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translational proteomics

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https://www.readbyqxmd.com/read/28526562/new-intracellular-activities-of-matrix-metalloproteinases-shine-in-the-moonlight
#1
REVIEW
Parker G Jobin, Georgina S Butler, ChristopherM Overall
Adaption of a single protein to perform multiple independent functions facilitates functional plasticity of the proteome allowing a limited number of protein-coding genes to perform a multitude of cellular processes. Multifunctionality is achievable by post-translational modifications and by modulating subcellular localization. Matrix metalloproteinases (MMPs), classically viewed as degraders of the extracellular matrix (ECM) responsible for matrix protein turnover, are more recently recognized as regulators of a range of extracellular bioactive molecules including chemokines, cytokines, and their binders...
May 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28525563/omics-biomarkers-in-ophthalmology
#2
Susette Lauwen, Eiko K de Jong, Dirk J Lefeber, Anneke I den Hollander
"Omics" refers to high-throughput analyses of genes, proteins, or metabolites in a biological system, and is increasingly used for ophthalmic research. These system-based approaches can unravel disease-related processes and are valuable for biomarker discovery. Furthermore, potential therapeutic targets can be identified based on omics results, and targeted follow-up experiments can be designed to gain molecular understanding of the disease and to test new therapies. Here, we review the application of omics techniques in eye diseases, focusing on age-related macular degeneration (AMD), diabetic retinopathy (DR), retinal detachment (RD), myopia, glaucoma, Fuchs' corneal dystrophy (FCD), cataract, keratoconus, and dry eyes...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28524877/optimized-fragmentation-schemes-and-data-analysis-strategies-for-proteome-wide-cross-link-identification
#3
Fan Liu, Philip Lössl, Richard Scheltema, Rosa Viner, Albert J R Heck
We describe optimized fragmentation schemes and data analysis strategies substantially enhancing the depth and accuracy in identifying protein cross-links using non-restricted whole proteome databases. These include a novel hybrid data acquisition strategy to sequence cross-links at both MS2 and MS3 level and a new algorithmic design XlinkX v2.0 for data analysis. As proof-of-concept we investigated proteome-wide protein interactions in E. coli and HeLa cell lysates, respectively, identifying 1,158 and 3,301 unique cross-links at ∼1% false discovery rate...
May 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28522639/definition-of-a-rack1-interaction-network-in-drosophila-melanogaster-using-swath-ms
#4
Lauriane Kuhn, Karim Majzoub, Evelyne Einhorn, Johana Chicher, Pompon Julien, Jean-Luc Imler, Philippe Hammann, Carine Meignin
Receptor for Activated C kinase 1 (RACK1) is a scaffold protein that has been found in association with several signaling complexes, and with the 40S subunit of the ribosome. Using the model organism Drosophila melanogaster, we recently showed that RACK1 is required at the ribosome for IRES-mediated translation of viruses. Here, we report a proteomic characterization of the interactome of RACK1 in Drosophila S2 cells. We carried out Label-Free quantitation using both Data-Dependent and Data-Independent Acquisition and observed a significant advantage for the Sequential Window Acquisition of all THeoretical fragment-ion spectra (SWATH) method both in terms of identification of interactants and quantification of low abundance proteins...
May 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28521569/exploring-the-biochemistry-of-the-prenylome-and-its-role-in-disease-through-proteomics-progress-and-potential
#5
Maura Brioschi, Alma Martinez Fernandez, Cristina Banfi
Protein prenylation is a ubiquitous covalent post-translational modification characterized by the addition of farnesyl or geranylgeranyl isoprenoid groups to a cysteine residue located near the carboxyl terminal of a protein. It is essential for the proper localization and cellular activity of numerous proteins, including Ras family GTPases and G-proteins. In addition to its roles in cellular physiology, the prenylation process has important implications in human diseases and in the recent years, it has become attractive target of inhibitors with therapeutic potential...
May 18, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28518125/glycoproteomics-of-the-extracellular-matrix-a-method-for-intact-glycopeptide-analysis-using-mass-spectrometry
#6
Javier Barallobre-Barreiro, Ferheen Baig, Marika Fava, Xiaoke Yin, Manuel Mayr
Fibrosis is a hallmark of many cardiovascular diseases and is associated with the exacerbated secretion and deposition of the extracellular matrix (ECM). Using proteomics, we have previously identified more than 150 ECM and ECM-associated proteins in cardiovascular tissues. Notably, many ECM proteins are glycosylated. This post-translational modification affects protein folding, solubility, binding, and degradation. We have developed a sequential extraction and enrichment method for ECM proteins that is compatible with the subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of intact glycopeptides...
April 21, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28516784/in-culture-cross-linking-of-bacterial-cells-reveals-large-scale-dynamic-protein-protein-interactions-at-the-peptide-level
#7
Luitzen de Jong, Edward A de Koning, Winfried Roseboom, Hansuk Buncherd, Martin J Wanner, Irena Dapic, Petra J Jansen, Jan H van Maarseveen, Garry L Corthals, Peter J Lewis, Leendert Willem Hamoen, Chris G de Koster
Identification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram positive model bacterium Bacillus subtilis as an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species, Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28516777/improvements-in-mass-spectrometry-assay-library-generation-for-targeted-proteomics
#8
Johan Teleman, Simon Hauri, Johan Malmström
In data independent acquisition mass spectrometry (DIA-MS), targeted extraction of peptide signals in silico using mass spectrometry assay libraries is a successful method for the identification and quantification of proteins. Still, it remains unclear if high quality assay libraries with more accurate peptide ion coordinates can improve peptide target identification rates in DIA analysis. In this study, we systematically improved and evaluated the common algorithmic steps for assay library generation and demonstrate that increased assay quality results in substantially higher identification rates of peptide targets from mouse organ protein lysates measured by DIA-MS...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28508553/a-targeted-proteomic-assay-for-the-measurement-of-plasma-proteoforms-related-to-human-aging-phenotypes
#9
Richard D Semba, Pingbo Zhang, Min Zhu, Elisa Fabbri, Marta Gonzalez-Freire, Ruin Moaddel, Minghui Geng-Spyropoulos, Luigi Ferrucci
Circulating polypeptides and proteins have been implicated in reversing or accelerating aging phenotypes, including growth/differentiation factor 8 (GDF8), GDF11, eotaxin, and oxytocin. These proteoforms, which are defined as the protein products arising from a single gene due to alternative splicing and post-translational modifications, have been challenging to study. Both GDF8 and GDF11 have known antagonists such as follistatin (FST), and WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing proteins 1 and 2 (WFIKKN1, WFIKKN2)...
May 16, 2017: Proteomics
https://www.readbyqxmd.com/read/28508356/progress-and-potential-of-imaging-mass-spectrometry-applied-to-biomarker-discovery
#10
Jusal Quanico, Julien Franck, Maxence Wisztorski, Michel Salzet, Isabelle Fournier
Mapping provides a direct means to assess the impact of protein biomarkers and puts into context their relevance in the type of cancer being examined. To this end, mass spectrometry imaging (MSI) was developed to provide the needed spatial information which is missing in traditional liquid-based mass spectrometric proteomics approaches. Aptly described as a "molecular histology" technique, MSI gives an additional dimension in characterizing tumor biopsies, allowing for mapping of hundreds of molecules in a single analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28508355/neuroproteomics-studies-challenges-and-updates
#11
Naify Ramadan, Hussein Ghazale, Mohammad El-Sayyad, Mohamad El-Haress, Firas H Kobeissy
The Human Genome Project in 2003 has resulted in the complete sequence of ~99% of the human genome paving the road for the Human Proteome Project (HPP) assessing the full characterization of the translated protein map of the 20,300 protein-coding genes. Consequently, the emerging of the proteomics field has successfully been adopted as the method of choice for the proteome characterization. Proteomics is a term that is used to encompass multidisciplinary approaches combining different technologies that aim to study the entire spectrum of protein changes at a specific physiological condition...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28507225/phosphorylation-of-pkp1-by-ripk4-regulates-epidermal-differentiation-and-skin-tumorigenesis
#12
Philbert Lee, Shangwen Jiang, Yuanyuan Li, Jiping Yue, Xuewen Gou, Shao-Yu Chen, Yingming Zhao, Markus Schober, Minjia Tan, Xiaoyang Wu
Tissue homeostasis of skin is sustained by epidermal progenitor cells localized within the basal layer of the skin epithelium. Post-translational modification of the proteome, such as protein phosphorylation, plays a fundamental role in the regulation of stemness and differentiation of somatic stem cells. However, it remains unclear how phosphoproteomic changes occur and contribute to epidermal differentiation. In this study, we survey the epidermal cell differentiation in a systematic manner by combining quantitative phosphoproteomics with mammalian kinome cDNA library screen...
May 15, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28504707/regulation-of-mitochondrial-biogenesis-in-erythropoiesis-by-mtorc1-mediated-protein%C3%A2-translation
#13
Xin Liu, Yuannyu Zhang, Min Ni, Hui Cao, Robert A J Signer, Dan Li, Mushan Li, Zhimin Gu, Zeping Hu, Kathryn E Dickerson, Samuel E Weinberg, Navdeep S Chandel, Ralph J DeBerardinis, Feng Zhou, Zhen Shao, Jian Xu
Advances in genomic profiling present new challenges of explaining how changes in DNA and RNA are translated into proteins linking genotype to phenotype. Here we compare the genome-scale proteomic and transcriptomic changes in human primary haematopoietic stem/progenitor cells and erythroid progenitors, and uncover pathways related to mitochondrial biogenesis enhanced through post-transcriptional regulation. Mitochondrial factors including TFAM and PHB2 are selectively regulated through protein translation during erythroid specification...
May 15, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28501217/edta-functionalized-magnetic-nanoparticles-a-suitable-platform-for-the-analysis-of-low-abundance-urinary-proteins
#14
Paulo Bastos, Fábio Trindade, Rita Ferreira, Adelino Leite-Moreira, Inês Falcão-Pires, Bruno Manadas, Ana L Daniel-da-Silva, Rui Vitorino
Urine is a highly attractive source of biological information and disease biomarkers, whose proteome characterization is ongoing. To that end, depletion/enrichment strategies for protein analysis can be of great convenience. We have thus developed a method based on the use of EDTA-functionalized magnetic nanoparticles (NPs@EDTA), to fractionate urine samples before liquid chromatography-mass spectrometry analysis and compared the identified proteins with those obtained from ultrafiltrated/unfractionated (UF) urine samples...
August 1, 2017: Talanta
https://www.readbyqxmd.com/read/28500777/a-comprehensive-investigation-of-starch-degradation-process-and-identification-of-a-transcriptional-activator-mabhlh6-during-banana-fruit-ripening
#15
Yun-Yi Xiao, Jian-Fei Kuang, Xin-Na Qi, Yu-Jie Ye, Zhen-Xian Wu, Jian-Ye Chen, Wang-Jin Lu
Although starch degradation has been well studied in model systems such as Arabidopsis leaves and cereal seeds, this process in starchy fruits during ripening, especially in bananas, is largely unknown. In this study, 38 genes encoding starch degradation-related proteins were identified and characterized from banana fruit. Expression analysis revealed that 27 candidate genes were significantly induced during banana fruit ripening, with concomitant conversion of starch-to-sugars. Furthermore, iTRAQ-based proteomics experiments identified 18 starch degradation-associated enzymes bound to the surface of starch granules, of which 10 were markedly up-regulated during ripening...
May 13, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28500593/assessment-of-protein-carbonylation-and-protein-tyrosine-phosphatase-ptp-oxidation-in-vascular-smooth-muscle-cells-vsmcs-using-immunoblotting-approaches
#16
Sofia Tsiropoulou, Rhian M Touyz
Post-translational modification of proteins, such as phosphorylation and oxidation, plays a major role in cellular signaling by influencing protein structure and function. In vascular cells, in addition to influencing phosphorylation, angiotensin II (Ang II) induces oxidation of proteins, important in redox signaling in the cardiovascular and renal systems. The present chapter describes immunoblotting approaches to assess irreversible protein carbonylation and protein tyrosine phosphatase (PTPs) oxidation status in the proteome of vascular smooth muscle cells (VSMC)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28500349/quantitative-succinyl-proteome-profiling-of-camellia-sinensis-cv-anji-baicha-during-periodic-albinism
#17
Yan-Xia Xu, Chen-Jia Shen, Jian-Qiang Ma, Wei Chen, Juan Mao, Yan-Yan Zhou, Liang Chen
Lysine succinylation is a novel dynamic and evolutionarily conserved post-translational modification (PTM) that regulates various biological processes. 'Anji Baicha' is an albino tea variety that exhibits temperature-based variability of leaf colour and amino acid concentrations. However, the mechanism underlying albinism in 'Anji Baicha' has not been investigated at the level of succinylation. Here, we identify 3530 lysine succinylation sites mapped to 2132 proteins in 'Anji Baicha', representing the first extensive data on the lysine succinylome in the tea plant...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28500236/identification-of-the-serine-biosynthesis-pathway-as-a-critical-component-of-braf-inhibitor-resistance-of-melanoma-pancreatic-and-non-small-cell-lung-cancer-cells
#18
Kayleigh C Ross, Andrew J Andrews, Christopher D Marion, Timothy J Yen, Vikram Bhattacharjee
Metastatic melanoma cells commonly acquire resistance to BRAF V600E inhibitors (BRAFis). In this study, we identified serine biosynthesis as a critical mechanism of resistance. Proteomic assays revealed differential protein expression of serine biosynthetic enzymes PHGDH, PSPH, and PSAT1 following vemurafenib (BRAFi) treatment in sensitive versus acquired resistant melanoma cells. Ablation of PHGDH via siRNA sensitized acquired resistant cells to vemurafenib. Inhibiting the folate cycle, directly downstream of serine synthesis, with methotrexate also displayed similar sensitization...
May 12, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28500030/translating-divergent-environmental-stresses-into-a-common-proteome-response-through-hik33-in-a-model-cyanobacterium
#19
Haitao Ge, Longfa Fang, Xiahe Huang, Jinlong Wang, Weiyang Chen, Ye Liu, Yuanya Zhang, Xiaorong Wang, Wu Xu, Qingfang He, Yingchun Wang
The histidine kinase Hik33 plays important roles in mediating cyanobacterial response to divergent types of abiotic stresses including cold, salt, high light (HL), and osmotic stresses. However, how these functions are regulated by Hik33 remains to be addressed. Using a hik33-deficient strain (Δhik33) of Synechocystis sp. PCC 6803 (Synechocystis) and quantitative proteomics, we found that Hik33 depletion induces differential protein expression highly similar to that induced by divergent types of stresses. This typically includes downregulation of proteins in photosynthesis and carbon assimilation that are necessary for cell propagation, and upregulation of heat shock proteins, chaperons, and proteases that are important for cell survival...
May 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28497061/mining-of-microbial-genomes-for-the-novel-sources-of-nitrilases
#20
Nikhil Sharma, Neerja Thakur, Tilak Raj, Savitri, Tek Chand Bhalla
Next-generation DNA sequencing (NGS) has made it feasible to sequence large number of microbial genomes and advancements in computational biology have opened enormous opportunities to mine genome sequence data for novel genes and enzymes or their sources. In the present communication in silico mining of microbial genomes has been carried out to find novel sources of nitrilases. The sequences selected were analyzed for homology and considered for designing motifs. The manually designed motifs based on amino acid sequences of nitrilases were used to screen 2000 microbial genomes (translated to proteomes)...
2017: BioMed Research International
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