Quantitative proteomics identifies the core proteome of exosomes with syntenin-1 as the highest abundant protein and a putative universal biomarker

2021 ◽  
Author(s):  
Fernanda G. Kugeratski ◽  
Kelly Hodge ◽  
Sergio Lilla ◽  
Kathleen M. McAndrews ◽  
Xunian Zhou ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Abundant Protein ◽  
The Core ◽  
Core Proteome

scholarly journals Proteomics of spatially identified tissues in whole organs

2021 ◽  
Author(s):  
Harsharan Singh Bhatia ◽  
Andreas-David Brunner ◽  
Zhouyi Rong ◽  
Hongcheng Mai ◽  
Marvin Thielert ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Proteome Analysis ◽  
High Sensitivity ◽  
Molecular Profiling ◽  
Compositional Heterogeneity ◽  
Proteomics Data ◽  
Qualitative And Quantitative ◽  
The Core ◽  
Core Proteome ◽  
Novel Biomarkers

Spatial molecular profiling of complex tissues is essential to investigate cellular function in physiological and pathological states. However, methods for molecular analysis of biological specimens imaged in 3D as a whole are lacking. Here, we present DISCO-MS, a technology combining whole-organ imaging, deep learning-based image analysis, and ultra-high sensitivity mass spectrometry. DISCO-MS yielded qualitative and quantitative proteomics data indistinguishable from uncleared samples in both rodent and human tissues. Using DISCO-MS, we investigated microglia activation locally along axonal tracts after brain injury and revealed known and novel biomarkers. Furthermore, we identified initial individual amyloid-beta plaques in the brains of a young familial Alzheimer's disease mouse model, characterized the core proteome of these aggregates, and highlighted their compositional heterogeneity. Thus, DISCO-MS enables quantitative, unbiased proteome analysis of target tissues following unbiased imaging of entire organs, providing new diagnostic and therapeutic opportunities for complex diseases, including neurodegeneration.

scholarly journals Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 289
Author(s):  
Marios Nikolaidis ◽  
Dimitris Mossialos ◽  
Stephen G. Oliver ◽  
Grigorios D. Amoutzias
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Pseudomonas Syringae ◽  
Pseudomonas Stutzeri ◽  
Phylogenomic Analysis ◽  
Pseudomonas Chlororaphis ◽  
Phylogenetic Groups ◽  
The Core ◽  
Core Proteins ◽  
Core Proteome ◽  
Species Specific

The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, with P. aeruginosa having the highest number of these and P. fluorescens having none. We identified several P. aeruginosa-specific core proteins (such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC) that are known to play an important role in its pathogenicity. Finally, a holin family bacteriocin and a mitomycin-like biosynthetic protein were found to be core-specific for P. cholororaphis and we hypothesize that these proteins may confer a competitive advantage against other root-colonizers.

scholarly journals EpitoCore: Mining Conserved Epitope Vaccine Candidates in the Core Proteome of Multiple Bacteria Strains

2020 ◽  
Vol 11 ◽  
Author(s):  
Tayna S. Fiuza ◽  
João P. M. S. Lima ◽  
Gustavo A. de Souza
Keyword(s):  
Epitope Vaccine ◽  
Vaccine Candidates ◽  
The Core ◽  
Core Proteome ◽  
Conserved Epitope

scholarly journals Culture medium associated changes in the core proteome of macrophages and in their responses to copper oxide nanoparticles

PROTEOMICS ◽  
2016 ◽  
Vol 16 (22) ◽  
pp. 2864-2877 ◽  
Author(s):  
Bastien Dalzon ◽  
Hélène Diemer ◽  
Véronique Collin-Faure ◽  
Sarah Cianférani ◽  
Thierry Rabilloud ◽  
...  
Keyword(s):  
Copper Oxide ◽  
Culture Medium ◽  
Copper Oxide Nanoparticles ◽  
Oxide Nanoparticles ◽  
The Core ◽  
Core Proteome

scholarly journals Next-Generation Proteomics Reveals a Greater Antioxidative Response to Drought in Coffea arabica Than in Coffea canephora

Agronomy ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 148
Author(s):  
Isabel Marques ◽  
Duarte Gouveia ◽  
Jean-Charles Gaillard ◽  
Sónia Martins ◽  
Magda C. Semedo ◽  
...  
Keyword(s):  
Coffea Arabica ◽  
Shotgun Proteomics ◽  
Coffea Canephora ◽  
Label Free ◽  
Major Threat ◽  
The Core ◽  
Antioxidative Response ◽  
Core Proteome ◽  
Proteomic Response ◽  
The Impact

Drought is a major threat to coffee, compromising the quality and quantity of its production. We have analyzed the core proteome of 18 Coffea canephora cv. Conilon Clone 153 and C. arabica cv. Icatu plants and assessed their responses to moderate (MWD) and severe (SWD) water deficits. Label-free quantitative shotgun proteomics identified 3000 proteins in both genotypes, but less than 0.8% contributed to ca. 20% of proteome biomass. Proteomic changes were dependent on the severity of drought, being stronger under SWD and with an enrolment of different proteins, functions, and pathways than under MWD. The two genotypes displayed stress-responsive proteins under SWD, but only C. arabica showed a higher abundance of proteins involved in antioxidant detoxification activities. Overall, the impact of MWD was minor in the two genotypes, contrary to previous studies. In contrast, an extensive proteomic response was found under SWD, with C. arabica having a greater potential for acclimation/resilience than C. canephora. This is likely supported by a wider antioxidative response and an ability to repair photosynthetic structures, being crucial to develop new elite genotypes that assure coffee supply under water scarcity levels.

scholarly journals EpitoCore: mining conserved epitope vaccine candidates in the core proteome of multiple bacteria strains

2019 ◽  
Author(s):  
T.S. Fiuza ◽  
J.P.M.S. Lima ◽  
G.A. de Souza
Keyword(s):  
Peptide Vaccine ◽  
Computational Prediction ◽  
Reverse Vaccinology ◽  
Automated Identification ◽  
Single Strain ◽  
Vaccine Candidates ◽  
The Core ◽  
Core Proteins ◽  
Conserved Genes ◽  
Core Proteome

ABSTRACTIn reverse vaccinology approaches, complete proteomes of bacteria are submitted to multiple computational prediction steps in order to filter proteins that are possible vaccine candidates. Most available tools perform such analysis only in a single strain, or a very limited number of strains. But the vast amount of genomic data had shown that most bacteria contain pangenomes, i.e. their genomic information contains core, conserved genes, and random accessory genes specific to each strain. Therefore, it is of the utmost importance to define core proteins, and also core epitopes, in reverse vaccinology methods. EpitoCore is a decision-tree pipeline developed to fulfill that need. It provides surfaceome prediction of proteins from related strains, defines clusters of core proteins within those, calculate the immunogenicity of such clusters, predicts epitopes for a given set of MHC alleles defined by the user, and then reports if epitopes are located extracellularly and if they are conserved among the core homologues. Pipeline performance is illustrated by mining peptide vaccine candidates in Mycobacterium avium hominissuis strains. From a total proteome of approximately 4,800 proteins per strain, EpitoCore mined 103 highly immunogenic core homologues located at cell surface, many of those related to virulence and drug resistance. Conserved epitopes identified among these homologues allows the users to define sets of peptides with potential to immunize the largest coverage of tested HLA alleles using peptide-based vaccines. Therefore, EpitoCore is able to provide automated identification of conserved epitopes in bacterial pangenomic datasets.

Proteogenomic insights into the core-proteome of female reproductive tissues from crustacean amphipods

2016 ◽  
Vol 135 ◽  
pp. 51-61 ◽  
Author(s):  
Judith Trapp ◽  
Christine Almunia ◽  
Jean-Charles Gaillard ◽  
Olivier Pible ◽  
Arnaud Chaumot ◽  
...  
Keyword(s):  
The Core ◽  
Reproductive Tissues ◽  
Core Proteome

scholarly journals Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points

2016 ◽  
Author(s):  
Uri Barenholz ◽  
Dan Davidi ◽  
Ed Reznik ◽  
Yinon Bar-On ◽  
Niv Antonovsky ◽  
...  
Keyword(s):  
Kinetic Parameters ◽  
Chemical Reactions ◽  
Carbon Metabolism ◽  
Quantitative Proteomics ◽  
Central Carbon Metabolism ◽  
Branch Points ◽  
The Core ◽  
Intermediate Metabolites ◽  
Central Carbon ◽  
Substrate Saturation

AbstractA set of chemical reactions that require a metabolite to synthesize more of that metabolite is an autocatalytic cycle. Here we show that most of the reactions in the core of central carbon metabolism are part of compact autocatalytic cycles. Such metabolic designs must meet specific conditions to support stable fluxes, hence avoiding depletion of intermediate metabolites. As such, they are subjected to constraints that may seem counter-intuitive: the enzymes of branch reactions out of the cycle must be overexpressed and the affinity of these enzymes to their substrates must be relatively weak. We use recent quantitative proteomics and fluxomics measurements to show that the above conditions hold for functioning cycles in central carbon metabolism of E.coli. This work demonstrates that the topology of a metabolic network can shape kinetic parameters of enzymes and lead to seemingly wasteful enzyme usage.

scholarly journals Identification of potential bladder cancer markers in urine by abundant-protein depletion coupled with quantitative proteomics

2013 ◽  
Vol 85 ◽  
pp. 28-43 ◽  
Author(s):  
Chien-Lun Chen ◽  
Tsung-Shih Lin ◽  
Cheng-Han Tsai ◽  
Chih-Ching Wu ◽  
Ting Chung ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Quantitative Proteomics ◽  
Cancer Markers ◽  
Abundant Protein ◽  
Protein Depletion
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