Breast cancer is the most prevalent cancer in women worldwide. Its molecular subtypes are based on the presence/absence of estrogen receptor (ER), progesterone receptor (PR), and human epidermal ...growth factor receptor 2 (HER2). MACL‐1 and MGSO‐3 are cell lines derived from primary tumor sites of patients diagnosed with luminal A subtype carcinoma (ER+/PR+/HER2−) and ductal carcinoma in situ (ER−/PR−/HER2+), respectively. However, these cell lines lost the expression of these markers over cell culturing, and both have triple‐negative phenotypes (ER−/PR−/HER2−), which has the poorest prognosis. Here, we sought to study the proteome signature of MGSO‐3 and MACL‐1, comparing them with the epithelial cell line MCF‐10A and the well‐established metastatic‐derived breast cancer cell line MDA‐MB‐231. Our results showed that proteins associated with the tricarboxylic acid cycle (TCA) and oxidative phosphorylation (OXPHOS) were upregulated in MGSO‐3 and MACL‐1 cells. These cell lines also showed upregulation of pro‐apoptotic proteins when compared with MDA‐MB‐231. The molecular differences highlighted in this study may clarify the molecular basis behind cancer cells functioning and may reveal novel signatures across the breast cancer cell models.
•The review presents the main proteomic approaches used to study filamentous fungi secretomes.•Data on the secretomes from Trichoderma and Aspergillus species is presented.•Perspectives on fungi ...secretome analysis are discussed.
Filamentous fungal secretomes comprise highly dynamic sets of proteins, including multiple carbohydrate active enzymes (CAZymes) which are able to hydrolyze plant biomass polysaccharides into products of biotechnological interest such as fermentable sugars. In recent years, proteomics has been used to identify and quantify enzymatic and non-enzymatic polypeptides present in secretomes of several fungi species. The resulting data have widened the scientific understanding of the way filamentous fungi perform biomass degradation and offered novel perspectives for biotechnological applications. The present review discusses proteomics approaches that have been applied to the study of fungal secretomes, focusing on two of the most studied filamentous fungi genera: Trichoderma and Aspergillus.
Sphingobium yanoikuyae S72 was isolated from the rhizosphere of sorghum plant in Mexico and we evaluated its survival and role in the degradation of some selected monoaromatic hydrocarbons and ...polycyclic aromatic hydrocarbons (PAHs) using minimal medium (Bushnell Hass medium (BH)) in which each of the hydrocarbons (naphthalene, phenanthrene, xylene, toluene, and biphenyl) served as sole carbon source. Gas column chromatography–mass spectrometry analysis was used to evaluate the effect of S72’s growth in the medium with the hydrocarbons. The genome of the S72 was sequenced to determine the genetic basis for the degradation of the selected hydrocarbon in S72. The genome was assembled de novo with Spades assembler and Velvet assembler and the obtained contigs were reduced to 1 manually using Consed software. Genome annotation was carried out Prokka version 1.12, and gene calling and further annotation was carried out with NCBI PGAAP. Pangenome analysis and COG annotation were done with bacteria pangenome analysis tool (BPGA) and with PATRIC online server, respectively. S72 grew effectively in the culture medium with the hydrocarbon with concentration ranging from 20–100 mg/mL for each hydrocarbon tested. S72 degraded biphenyl by 85%, phenanthrene by 93%, naphthalene by 81%, xylene by 19%, and toluene by 30%. The sequenced S72 genome was reduced to 1 contig and genome analysis revealed the presence of genes essential for the degradation of hydrocarbons in S72. A total of 126 unique genes in S72 are associated with the degradation of hydrocarbons and xenobiotics. S72 grew effectively in the tested hydrocarbon and shows good degradation efficiency. S72 will therefore be a good candidate for bioremediation of hydrocarbon contaminated soil.
In this novel large-scale multiplexed immunofluorescence study we comprehensively characterized and compared layer-specific proteomic features within regions of interest of the widely divergent ...dorsolateral prefrontal cortex (A46) and primary visual cortex (A17) of adult rhesus monkeys. Twenty-eight markers were imaged in rounds of sequential staining, and their spatial distribution precisely quantified within gray matter layers and superficial white matter. Cells were classified as neurons, astrocytes, oligodendrocytes, microglia, or endothelial cells. The distribution of fibers and blood vessels were assessed by quantification of staining intensity across regions of interest. This method revealed multivariate similarities and differences between layers and areas. Protein expression in neurons was the strongest determinant of both laminar and regional differences, whereas protein expression in glia was more important for intra-areal laminar distinctions. Among specific results, we observed a lower glia-to-neuron ratio in A17 than in A46 and the pan-neuronal markers HuD and NeuN were differentially distributed in both brain areas with a lower intensity of NeuN in layers 4 and 5 of A17 compared to A46 and other A17 layers. Astrocytes and oligodendrocytes exhibited distinct marker-specific laminar distributions that differed between regions; notably, there was a high proportion of ALDH1L1-expressing astrocytes and of oligodendrocyte markers in layer 4 of A17. The many nuanced differences in protein expression between layers and regions observed here highlight the need for direct assessment of proteins, in addition to RNA expression, and set the stage for future protein-focused studies of these and other brain regions in normal and pathological conditions.
Purpose
Although the pathophysiological response of cardiac tissue to pro‐hypertrophic stimulus is well characterized, a comprehensive characterization of the molecular events underlying the ...pathological hypertrophy in cardiomyocytes during the early compensated cardiac hypertrophy is currently lacking.
Experimental design
A quantitative label‐free proteomic analysis of cardiomyocytes isolated was conducted from mice treated subcutaneously with isoproterenol (ISO) during 7 days in comparison with cardiomyocytes from control animals (CT).
Results
Canonical pathway analysis of dysregulated proteins indicated that ISO‐hypertrophy drives the activation of actin cytoskeleton and integrin‐linked kinase (ILK) signaling, and inhibition of the sirtuin signaling. Alteration in cardiac contractile function and calcium signaling are predicted as downstream effects of ISO‐hypertrophy probably due to the upregulation of key elements such as myosin‐7 (MYH7). Confocal microscopy corroborated that indeed ISO‐treatment led to increased abundance of MYH7. Potential early markers for cardiac hypertrophy as APBB1, GOLGA4, HOOK1, KATNA1, KIFBP, MAN2B2, and SLC16A1 are also reported.
Conclusions and clinical relevance
The data consist in a complete molecular mapping of ISO‐induced compensated cardiac hypertrophy model at cardiomyocyte level. Marker candidates reported may assist early diagnosis of cardiac hypertrophy and ultimately heart failure.
The Stenopelmatus talpa species-group (Stenopelmatidae) comprises cricket-like orthopterans distributed across the Trans-Mexican Volcanic Belt (TMVB) morphotectonic province and adjacent areas in ...central Mexico. Despite recent efforts, the taxonomy and evolutionary relationships for members of this complex still are far from completely known. Here we generated and characterized the mitochondrial (mt) genome of 14 specimens of the S. talpa species-group and evaluated its species limits with the cox1 barcoding locus. Moreover, based on the mt genome DNA sequence data, we also reconstructed its phylogenetic relationships and made inferences about its biogeographic history based on a relaxed molecular clock analysis. A total of 9 species were delimited using a 2% pairwise distance criterion, which were consistent with our best estimate of phylogeny. The relationships recovered for the S. talpa species-group were similar although with more recent divergence time estimates than those obtained in a previous phylogenetic study, suggesting that its origin and subsequent diversification in the TMVB followed an east-central pattern, with its earliest divergence occurring during the late Pliocene to early Pleistocene.
Unveiling the Trypanosoma cruzi Nuclear Proteome dos Santos Júnior, Agenor de Castro Moreira; Kalume, Dário Eluan; Camargo, Ricardo ...
PloS one,
09/2015, Letnik:
10, Številka:
9
Journal Article
Recenzirano
Odprti dostop
Replication of Trypanosoma cruzi, the etiological agent of Chagas disease, displays peculiar features, such as absence of chromosome condensation and closed mitosis. Although previous proteome and ...subproteome analyses of T. cruzi have been carried out, the nuclear subproteome of this protozoan has not been described. Here, we report, for the first time to the best of our knowledge, the isolation and proteome analysis of T. cruzi nuclear fraction. For that, T. cruzi epimastigote cells were lysed and subjected to cell fractionation using two steps of sucrose density gradient centrifugation. The purity of the nuclear fraction was confirmed by phase contrast and fluorescence microscopy. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) allowed the identification of 864 proteins. Among those, 272 proteins were annotated as putative uncharacterized, and 275 had not been previously reported on global T. cruzi proteome analysis. Additionally, to support our enrichment method, bioinformatics analysis in DAVID was carried out. It grouped the nuclear proteins in 65 gene clusters, wherein the clusters with the highest enrichment scores harbor members with chromatin organization and DNA binding functions.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The present work aims at characterizing T. harzianum secretome when the fungus is grown in synthetic medium supplemented with one of the four substrates: glucose, cellulose, xylan, and sugarcane ...bagasse (SB). The characterization was done by enzymatic assays and proteomic analysis using 2-DE/MALDI-TOF and gel-free shotgun LC–MS/MS. The results showed that SB induced the highest cellulolytic and xylanolytic activities when compared with the other substrates, while remarkable differences in terms of number and distribution of protein spots in 2-DE gels were also observed among the samples. Additionally, treatment of the secretomes with PNGase F revealed that most spot trails in 2-DE gels corresponded to N-glycosylated proteoforms. The LC–MS/MS analysis of the samples identified 626 different protein groups, including carbohydrate-active enzymes and accessory, noncatalytic, and cell-wall-associated proteins. Although the SB-induced secretome displayed the highest cellulolytic and xylanolytic activities, it did not correspond to a higher proteome complexity because CM-cellulose-induced secretome was significantly more diverse. Among the identified proteins, 73% were exclusive to one condition, while only 5% were present in all samples. Therefore, this study disclosed the variation of T. harzianum secretome in response to different substrates and revealed the diversity of the fungus enzymatic toolbox.
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