TOF MS Profiling for the differentiation of biological samples submitted to different treatments. We compared the bacterium Xanthomonas campestris pv. campestris (Xcc), grown in culture medium and in vivo (recovered from the plant). Plant samples were also analyzed and included explants at different somatic embryogenesis (SE) stages, as well as leaves from Brassica oleracea and Arabidopsis thaliana inoculated with Xcc, at different time points. The results showed that bacteria and highly divergent plant samples, such as those from embryogenic stages, can be unequivocal...
Source: Journal of Proteomics - December 14, 2019 Category: Biochemistry Authors: Ribeiro DG, Carmo LST, Santos IR, Almeida RF, Silva LP, Oliveira-Neto OB, Scherwinski-Pereira JE, Mehta A Tags: J Proteomics Source Type: research

Comprehensive analysis of human IgG Fc N-glycopeptides and construction of a screening model for colorectal cancer.
In this study, we proposed a strategy for obtaining and analyzing IgG glycopeptides using CS@PGMA@IDA nanomaterial in combination with MALDI-TOF-MS. Using this strategy, IgG Fc N-glycopeptides were analyzed in the plasma of CRC patients, and our findings indicated that glycosylation levels in the IgG Fc region were closely related to CRC. By using the IgG N-glycopeptide enrichment method and screening model designed in this study, early large-scale colorectal cancer screening can be implemented easily and fast. PMID: 31846768 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - December 14, 2019 Category: Biochemistry Authors: Zou Y, Hu J, Jie J, Lai J, Li M, Liu Z, Zou X Tags: J Proteomics Source Type: research

SILAC-based quantitative proteomics reveals pleiotropic, phenotypic modulation in primary murine macrophages infected with the protozoan pathogen Leishmania donovani.
This study describes a SILAC-based quantitative proteomics approach to characterise changes of bone marrow-derived macrophages infected with L. donovani promastigotes for 72 h. With the application of SILAC and the use of SAX and GEL fractionation methods, we have tested new routes for proteome quantification of primary macrophages. The protocols developed here can be applicable to other diseases and pathologies. Moreover, this study sheds important new light on the "proteomic reprogramming" of infected macrophages in response to L. donovani promastigotes that affects primary metabolism, cellular catabolic proc...
Source: Journal of Proteomics - December 14, 2019 Category: Biochemistry Authors: Smirlis D, Dingli F, Pescher P, Prina E, Loew D, Rachidi N, Späth GF Tags: J Proteomics Source Type: research

UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase).
Abstract UniprotR is a software package designed to easily retrieve, cluster and visualize protein data from UniProt knowledgebase (UniProtKB) using R language. The package is implemented mainly to process, parse and illustrate proteomics data in a handy and time-saving approach allowing researchers to summarize all required protein information available at UniProtKB in a readable data frame, Excel CSV file, and/or graphical output. UniprotR generates a set of graphics including gene ontology, chromosomal location, protein scoring and status, protein networking, sequence phylogenetic tree, and physicochemical prop...
Source: Journal of Proteomics - December 13, 2019 Category: Biochemistry Authors: Soudy M, Anwar A, Ahmed EA, Osama A, Ezzeldin S, Mahgoub S, Magdeldin S Tags: J Proteomics Source Type: research

Alterations in plasma concentrations of energy-balance-related metabolites in patients with lung, or head & neck, cancers: Effects of radiotherapy.
This study analyzed the changes produced in the plasma concentrations of energy-balance-related metabolites in patients with lung cancer or head and neck cancer. The results obtained identified glutamate as the parameter with the highest discrimination capacity between patients and the control group. The relationships between various metabolites and clinical outcomes were also analyzed. These results extend the knowledge of metabolic alterations in cancer, thus facilitating the search for biomarkers and therapeutic targets. PMID: 31841666 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - December 10, 2019 Category: Biochemistry Authors: Rodríguez-Tomàs E, Arguís M, Arenas M, Fernández-Arroyo S, Murcia M, Sabater S, Torres L, Baiges-Gayà G, Hernández-Aguilera A, Camps J, Joven J Tags: J Proteomics Source Type: research

Enrichment and identification of small proteins in a simplified human gut microbiome.
This study improves the assessment of sProtein detection and enables their functional characterization in future experiments. SIGNIFICANCE: Small proteins have great potential and are therefore obtaining high interest. Especially in human microbiota, many undiscovered and uncharacterized small proteins promote the understanding of complex host-microbiome and bacteria-bacteria interactions. However, a major challenge lies in the detection of small proteins using bottom-up proteomics. Our study leads to an improved identification of small proteins in bacterial communities. It further describes properties and potential functi...
Source: Journal of Proteomics - December 10, 2019 Category: Biochemistry Authors: Petruschke H, Anders J, Stadler PF, Jehmlich N, von Bergen M Tags: J Proteomics Source Type: research

Integration of transcriptomics and metabolomics profiling reveals the metabolic pathways affected in dictamnine-induced hepatotoxicity in mice.
This study is the first to utilize integrated transcriptomics and metabolomics in combination with general toxicity evaluation to characterize the potential molecular mechanism in DTN-induced hepatotoxicity in mice. We found that acute exposure to higher dose of DTN induced hepatocellular liver injury with more changes in biochemical parameters, genes and metabolites. Gene expression and metabolite profiles were more sensitive than general toxicity studies for detecting earlier hepatotoxicity. Integrated analysis suggested that oxidative damage, ABC transporters and lipid metabolism were closely correlated with DTN-induced...
Source: Journal of Proteomics - December 5, 2019 Category: Biochemistry Authors: Li ZQ, Wang LL, Zhou J, Zheng X, Jiang Y, Li P, Li HJ Tags: J Proteomics Source Type: research

Protein methylome analysis in Arabidopsis reveals regulation in RNA-related processes.
This study was the first proteome-scale identification of lysine and arginine methylation in plants. We found that methylation occurred widely on non-histone proteins in Arabidopsis and was involved in diverse biological functions. The results provide foundations for the investigation of the protein methylome in Arabidopsis and provide powerful resources for the functional analysis of protein methylation in plants. PMID: 31809900 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - December 3, 2019 Category: Biochemistry Authors: Liang Q, Geng Q, Jiang L, Liang M, Li L, Zhang C, Wang W Tags: J Proteomics Source Type: research

Proteomic analysis of whole saliva in chronic periodontitis.
In conclusion, few specific salivary proteins were associated with CP. These findings may contribute to the identification of disease indicators or signatures for the improvement of periodontal diagnosis. SIGNIFICANCE: Periodontitis is a chronic inflammatory disease that results in periodontal attachment destruction, bone resorption and eventual tooth loss. Salivary biomarkers have been sought to predict periodontitis. The analysis of the salivary proteome of individuals with chronic periodontitis indicated that several proteins of various functions were significantly reduced in these individuals, except for salivary acidi...
Source: Journal of Proteomics - December 3, 2019 Category: Biochemistry Authors: Hartenbach FARR, Velasquez É, Nogueira FCS, Domont GB, de Oliveira Ferreira E, Colombo APV Tags: J Proteomics Source Type: research

Proteomic analyses on xylem sap provides insights into the defense response of Gossypium hirsutum against Verticillium dahliae.
Abstract Verticillium dahliae seriously affects the yield of cotton. Here, V. dahliae infection induced the significant reduction of protein concentration in cotton xylem sap (CXS), suggesting that the protein composition have changed. Thus, the proteomics in CXS from resistant Gossypium hirsutum cv. ND601 and susceptible CCRI8 infected by V. dahliae were analyzed using the label-free method. A total of 3047 proteins were identified across all four CXS sample groups. 1717 and 1476 proteins were differentially accumulated in ND601 and CCRI8 after infection with V. dahliae, respectively. The majority of up-accumulat...
Source: Journal of Proteomics - December 3, 2019 Category: Biochemistry Authors: Yang J, Wang X, Xie M, Wang G, Li Z, Zhang Y, Wu L, Zhang G, Ma Z Tags: J Proteomics Source Type: research

Proteomics fingerprints of systemic mechanisms of adaptation to bile in Lactobacillus fermentum.
Abstract Lactobacillus fermentum is a natural resident of the human GIT and is used as a probiotic. A unique property of L. fermentum is its ability to tolerate, colonize, and survive in the harsh conditions of bile, which facilitates transient colonization of the host colon. In the current study, we investigated the key mechanisms of action involved in bacterial survival in the presence of bile, using high-resolution mass spectrometry. A total of 1071 proteins were identified, among which 378 were up-regulated and 368 down-regulated by ≥2-fold (t-test, p 
Source: Journal of Proteomics - December 2, 2019 Category: Biochemistry Authors: Ali SA, Singh P, Tomar SK, Mohanty AK, Behare P Tags: J Proteomics Source Type: research

ITRAQ-based quantitative proteomics reveals the first proteome profiles of piglets infected with porcine circovirus type 3.
This study attempted for the first time to investigate the protein profile of PCV3-infected piglets using iTRAQ technology; our findings provide valuable information to better understand the mechanisms underlying the host responses to PCV3 infection in piglets. SIGNIFICANCE: Our study identified differentially abundant proteins related to a variety of potential signaling pathways in the lungs of PCV3-infected piglets. These findings provide valuable information to better understand the mechanisms of host responses to PCV3 infection. PMID: 31785380 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - November 27, 2019 Category: Biochemistry Authors: Jiang H, Wei L, Wang D, Wang J, Zhu S, She R, Liu T, Tian J, Quan R, Hou L, Li Z, Chu J, Zhou J, Guo Y, Xi Y, Song H, Yuan F, Liu J Tags: J Proteomics Source Type: research

Comparative analysis of iTRAQ-based proteome profiles of Schistosoma japonicum female worms coming from single-sex infections and bisexual infections.
In this study, isobaric tags for relative and absolute quantitation (iTRAQ)-coupled LC-MS/MS was used to explore the proteome of FSS and FMS of Schistosoma japonicum. A total of 1477 differentially expressed proteins (fold change>1.2, P 
Source: Journal of Proteomics - November 25, 2019 Category: Biochemistry Authors: Li X, Qiao H, Qin F, Cheng G, Liu J, Li H, Gu S, Jin Y Tags: J Proteomics Source Type: research

A meta-analysis of affinity purification-mass spectrometry experimental systems used to identify eukaryotic and chlamydial proteins at the Chlamydia trachomatis inclusion membrane.
This study provides important guidelines and considerations for using this methodology to study intracellular pathogens residing within a membrane-bound compartment. SIGNIFICANCE: Chlamydia trachomatis, an obligate intracellular pathogen, grows within a membrane-bound vacuole termed the inclusion. The inclusion is studded with bacterial membrane proteins that likely orchestrate numerous interactions with the host cell. Although maintenance of the intracellular niche is vital, an understanding of the host-pathogen interactions that occur at the inclusion membrane is limited by the difficulty in purifying membrane protein fr...
Source: Journal of Proteomics - November 21, 2019 Category: Biochemistry Authors: Olson MG, Ouellette SP, Rucks EA Tags: J Proteomics Source Type: research

Transcriptomic and proteomic approaches reveal biological basis of intraoperative radiotherapy-treated tumor bed modification in breast cancer patients: A pilot study.
This study designed to investigate short-term molecular effects of 12Gy as Boost versus 21Gy as Radical dose of IOeRT using high throughput approaches. MATERIALS AND METHODS: Six BC patients as a pilot study were treated with IOeRT following two separate strategies, including Boost and Radical doses. Approximately 100 mg of tumor bed tissue retrieved from each patient (before IOeRT,immediately, 24 h post-treatment). mRNA sequencing also Isobaric tag for relative and absolute quantitation (iTRAQ) were performed to study the transcriptome and proteome profile of IOeRT-treated tumor bed. RESULTS: Using NGS, ~6 G...
Source: Journal of Proteomics - November 20, 2019 Category: Biochemistry Authors: Shahani M, Shakeri J, Akbari ME, Arefnezhad B, Tafti A, Zali H, Nafisi N, Hashemi M, Rezaei-Tavirani M, Mohammadpour S, Salami SAR, Mirzai HR, Samsami M, Ezabady SHJ, Akbari A Tags: J Proteomics Source Type: research

Site- and structure-specific quantitative N-glycoproteomics study of differential N-glycosylation in MCF-7 cancer cells.
Abstract Glycosylation is a common protein PTM, and its aberrant regulation has been widely linked to various pathological conditions including cancers. Our recent development of intact N-glycopeptide search engine GPSeeker has enabled relatively quantitative structure-specific characterization of differentially expressed intact N-glycopeptides (DEGPs) with isotopic labeling of the peptide backbones and structure-specific fragment ions of the N-glycan moieties. Here we report our site- and structure-specific relatively quantitative N-glycoproteomics study of breast MCF-7 cancer cells (relative to epithelial MCF-10...
Source: Journal of Proteomics - November 20, 2019 Category: Biochemistry Authors: Xue B, Xiao K, Wang Y, Tian Z Tags: J Proteomics Source Type: research