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https://www.readbyqxmd.com/read/29666630/the-interactomic-analysis-reveals-pathogenic-protein-networks-in-phomopsis-longicolla-underlying-seed-decay-of-soybean
#1
Shuxian Li, Bryan Musungu, David Lightfoot, Pingsheng Ji
Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla ) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein-protein interactions (PPI) and to identify conserved global networks and pathogenicity subnetworks in P. longicolla including orthologous pathways for cell signaling and pathogenesis. The interlog method used in the study identified 215,255 unique PPIs among 3,868 proteins...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29666374/hatric-based-identification-of-receptors-for-orphan-ligands
#2
Nadine Sobotzki, Michael A Schafroth, Alina Rudnicka, Anika Koetemann, Florian Marty, Sandra Goetze, Yohei Yamauchi, Erick M Carreira, Bernd Wollscheid
Cellular responses depend on the interactions of extracellular ligands, such as nutrients, growth factors, or drugs, with specific cell-surface receptors. The sensitivity of these interactions to non-physiological conditions, however, makes them challenging to study using in vitro assays. Here we present HATRIC-based ligand receptor capture (HATRIC-LRC), a chemoproteomic technology that successfully identifies target receptors for orphan ligands on living cells ranging from small molecules to intact viruses...
April 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29665004/thiostrepton-degrades-mutant-p53-by-eliciting-an-autophagic-response-in-sw480-cells
#3
Dhanya Kalathil, Manu Prasad, Maharrish Chelladurai, Samu John, Asha S Nair
Mutations in p53 gene are one of the hallmarks of tumor development. Specific targeting of mutant p53 protein has a promising role in cancer therapeutics. Our preliminary observation showed destabilization of mutant p53 protein in SW480, MiaPaCa and MDAMB231 cell lines upon thiostrepton treatment. In order to elucidate the mechanism of thiostrepton triggered mutant p53 degradation, we explored the impact of proteasome inhibition on activation of autophagy. Combined treatment of thiostrepton and cycloheximide/chloroquine prevented the degradation of mutant p53 protein, reinforcing autophagy as the means of mutant p53 destabilization...
April 17, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29663027/molecular-interactions-at-the-surface-of-extracellular-vesicles
#4
REVIEW
Edit I Buzás, Eszter Á Tóth, Barbara W Sódar, Katalin É Szabó-Taylor
Extracellular vesicles such as exosomes, microvesicles, apoptotic bodies, and large oncosomes have been shown to participate in a wide variety of biological processes and are currently under intense investigation in many different fields of biomedicine. One of the key features of extracellular vesicles is that they have relatively large surface compared to their volume. Some extracellular vesicle surface molecules are shared with those of the plasma membrane of the releasing cell, while other molecules are characteristic for extracellular vesicular surfaces...
April 16, 2018: Seminars in Immunopathology
https://www.readbyqxmd.com/read/29662892/revealing-the-amylase-interactome-in-whole-saliva-using-proteomic-approaches
#5
Karla Tonelli Bicalho Crosara, David Zuanazzi, Eduardo Buozi Moffa, Yizhi Xiao, Maria Aparecida de Andrade Moreira Machado, Walter Luiz Siqueira
Understanding proteins present in saliva and their function when isolated is not enough to describe their real role in the mouth. Due to protein-protein interactions, structural changes may occur in macromolecules leading to functional modulation or modification. Besides amylase's function in carbohydrate breakdown, amylase can delay proteolytic degradation of protein partners (e.g., histatin 1) when complexed. Due to its biochemical characteristics and high abundance in saliva, amylase probably interacts with several proteins acting as a biological carrier...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29662057/quantitative-assessment-of-protein-activity-in-orphan-tissues-and-single-cells-using-the-metaviper-algorithm
#6
Hongxu Ding, Eugene F Douglass, Adam M Sonabend, Angeliki Mela, Sayantan Bose, Christian Gonzalez, Peter D Canoll, Peter A Sims, Mariano J Alvarez, Andrea Califano
We and others have shown that transition and maintenance of biological states is controlled by master regulator proteins, which can be inferred by interrogating tissue-specific regulatory models (interactomes) with transcriptional signatures, using the VIPER algorithm. Yet, some tissues may lack molecular profiles necessary for interactome inference (orphan tissues), or, as for single cells isolated from heterogeneous samples, their tissue context may be undetermined. To address this problem, we introduce metaVIPER, an algorithm designed to assess protein activity in tissue-independent fashion by integrative analysis of multiple, non-tissue-matched interactomes...
April 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29657132/structure-of-radical-induced-cell-death1-hub-domain-reveals-a-common-%C3%AE-%C3%AE-scaffold-for-disorder-in-transcriptional-networks
#7
Katrine Bugge, Lasse Staby, Katherine R Kemplen, Charlotte O'Shea, Sidsel K Bendsen, Mikael K Jensen, Johan G Olsen, Karen Skriver, Birthe B Kragelund
Communication within cells relies on a few protein nodes called hubs, which organize vast interactomes with many partners. Frequently, hub proteins are intrinsically disordered conferring multi-specificity and dynamic communication. Conversely, folded hub proteins may organize networks using disordered partners. In this work, the structure of the RST domain, a unique folded hub, is solved by nuclear magnetic resonance spectroscopy and small-angle X-ray scattering, and its complex with a region of the transcription factor DREB2A is provided through data-driven HADDOCK modeling and mutagenesis analysis...
April 12, 2018: Structure
https://www.readbyqxmd.com/read/29651153/decipher-reliable-biomarkers-of-brain-aging-by-integrating-literature-based-evidence-with-interactome-data
#8
Sang-Hun Bae, Han Wool Kim, SeoJeong Shin, Joopyung Kim, Yun-Hwa Jeong, Jisook Moon
Aging is an inevitable progressive decline in every physiological function and serves as a primary risk factor for cognitive decline and Alzheimer's disease. Thus, age-dependent impairments in cognitive function must be understood in association with general aging processes with an integrative approach in a systemic manner. An integrative aging gene network was constructed based on mutual molecular interactions using literature-curated interactome data and separated into functionally distinct modules. To investigate key surrogate biomarkers of the aging brain in the context of the general aging process, co-expression networks were built on post-mortem and Alzheimer's brain transcriptome data...
April 13, 2018: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29648920/functional-domain-analysis-of-sox18-transcription-factor-using-a-single-chain-variable-fragment-based-approach
#9
Frank R Fontaine, Stephen Goodall, Jeremy W Prokop, Christopher B Howard, Mehdi Moustaqil, Somuah Kumble, Daniel T Rasicci, Geoffrey W Osborne, Yann Gambin, Emma Sierecki, Martina L Jones, Johannes Zuegg, Stephen Mahler, Mathias Francois
Antibodies are routinely used to study the activity of transcription factors, using various in vitro and in vivo approaches such as electrophoretic mobility shift assay, enzyme-linked immunosorbent assay, genome-wide method analysis coupled with next generation sequencing, or mass spectrometry. More recently, a new application for antibodies has emerged as crystallisation scaffolds for difficult to crystallise proteins, such as transcription factors. Only in a few rare cases, antibodies have been used to modulate the activity of transcription factors, and there is a real gap in our knowledge on how to efficiently design antibodies to interfere with transcription...
April 12, 2018: MAbs
https://www.readbyqxmd.com/read/29642908/putative-human-sperm-interactome-a-networks-study
#10
Alessandra Ordinelli, Nicola Bernabò, Massimiliano Orsini, Mauro Mattioli, Barbara Barboni
BACKGROUND: For over sixty years, it has been known that mammalian spermatozoa immediately after ejaculation are virtually infertile. They became able to fertilize only after they reside for long time (hours to days) within female genital tract where they complete their functional maturation, the capacitation. This process is finely regulated by the interaction with the female environment and involves, in spermatozoa, a myriad of molecules as messengers and target of signals. Since, to date, a model able to represent the molecular interaction that characterize sperm physiology does not exist, we realized the Human Sperm Interactme Network3...
April 11, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29615496/crispr-cas9-mediated-genomic-editing-of-cluap1-ift38-reveals-a-new-role-in-actin-arrangement
#11
Tina Beyer, Sylvia Bolz, Katrin Junger, Nicola Horn, Muhammad Moniruzzaman, Yasmin Wissinger, Marius Ueffing, Karsten Boldt
CRISPR/Cas9-mediated gene editing allows manipulation of a gene of interest in its own chromosomal context. When applied to the analysis of protein interactions, and in contrast to exogenous expression of a protein, this can be studied maintaining physiological stoichiometry, topology and context. We have used CRISPR/Cas9-mediated genomic editing to investigate Cluap1/ IFT38, a component of the intraflagellar transport complex B (IFT-B). Cluap1 has been implicated in human development as well as in cancer progression...
April 3, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29609142/an-efficient-strategy-for-identifying-cancer-related-key-genes-based-on-graph-entropy
#12
Wei Zhang, Shu-Lin Wang
Gene networks are beneficial to identify functional genes that are highly relevant to clinical outcomes. Most of the current methods require information about the interaction of genes or proteins to construct genetic network connection. However, the conclusion of these methods may be bias because of the current incompleteness of human interactome. In this paper, we propose an efficient strategy to use gene expression data and gene mutation data for identifying cancer-related key genes based on graph entropy (iKGGE)...
March 21, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29606589/the-h3k36me2-methyltransferase-nsd1-demarcates-prc2-mediated-h3k27me2-and-h3k27me3-domains-in-embryonic-stem-cells
#13
Gundula Streubel, Ariane Watson, Sri Ganesh Jammula, Andrea Scelfo, Darren J Fitzpatrick, Giorgio Oliviero, Rachel McCole, Eric Conway, Eleanor Glancy, Gian Luca Negri, Eugene Dillon, Kieran Wynne, Diego Pasini, Nevan J Krogan, Adrian P Bracken, Gerard Cagney
The Polycomb repressor complex 2 (PRC2) is composed of the core subunits Ezh1/2, Suz12, and Eed, and it mediates all di- and tri-methylation of histone H3 at lysine 27 in higher eukaryotes. However, little is known about how the catalytic activity of PRC2 is regulated to demarcate H3K27me2 and H3K27me3 domains across the genome. To address this, we mapped the endogenous interactomes of Ezh2 and Suz12 in embryonic stem cells (ESCs), and we combined this with a functional screen for H3K27 methylation marks. We found that Nsd1-mediated H3K36me2 co-locates with H3K27me2, and its loss leads to genome-wide expansion of H3K27me3...
March 22, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29606212/review-plant-g-quadruplex-g4-motifs-in-dna-and-rna-abundant-intriguing-sequences-of-unknown-function
#14
REVIEW
Brianna D Griffin, Hank W Bass
DNA sequences capable of forming G-quadruplex (G4) structures can be predicted and mapped in plant genomes using computerized pattern search programs. Non-telomeric G4 motifs have recently been found to number in the thousands across many plant species and enriched around gene promoters, prompting speculation that they may represent a newly uncovered and ubiquitous family of cis-acting elements. Comparative analysis shows that monocots exhibit five to ten times higher G4 motif density than eudicots, but the significance of this difference has not been determined...
April 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29600765/network-pharmacology-exploring-the-resources-and-methodologies
#15
Junaid Muhammd, Abbas Khan, Arif Ali, Li Fang, Wang Yanjing, Qin Xu, Donqing Wei
Multi-target and combinatorial therapies have been focused for the past several decades. These approaches achieved considerable therapeutic efficacy by modulating the activities of the targets in complex diseases such as HIV-1 infection, cancer and diabetes disease. Most of the diseases cannot be treated efficiently in terms of single gene target, because it involves the cessation of the coordinated function of distinct gene groups. Most of the cellular components work efficiently by interacting with other cellular components and all these interactions together represent interactome...
March 30, 2018: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/29588451/identification-of-the-functional-pathways-altered-by-placental-cell-exposure-to-high-glucose-lessons-from-the-transcript-and-metabolite-interactome
#16
C H Hulme, A Stevens, W Dunn, A E P Heazell, K Hollywood, P Begley, M Westwood, J E Myers
The specific consequences of hyperglycaemia on placental metabolism and function are incompletely understood but likely contribute to poor pregnancy outcomes associated with diabetes mellitus (DM). This study aimed to identify the functional biochemical pathways perturbed by placental exposure to high glucose levels through integrative analysis of the trophoblast transcriptome and metabolome. The human trophoblast cell line, BeWo, was cultured in 5 or 25 mM glucose, as a model of the placenta in DM. Transcriptomic analysis using microarrays, demonstrated 5632 differentially expressed gene transcripts (≥± 1...
March 27, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29581850/interactome-analysis-of-transforming-growth-factor-%C3%AE-activated-kinase-1-in-helicobacter-pylori-infected-cells-revealed-novel-regulators-tripartite-motif-28-and-cdc37
#17
Olga Sokolova, Thilo Kähne, Kenneth Bryan, Michael Naumann
Transforming growth factor-β (TGFβ)-activated kinase 1 (TAK1) plays a central role in controlling the cellular pro-inflammatory response via the activation of the nuclear factor κB (NF-κB)- and mitogen-activated protein (MAP) kinases-dependent transcriptional programs. Here, we show that depletion of TAK1 and the TAK1-binding proteins TAB1 and TAB2 affects NF-κB, JNK and p38 phosphorylation and suppresses NF-κB activity in AGS cells infected with Helicobacter pylori or stimulated with the cytokines TNF and IL-1β...
March 6, 2018: Oncotarget
https://www.readbyqxmd.com/read/29577053/hsa_circ_0001859-regulates-atf2-expression-by-functioning-as-an-mir-204-211-sponge-in-human-rheumatoid-arthritis
#18
Bingrui Li, Nianyu Li, Le Zhang, Kai Li, Yingtian Xie, Meilan Xue, Zheng Zheng
Background: circRNAs are part of the competitive endogenous RNA network, which putatively function as miRNA sponges and play a crucial role in the development of numerous diseases. However, studies of circRNAs in rheumatoid arthritis (RA) disease are limited. This work aims to identify the expression pattern of circRNAs in synovial tissues and their inflammatory regulation mechanism. Methods: We first compared the mRNA expression in rheumatoid arthritis patients with that in healthy volunteers by GEO database mining to identify gene loci specifically expressed in synovial tissues...
2018: Journal of Immunology Research
https://www.readbyqxmd.com/read/29576399/chemical-diversity-in-the-g-protein-coupled-receptor-superfamily
#19
REVIEW
Márton Vass, Albert J Kooistra, Dehua Yang, Raymond C Stevens, Ming-Wei Wang, Chris de Graaf
G protein-coupled receptors (GPCRs) are the largest family of cell signaling transmembrane proteins that can be modulated by a plethora of chemical compounds. Systematic cheminformatics analysis of structurally and pharmacologically characterized GPCR ligands shows that cocrystallized GPCR ligands cover a significant part of chemical ligand space, despite their limited number. Many GPCR ligands and substructures interact with multiple receptors, providing a basis for polypharmacological ligand design. Experimentally determined GPCR structures represent a variety of binding sites and receptor-ligand interactions that can be translated to chemically similar ligands for which structural data are lacking...
March 22, 2018: Trends in Pharmacological Sciences
https://www.readbyqxmd.com/read/29569085/the-nmr-contribution-to-protein-protein-networking-in-fe-s-protein-maturation
#20
REVIEW
Lucia Banci, Francesca Camponeschi, Simone Ciofi-Baffoni, Mario Piccioli
Iron-sulfur proteins were among the first class of metalloproteins that were actively studied using NMR spectroscopy tailored to paramagnetic systems. The hyperfine shifts, their temperature dependencies and the relaxation rates of nuclei of cluster-bound residues are an efficient fingerprint of the nature and the oxidation state of the Fe-S cluster. NMR significantly contributed to the analysis of the magnetic coupling patterns and to the understanding of the electronic structure occurring in [2Fe-2S], [3Fe-4S] and [4Fe-4S] clusters bound to proteins...
March 22, 2018: Journal of Biological Inorganic Chemistry: JBIC
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