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1.
Immunogenetics ; 71(8-9): 519-530, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31520135

RESUMO

Human CD4+ T lymphocytes play an important role in inducing potent immune responses. T cells are activated and stimulated by peptides presented in human leucocyte antigen (HLA)-class II molecules. These HLA-class II molecules typically present peptides of between 12 and 20 amino acids in length. The region that interacts with the HLA molecule, designated as the peptide-binding core, is highly conserved in the residues which anchor the peptide to the molecule. In addition, as these peptides are the product of proteolytic cleavages, certain conserved residues may be expected at the N- and C-termini outside the binding core. To study whether similar conserved residues are present in different cell types, potentially harbouring different proteolytic enzymes, the ligandomes of HLA-DRB1*03:01/HLA-DRB > 1 derived from two different cell types (dendritic cells and EBV-transformed B cells) were identified with mass spectrometry and the binding core and N- and C-terminal residues of a total of 16,568 peptides were analysed using the frequencies of the amino acids in the human proteome. Similar binding motifs were found as well as comparable conservations in the N- and C-terminal residues. Furthermore, the terminal conservations of these ligandomes were compared to the N- and C-terminal conservations of the ligandome acquired from dendritic cells homozygous for HLA-DRB1*04:01. Again, comparable conservations were evident with only minor differences. Taken together, these data show that there are conservations in the terminal residues of peptides, presumably the result of the activity of proteases involved in antigen processing.


Assuntos
Linfócitos B/metabolismo , Células Dendríticas/metabolismo , Antígenos HLA-DR/classificação , Antígenos HLA-DR/metabolismo , Fragmentos de Peptídeos/metabolismo , Proteoma/metabolismo , Motivos de Aminoácidos , Linfócitos B/citologia , Células Cultivadas , Células Dendríticas/citologia , Humanos , Ligantes , Ligação Proteica
2.
Vet Parasitol ; 272: 44-52, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31395204

RESUMO

In the present study, a quantitative proteomic approach to study changes in saliva proteins associated with canine leishmaniosis (CanL) was performed. For this, canine salivary proteins were analysed and compared between dogs before (T0) and after (T1) experimental infection with Leishmania infantum by high-throughput label-based quantitative LC-MS/MS proteomic approach and bioinformatic analysis of the in silico inferred interactome protein network was created from the initial list of differential proteins. More than 2000 proteins were identified, and of the 90 differentially expressed proteins between T0 and T1, 12 were down-regulated with log2 fold change lower than -0.5849, and 19 were up-regulated with log2 fold change greater than 0.5849. This study provides evidence of changes in salivary proteome that can occur in canine leishmaniosis and revealed biological pathways in saliva modulated in canine leishmaniosis with potential for further targeted research.


Assuntos
Doenças do Cão/fisiopatologia , Leishmaniose/veterinária , Saliva , Proteínas e Peptídeos Salivares/genética , Proteínas e Peptídeos Salivares/metabolismo , Animais , Cromatografia Líquida , Simulação por Computador , Cães , Regulação da Expressão Gênica , Leishmaniose/fisiopatologia , Proteoma/genética , Proteoma/metabolismo , Proteômica , Saliva/química , Saliva/metabolismo , Espectrometria de Massas em Tandem
3.
Sci Total Environ ; 687: 839-848, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31412487

RESUMO

The adverse effects of air pollution have been long studied in the lung and respiratory systems, but the molecular changes that this causes at the central nervous system level have yet to be fully investigated and understood. To explore the evolution with time of protein expression levels in the brain of rats exposed to particulate matter of different sizes, we carried out two-dimensional gel electrophoresis followed by determination of dysregulated proteins through Coomassie blue staining-based densities (SameSpots software) and subsequent protein identification using MALDI-based mass spectrometry. Expression differences in dysregulated proteins were found to be statistically significant with p-value <0.05. A systems biology-based approach was utilized to determine critical biochemical pathways involved in the rats' brain response. Our results suggest that rats' brains have a particulate matter size dependent-response, being the mitochondrial activity and the astrocyte function severely affected. Our proteomic study confirms the dysregulation of different biochemical pathways involving energy metabolism, mitochondrial activity, and oxidative pathways as some of the main effects of PM exposure on the rat brain. SIGNIFICANCE: Rat brains exposed to particulate matter with origin in car engines are affected in two main areas: mitochondrial activity, by the dysregulation of many pathways linked to the respiratory chain, and neuronal and astrocytic function, which stimulates brain changes triggering tumorigenesis and neurodegeneration.


Assuntos
Poluentes Atmosféricos/toxicidade , Encéfalo/metabolismo , Material Particulado/toxicidade , Proteoma/metabolismo , Poluição do Ar/estatística & dados numéricos , Animais , Metabolismo Energético/efeitos dos fármacos , Masculino , Estresse Oxidativo/fisiologia , Proteômica , Ratos
4.
Clin Exp Rheumatol ; 37 Suppl 118(3): 240-248, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31464680

RESUMO

In the era of personalised medicine new biomarkers are required to early diagnose Sjögren's syndrome (SS), to define different disease subsets and to direct patients' clinical management and therapeutic intervention. In the last few years, several efforts have evaluated saliva proteome to detect and monitor primary SS. Although clinically valuable, these studies presented some limitations that have partially prevented the use of salivary biomarkers in clinical practice. Nowadays, proteomic of extracellular vesicle (EV) represents an emerging and promising field in the discovery of -omic biomarkers for pSS. EV is a relatively new term that includes exosomes, microvesicles and apoptotic body. EVs are packed with proteins, growth factors, cytokines, bioactive lipids, but also nucleic acids and in particular: mRNA, microRNA, long non-coding RNA, tRNA and rRNA. Therefore, they may represent a useful source for diagnostic, prognostic and therapeutic biomarkers in several conditions. In this review we will specifically focus on EV proteomics as a tool for the identification of novel biomarkers for pSS. In the first part we focused on the state of the art of the studies on proteomics in SS existing in the literature. In the second part we provided a definition of EV with an update on biological sample collection and processing for EV proteomic studies. Finally, we summarised the state of the art of EV -omics in SS highlighting the potential advantages of this novel approach compared to the overall traditional concept of analysing the proteome of blood or saliva.


Assuntos
Vesículas Extracelulares , Proteômica/métodos , Síndrome de Sjogren , Biomarcadores/metabolismo , Vesículas Extracelulares/metabolismo , Humanos , Proteoma/metabolismo , Saliva/metabolismo , Síndrome de Sjogren/metabolismo
5.
Nat Commun ; 10(1): 3035, 2019 07 10.
Artigo em Inglês | MEDLINE | ID: mdl-31292443

RESUMO

Mycobacterium tuberculosis readily adapts to survive a wide range of assaults by modifying its physiology and establishing a latent tuberculosis (TB) infection. Here we report a sophisticated mode of regulation by a tRNA-cleaving toxin that enlists highly selective ribosome stalling to recalibrate the transcriptome and remodel the proteome. This toxin, MazF-mt9, exclusively inactivates one isoacceptor tRNA, tRNALys43-UUU, through cleavage at a single site within its anticodon (UU↓U). Because wobble rules preclude compensation for loss of tRNALys43-UUU by the second M. tuberculosis lysine tRNA, tRNALys19-CUU, ribosome stalling occurs at in-frame cognate AAA Lys codons. Consequently, the transcripts harboring these stalled ribosomes are selectively cleaved by specific RNases, leading to their preferential deletion. This surgically altered transcriptome generates concomitant changes to the proteome, skewing synthesis of newly synthesized proteins away from those rich in AAA Lys codons toward those harboring few or no AAA codons. This toxin-mediated proteome reprogramming may work in tandem with other pathways to facilitate M. tuberculosis stress survival.


Assuntos
Proteínas de Bactérias/metabolismo , Endorribonucleases/metabolismo , Mycobacterium tuberculosis/fisiologia , Proteoma/genética , Ribossomos/metabolismo , Sistemas Toxina-Antitoxina/fisiologia , Toxinas Bacterianas/metabolismo , Tuberculose Latente/microbiologia , Mycobacterium tuberculosis/patogenicidade , Proteoma/metabolismo , RNA Bacteriano/metabolismo , RNA de Transferência/metabolismo , Transcriptoma/genética
6.
Chemistry ; 25(54): 12644-12651, 2019 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-31310394

RESUMO

The illudin natural product family are fungal secondary metabolites with a characteristic spirocyclopropyl-substituted fused 6,5-bicyclic ring system. They have been extensively studied for their cytotoxicity in various tumor cell types, and semisynthetic derivatives with improved therapeutic characteristics have progressed to clinical trials. Although it is believed that this potent alkylating compound class acts mainly through DNA modification, little is known about its binding to protein sites in a cellular context. To reveal putative protein targets of the illudin family in live cancer cells, we employed a semisynthetic strategy to access a series of illudin-based probes for activity-based protein profiling (ABPP). While the probes largely retained potent cytotoxicity, proteomic profiling studies unraveled multiple protein hits, suggesting that illudins exert their mode of action not from addressing a specific protein target but rather from DNA modification and unselective protein binding.


Assuntos
Proteínas/química , Proteoma/química , Sesquiterpenos/farmacologia , Compostos de Espiro/farmacologia , Células A549 , Alquilação , Antineoplásicos/química , Antineoplásicos/farmacologia , Sítios de Ligação , Sobrevivência Celular , Humanos , Ligação Proteica , Proteínas/metabolismo , Proteoma/metabolismo , Metabolismo Secundário , Sesquiterpenos/química , Compostos de Espiro/química
7.
BMC Bioinformatics ; 20(1): 398, 2019 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-31315557

RESUMO

BACKGROUND: Utilization of quantitative proteomics data on the network level is still a challenge in proteomics data analysis. Currently existing models use sophisticated, sometimes hard to implement analysis techniques. Our aim was to generate a relatively simple strategy for quantitative proteomics data analysis in order to utilize as much of the data generated in a proteomics experiment as possible. RESULTS: In this study, we applied label-free proteomics, and generated a network model utilizing both qualitative, and quantitative data, in order to examine the early host response to Human Immunodeficiency Virus type 1 (HIV-1). A weighted network model was generated based on the amount of proteins measured by mass spectrometry, and analysis of weighted networks and functional sub-networks revealed upregulation of proteins involved in translation, transcription, and DNA condensation in the early phase of the viral life-cycle. CONCLUSION: A relatively simple strategy for network analysis was created and applied to examine the effect of HIV-1 on host cellular proteome. We believe that our model may prove beneficial in creating algorithms, allowing for both quantitative and qualitative studies of proteome change in various biological and pathological processes by quantitative mass spectrometry.


Assuntos
HIV-1/fisiologia , Proteômica/métodos , HIV-1/genética , Humanos , Espectrometria de Massas , Mapeamento de Interação de Proteínas , Proteoma/metabolismo , Transdução Genética
8.
Aquat Toxicol ; 214: 105244, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31352074

RESUMO

High-throughput proteomics can be performed on animal sentinels for discovering key molecular biomarkers signing the physiological response and adaptation of organisms. Ecotoxicoproteomics is today amenable by means of proteogenomics to small arthropods such as Gammarids which are well known sentinels of aquatic environments. Here, we analysed two regional Gammarus pulex populations to characterize the potential proteome divergence induced in one site by natural bioavailable mono-metallic contamination (cadmium) compared to a non-contaminated site. Two RNAseq-derived protein sequence databases were established previously on male and female individuals sampled from the reference site. Here, individual proteomes were acquired on 10 male and 10 female paired organisms sampled from each site. Proteins involved in protein lipidation, carbohydrate metabolism, proteolysis, innate immunity, oxidative stress response and lipid transport were found more abundant in animals exposed to cadmium, while hemocyanins were found in lower abundance. The intrapopulation proteome variability of long-term exposed G. pulex was inflated relatively to the non-contaminated population. These results show that, while remaining a challenge for such organisms with not yet sequenced genomes, taking into account intrapopulation variability is important to better define the molecular players induced by toxic stress in a comparative field proteomics approach.


Assuntos
Anfípodes/metabolismo , Cádmio/toxicidade , Proteoma/metabolismo , Proteômica , Anfípodes/efeitos dos fármacos , Animais , Análise por Conglomerados , Feminino , Masculino , Análise de Componente Principal , Poluentes Químicos da Água/toxicidade
9.
BMC Genomics ; 20(Suppl 7): 535, 2019 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-31291891

RESUMO

BACKGROUND: Purpose of study is revealing significant differences in serum proteomes in schizophrenia and bipolar disorder (BD). RESULTS: Quantitative mass-spectrometry based proteomic analysis was used to quantify proteins in the blood serum samples after the depletion of six major blood proteins. Comparison of proteome profiles of different groups revealed 27 proteins being specific for schizophrenia, and 18 - for BD. Protein set in schizophrenia was mostly associated with immune response, cell communication, cell growth and maintenance, protein metabolism and regulation of nucleic acid metabolism. Protein set in BD was mostly associated with immune response, regulating transport processes across cell membrane and cell communication, development of neurons and oligodendrocytes and cell growth. Concentrations of ankyrin repeat domain-containing protein 12 (ANKRD12) and cadherin 5 in serum samples were determined by ELISA. Significant difference between three groups was revealed in ANKRD12 concentration (p = 0.02), with maximum elevation of ANKRD12 concentration (median level) in schizophrenia followed by BD. Cadherin 5 concentration differed significantly (p = 0.035) between schizophrenic patients with prevailing positive symptoms (4.78 [2.71, 7.12] ng/ml) and those with prevailing negative symptoms (1.86 [0.001, 4.11] ng/ml). CONCLUSIONS: Our results are presumably useful for discovering the new pathways involved in endogenous psychotic disorders.


Assuntos
Transtorno Bipolar/metabolismo , Proteoma/metabolismo , Esquizofrenia/metabolismo , Adulto , Antígenos CD/metabolismo , Caderinas/metabolismo , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Proteínas Nucleares/metabolismo , Adulto Jovem
10.
Environ Pollut ; 252(Pt A): 427-439, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31158671

RESUMO

Natural environments are receiving an increasing number of contaminants. Therefore, the evaluation and identification of early responses to pollution in these complex habitats is an urgent and challenging task. Doñana National Park (DNP, SW Spain) has been widely used as a model area for environmental studies because, despite its strictly protected core, it is surrounded by numerous threat sources from agricultural, mining and industrial activities. Since many pollutants often induce oxidative stress, redox proteomics was used to detect redox-based variations within the proteome of Mus spretus mice captured in DNP and the surrounding areas. Functional analysis showed that most differentially oxidized proteins are involved in the maintenance of homeostasis, by eliciting mechanisms to respond to toxic substances and oxidative stress, such as antioxidant and biotransformation processes, immune and inflammatory responses, and blood coagulation. Furthermore, changes in the overall protein abundance were also analysed by label-free quantitative proteomics. The upregulation of phase I and II biotransformation enzymes in mice from Lucio del Palacio may be an alert for organic pollution in the area located at the heart of DNP. Metabolic processes involved in protein turnover (proteolysis, amino acid catabolism, new protein biosynthesis and folding) were activated in response to oxidative damage to these biomolecules. Consequently, aerobic respiratory metabolism increased to address the greater ATP demands. Alterations of cholesterol metabolism that could cause hepatic steatosis were also detected. The proteomic detection of globally altered metabolic and physiological processes offers a complete view of the main biological changes caused by environmental pollution in complex habitats.


Assuntos
Monitoramento Ambiental/métodos , Poluentes Ambientais/toxicidade , Substâncias Perigosas/toxicidade , Estresse Oxidativo/efeitos dos fármacos , Parques Recreativos , Proteoma/metabolismo , Animais , Antioxidantes/metabolismo , Biomarcadores Ambientais/efeitos dos fármacos , Camundongos , Mineração , Oxirredução , Proteômica , Espanha
11.
J Sci Food Agric ; 99(13): 5760-5770, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31162844

RESUMO

BACKGROUND: It has been reported that antagonistic microorganisms could effectively control the infection of Fusarium graminearum. However, there is limited information on the control of F. graminearum by Saccharomyces cerevisiae, while the possible control mechanisms involved through proteomic and transcriptomic techniques have also not been reported. RESULTS: The results of this study showed that S. cerevisiae Y-912 could significantly inhibit the growth of F. graminearum Fg1, and the spore germination rate and germ tube length of F. graminearum Fg1 were also significantly inhibited by S. cerevisiae Y-912. Proteomic analysis revealed that differentially expressed proteins which were made of some basic proteins and enzymes related to basal metabolism, such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate mutase (PGAM), enolase (ENO), fructose diphosphate aldolase (FBA) and so on, were all down-regulated. The transcriptomics of F. graminearum control by S. cerevisiae was also analyzed. CONCLUSION: The control mechanism of S. cerevisiae Y-912 on F. graminearum Fg1 was a very complex material and energy metabolic process in which the related proteins and genes involved in the glycolytic pathway, tricarboxylic acid (TCA) cycle and amino acid metabolism were all down-regulated. © 2019 Society of Chemical Industry.


Assuntos
Fusarium/genética , Saccharomyces cerevisiae/genética , Transcriptoma , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Fusarium/crescimento & desenvolvimento , Fusarium/metabolismo , Proteoma/genética , Proteoma/metabolismo , Saccharomyces cerevisiae/crescimento & desenvolvimento , Saccharomyces cerevisiae/metabolismo , Esporos Fúngicos/genética , Esporos Fúngicos/crescimento & desenvolvimento , Esporos Fúngicos/metabolismo
12.
Ecotoxicol Environ Saf ; 180: 780-788, 2019 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-31154203

RESUMO

Cadmium (Cd) is one of the most toxic heavy metals, and its accumulation in plants will seriously affect growth and yield. In this study, Cd-sensitive line D69 and Cd-tolerant line D28 were selected, which the Cd content of D28 was higher than D69 in both above and underground parts after Cd treatment. Using a combination of two-dimensional gel electrophoresis (2-DE) and MALDI-TOF-TOF MS/MS, the differential expression changes of phosphorylated proteins between D69 and D28 in leaves were classified and analyzed after Cd treatment. A total of 53 differentially expressed phosphoproteins were identified, which mainly involved in metabolism, signal transduction, gene expression regulation, material transport, and membrane fusion. The phosphorylated proteins of Cd-tolerant and Cd-sensitive lines were all analyzed, and found that some proteins associated with carbon metabolism, proteolytic enzymes, F-box containing transcription factors, RNA helicases, DNA replication/transcription/repair enzymes and ankyrins were detected in Cd-tolerant line D28, which might alleviate the abiotic stress caused by Cd treatment. These results will clarify the phosphorylated pathways in response and resistance to Cd stress in rice.


Assuntos
Cádmio/toxicidade , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Proteoma/metabolismo , Estresse Fisiológico/efeitos dos fármacos , Oryza/genética , Oryza/fisiologia , Fosforilação , Folhas de Planta/metabolismo , Folhas de Planta/fisiologia , Poluentes do Solo/toxicidade
13.
Plant Cell Physiol ; 60(8): 1811-1828, 2019 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-31179502

RESUMO

Diatoms are unicellular algae and evolved by secondary endosymbiosis, a process in which a red alga-like eukaryote was engulfed by a heterotrophic eukaryotic cell. This gave rise to plastids of remarkable complex architecture and ultrastructure that require elaborate protein importing, trafficking, signaling and intracellular cross-talk pathways. Studying both plastids and mitochondria and their distinctive physiological pathways in organello may greatly contribute to our understanding of photosynthesis, mitochondrial respiration and diatom evolution. The isolation of such complex organelles, however, is still demanding, and existing protocols are either limited to a few species (for plastids) or have not been reported for diatoms so far (for mitochondria). In this work, we present the first isolation protocol for mitochondria from the model diatom Thalassiosira pseudonana. Apart from that, we extended the protocol so that it is also applicable for the purification of a high-quality plastids fraction, and provide detailed structural and physiological characterizations of the resulting organelles. Isolated mitochondria were structurally intact, showed clear evidence of mitochondrial respiration, but the fractions still contained residual cell fragments. In contrast, plastid isolates were virtually free of cellular contaminants, featured structurally preserved thylakoids performing electron transport, but lost most of their stromal components as concluded from Western blots and mass spectrometry. Liquid chromatography electrospray-ionization mass spectrometry studies on mitochondria and thylakoids, moreover, allowed detailed proteome analyses which resulted in extensive proteome maps for both plastids and mitochondria thus helping us to broaden our understanding of organelle metabolism and functionality in diatoms.


Assuntos
Diatomáceas/metabolismo , Mitocôndrias/metabolismo , Plastídeos/metabolismo , Proteoma/metabolismo , Tilacoides/metabolismo
14.
BMC Plant Biol ; 19(1): 280, 2019 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-31242871

RESUMO

BACKGROUND: The xylem sap of vascular plants primarily transports water and mineral nutrients from the roots to the shoots and also transports heavy metals such as cadmium (Cd). Proteomic changes in xylem sap is an important mechanism for detoxifying Cd by plants. However, it is unclear how proteins in xylem sap respond to Cd. Here, we investigated the effects of Cd stress on the xylem sap proteome of Brassica napus using a label-free shotgun proteomic approach to elucidate plant response mechanisms to Cd toxicity. RESULTS: We identified and quantified 672 proteins; 67% were predicted to be secretory, and 11% (73 proteins) were unique to Cd-treated samples. Cd stress caused statistically significant and biologically relevant abundance changes in 28 xylem sap proteins. Among these proteins, the metabolic pathways that were most affected were related to cell wall modifications, stress/oxidoreductases, and lipid and protein metabolism. We functionally validated a plant defensin-like protein, BnPDFL, which belongs to the stress/oxidoreductase category, that was unique to the Cd-treated samples and played a positive role in Cd tolerance. Subcellular localization analysis revealed that BnPDFL is cell wall-localized. In vitro Cd-binding assays revealed that BnPDFL has Cd-chelating activity. BnPDFL heterologous overexpression significantly enhanced Cd tolerance in E. coli and Arabidopsis. Functional disruption of Arabidopsis plant defensin genes AtPDF2.3 and AtPDF2.2, which are mainly expressed in root vascular bundles, significantly decreased Cd tolerance. CONCLUSIONS: Several xylem sap proteins in Brassica napus are differentially induced in response to Cd treatment, and plant defensin plays a positive role in Cd tolerance.


Assuntos
Brassica napus/genética , Cádmio/efeitos adversos , Proteoma/efeitos dos fármacos , Poluentes do Solo/efeitos adversos , Xilema/fisiologia , Brassica napus/efeitos dos fármacos , Brassica napus/metabolismo , Proteoma/genética , Proteoma/metabolismo , Xilema/efeitos dos fármacos
15.
Environ Sci Pollut Res Int ; 26(22): 22529-22550, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31161543

RESUMO

Widespread application of silver nanoparticles (AgNPs), due to their antibacterial and antifungal properties, increases their release into the environment and potential detrimental impact on living organisms. Plants may serve as a potential pathway for AgNPs bioaccumulation and a route into the food chain, hence investigation of AgNP phytotoxic effects are of particular importance. Since proteins are directly involved in stress response, studies of their abundance changes can help elucidate the mechanism of the AgNP-mediated phytotoxicity. In this study, we investigated proteomic changes in tobacco (Nicotiana tabacum) exposed to AgNPs and ionic silver (AgNO3). A high overlap of differently abundant proteins was found in root after exposure to both treatments, while in leaf, almost a half of the proteins exhibited different abundance level between treatments, indicating tissue-specific responses. Majority of the identified proteins were down-regulated in both tissues after exposure to either AgNPs or AgNO3; in roots, the most affected proteins were those involved in response to abiotic and biotic stimuli and oxidative stress, while in leaf, both treatments had the most prominent effect on photosynthesis-related proteins. However, since AgNPs induced higher suppression of protein abundance than AgNO3, we conclude that AgNP effects can, at least partially, be attributed to nanoparticle form.


Assuntos
Nanopartículas Metálicas/toxicidade , Prata/toxicidade , Tabaco/fisiologia , Íons , Estresse Oxidativo/efeitos dos fármacos , Folhas de Planta/metabolismo , Proteoma/metabolismo , Proteômica , Nitrato de Prata/toxicidade , Tabaco/metabolismo
16.
PLoS Negl Trop Dis ; 13(5): e0007416, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31125353

RESUMO

BACKGROUND: Salmonella enterica subsp. enterica contains more than 2,600 serovars of which four are of major medical relevance for humans. While the typhoidal serovars (Typhi and Paratyphi A) are human-restricted and cause enteric fever, non-typhoidal Salmonella serovars (Typhimurium and Enteritidis) have a broad host range and predominantly cause gastroenteritis. METHODOLOGY/PRINCIPLE FINDINGS: We compared the core proteomes of Salmonella Typhi, Paratyphi A, Typhimurium and Enteritidis using contemporary proteomics. For each serovar, five clinical isolates (covering different geographical origins) and one reference strain were grown in vitro to the exponential phase. Levels of orthologous proteins quantified in all four serovars and within the typhoidal and non-typhoidal groups were compared and subjected to gene ontology term enrichment and inferred regulatory interactions. Differential expression of the core proteomes of the typhoidal serovars appears mainly related to cell surface components and, for the non-typhoidal serovars, to pathogenicity. CONCLUSIONS/SIGNIFICANCE: Our comparative proteome analysis indicated differences in the expression of surface proteins between Salmonella Typhi and Paratyphi A, and in pathogenesis-related proteins between Salmonella Typhimurium and Enteritidis. Our findings may guide future development of novel diagnostics and vaccines, as well as understanding of disease progression.


Assuntos
Proteínas de Bactérias/genética , Proteoma/genética , Infecções por Salmonella/microbiologia , Salmonella enterica/genética , Salmonella paratyphi A/genética , Salmonella typhi/genética , Salmonella typhimurium/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Humanos , Proteoma/metabolismo , Salmonella enterica/metabolismo , Salmonella enterica/patogenicidade , Salmonella paratyphi A/metabolismo , Salmonella paratyphi A/patogenicidade , Salmonella typhi/metabolismo , Salmonella typhi/patogenicidade , Salmonella typhimurium/metabolismo , Salmonella typhimurium/patogenicidade , Virulência
17.
PLoS Negl Trop Dis ; 13(5): e0007362, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31091291

RESUMO

BACKGROUND: Schistosomiasis is a neglected disease affecting hundreds of millions worldwide. Of the three main species affecting humans, Schistosoma haematobium is the most common, and is the leading cause of urogenital schistosomiasis. S. haematobium infection can cause different urogenital clinical complications, particularly in the bladder, and furthermore, this parasite has been strongly linked with squamous cell carcinoma. A comprehensive analysis of the molecular composition of its different proteomes will contribute to developing new tools against this devastating disease. METHODS AND FINDINGS: By combining a comprehensive protein fractionation approach consisting of OFFGEL electrophoresis with high-throughput mass spectrometry, we have performed the first in-depth characterisation of the different discrete proteomes of S. haematobium that are predicted to interact with human host tissues, including the secreted and tegumental proteomes of adult flukes and secreted and soluble egg proteomes. A total of 662, 239, 210 and 138 proteins were found in the adult tegument, adult secreted, soluble egg and secreted egg proteomes, respectively. In addition, we probed these distinct proteomes with urine to assess urinary antibody responses from naturally infected human subjects with different infection intensities, and identified adult fluke secreted and tegument extracts as being the best predictors of infection. CONCLUSION: We provide a comprehensive dataset of proteins from the adult and egg stages of S. haematobium and highlight their utility as diagnostic markers of infection intensity. Protein composition was markedly different between the different extracts, highlighting the distinct subsets of proteins that different development stages present in their different niches. Furthermore, we have identified adult fluke ES and tegument extracts as best predictors of infection using urine antibodies of naturally infected people. This study provides the first steps towards the development of novel tools to control this important neglected tropical disease.


Assuntos
Proteínas de Helminto/metabolismo , Proteoma/metabolismo , Schistosoma haematobium/metabolismo , Esquistossomose Urinária/parasitologia , Animais , Feminino , Proteínas de Helminto/química , Proteínas de Helminto/genética , Humanos , Masculino , Proteoma/química , Proteoma/genética , Proteômica , Schistosoma haematobium/química , Schistosoma haematobium/classificação , Schistosoma haematobium/genética
18.
Nature ; 570(7759): 117-121, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31068692

RESUMO

Aneuploidy, which refers to unbalanced chromosome numbers, represents a class of genetic variation that is associated with cancer, birth defects and eukaryotic micro-organisms1-4. Whereas it is known that each aneuploid chromosome stoichiometry can give rise to a distinct pattern of gene expression and phenotypic profile4,5, it remains a fundamental question as to whether there are common cellular defects that are associated with aneuploidy. Here we show the existence in budding yeast of a common aneuploidy gene-expression signature that is suggestive of hypo-osmotic stress, using a strategy that enables the observation of common transcriptome changes of aneuploidy by averaging out karyotype-specific dosage effects in aneuploid yeast-cell populations with random and diverse chromosome stoichiometry. Consistently, aneuploid yeast exhibited increased plasma-membrane stress that led to impaired endocytosis, and this defect was also observed in aneuploid human cells. Thermodynamic modelling showed that hypo-osmotic-like stress is a general outcome of the proteome imbalance that is caused by aneuploidy, and also predicted a relationship between ploidy and cell size that was observed in yeast and aneuploid cancer cells. A genome-wide screen uncovered a general dependency of aneuploid cells on a pathway of ubiquitin-mediated endocytic recycling of nutrient transporters. Loss of this pathway, coupled with the endocytic defect inherent to aneuploidy, leads to a marked alteration of intracellular nutrient homeostasis.


Assuntos
Aneuploidia , Pressão Osmótica , Proteoma/genética , Proteoma/metabolismo , Saccharomyces cerevisiae/citologia , Saccharomyces cerevisiae/genética , Estresse Fisiológico , Membrana Celular/metabolismo , Membrana Celular/patologia , Proteínas de Ligação a DNA/metabolismo , Endocitose , Complexos Endossomais de Distribuição Requeridos para Transporte/metabolismo , Homeostase , Humanos , Cariótipo , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Termodinâmica , Fatores de Transcrição/metabolismo , Transcriptoma/genética , Ubiquitina/metabolismo , Complexos Ubiquitina-Proteína Ligase/metabolismo
19.
Microb Cell Fact ; 18(1): 93, 2019 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-31138236

RESUMO

BACKGROUND: Polyhydroxyalkanoates (PHAs) have attracted much attention in recent years as natural alternatives to petroleum-based synthetic polymers that can be broadly used in many applications. Pseudomonas putida KT2440 is a metabolically versatile microorganism that is able to synthesize medium-chain-length PHAs (mcl-PHAs). The phenomena that drive mcl-PHAs synthesis and accumulation seems to be complex and are still poorly understood. Therefore, here we determine new insights into cellular responses of Pseudomonas putida KT2440 during biopolymers production using two-dimensional difference gel-electrophoresis (2D-DIGE) followed by MALDI TOF/TOF mass spectrometry. RESULTS: The maximum mcl-PHAs content in Pseudomonas putida KT2440 cells was 24% of cell dry weight (CDW) and was triggered by nitrogen depletion. Proteomic analysis allowed the detection of 150 and 131 protein spots differentially regulated at 24 h and 48 h relative to the cell growth stage (8 h), respectively. From those, we successfully identified 84 proteins that had altered expression at 24 h and 74 proteins at 48 h of the mcl-PHAs synthesis process. The protein-protein interactions network indicated that the majority of identified proteins were functionally linkage. The abundance of proteins involved in carbon metabolism were significantly decreased at 24 h and 48 h of the cultivations. Moreover, proteins associated with ATP synthesis were up-regulated suggesting that the enhanced energy metabolism was necessary for the mcl-PHAs accumulation. Furthermore, the induction of proteins involved in nitrogen metabolism, ribosome synthesis and transport was observed. Our results indicate that mcl-PHAs accumulated in the bacterial cells changed the protein abundance involved in stress response and cellular homeostasis. CONCLUSIONS: The presented data allow us to investigate time-course proteome rearrangement in response to nitrogen limitation and biopolyesters accumulation. Our results have pointed out novel proteins that might take part in cellular responses of mcl-PHA-accumulated bacteria. The study provides an additional knowledge that could be helpful to improve the efficiency of the bioprocess and make it more economically feasible.


Assuntos
Proteínas de Bactérias/metabolismo , Poli-Hidroxialcanoatos/biossíntese , Proteoma/metabolismo , Pseudomonas putida/metabolismo , Carbono/metabolismo , Homeostase , Nitrogênio/metabolismo , Poliésteres/metabolismo , Proteômica/métodos , Estresse Fisiológico , Eletroforese em Gel Diferencial Bidimensional/métodos
20.
BMC Bioinformatics ; 20(1): 270, 2019 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-31138107

RESUMO

BACKGROUND: Immunotherapy is an emerging approach in cancer treatment that activates the host immune system to destroy cancer cells expressing unique peptide signatures (neoepitopes). Administrations of cancer-specific neoepitopes in the form of synthetic peptide vaccine have been proven effective in both mouse models and human patients. Because only a tiny fraction of cancer-specific neoepitopes actually elicits immune response, selection of potent, immunogenic neoepitopes remains a challenging step in cancer vaccine development. A basic approach for immunogenicity prediction is based on the premise that effective neoepitope should bind with the Major Histocompatibility Complex (MHC) with high affinity. RESULTS: In this study, we developed MHCSeqNet, an open-source deep learning model, which not only outperforms state-of-the-art predictors on both MHC binding affinity and MHC ligand peptidome datasets but also exhibits promising generalization to unseen MHC class I alleles. MHCSeqNet employed neural network architectures developed for natural language processing to model amino acid sequence representations of MHC allele and epitope peptide as sentences with amino acids as individual words. This consideration allows MHCSeqNet to accept new MHC alleles as well as peptides of any length. CONCLUSIONS: The improved performance and the flexibility offered by MHCSeqNet should make it a valuable tool for screening effective neoepitopes in cancer vaccine development.


Assuntos
Antígenos de Histocompatibilidade Classe I/metabolismo , Modelos Biológicos , Redes Neurais (Computação) , Software , Alelos , Animais , Área Sob a Curva , Bases de Dados de Proteínas , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Camundongos , Peptídeos/química , Peptídeos/metabolismo , Ligação Proteica , Proteoma/metabolismo
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