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Protein turnover

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https://www.readbyqxmd.com/read/28090567/the-rna-polymerase-iii-subunit-polr3b-is-required-for-the-maintenance-of-small-intestinal-crypts-in-mice
#1
Julia Kieckhaefer, Sabina Lukovac, Diana Z Ye, Dolim Lee, Danielle J Beetler, Michael Pack, Klaus H Kaestner
BACKGROUND & AIMS: The continuously self-renewing mammalian intestinal epithelium, with high cellular turnover, depends on adequate protein synthesis for its proliferative capacity. RNA polymerase III activity is closely related to cellular growth and proliferation. Here, we studied the role of Polr3b, a large RNA polymerase III subunit, in the mammalian intestinal epithelium. METHODS: We derived mice with an intestinal epithelium-specific hypomorphic mutation of the Polr3b gene, using VillinCre-mediated gene ablation...
November 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28089450/a-structural-model-for-vinculin-insertion-into-pip2-containing-membranes-and-the-effect-of-insertion-on-vinculin-activation-and-localization
#2
Peter M Thompson, Srinivas Ramachandran, Lindsay B Case, Caitlin E Tolbert, Arpit Tandon, Mihir Pershad, Nikolay V Dokholyan, Clare M Waterman, Sharon L Campbell
Vinculin, a scaffolding protein that localizes to focal adhesions (FAs) and adherens junctions, links the actin cytoskeleton to the adhesive super-structure. While vinculin binds to a number of cytoskeletal proteins, it can also associate with phosphatidylinositol 4,5-bisphosphate (PIP2) to drive membrane association. To generate a structural model for PIP2-dependent interaction of vinculin with the lipid bilayer, we conducted lipid-association, nuclear magnetic resonance, and computational modeling experiments...
December 31, 2016: Structure
https://www.readbyqxmd.com/read/28089447/networks-of-dynamic-allostery-regulate-enzyme-function
#3
Michael Joseph Holliday, Carlo Camilloni, Geoffrey Stuart Armstrong, Michele Vendruscolo, Elan Zohar Eisenmesser
Many protein systems rely on coupled dynamic networks to allosterically regulate function. However, the broad conformational space sampled by non-coherently dynamic systems has precluded detailed analysis of their communication mechanisms. Here, we have developed a methodology that combines the high sensitivity afforded by nuclear magnetic resonance relaxation techniques and single-site multiple mutations, termed RASSMM, to identify two allosterically coupled dynamic networks within the non-coherently dynamic enzyme cyclophilin A...
December 27, 2016: Structure
https://www.readbyqxmd.com/read/28087841/single-cell-transcriptome-analysis-of-fish-immune-cells-provides-insight-into-the-evolution-of-vertebrate-immune-cell-types
#4
Santiago J Carmona, Sarah A Teichmann, Lauren Ferreira, Iain C Macaulay, Michael J T Stubbington, Ana Cvejic, David Gfeller
The immune system of vertebrate species consists of many different cell types that have distinct functional roles and are subject to different evolutionary pressures. Here, we first analysed conservation of genes specific for all major immune cell types in human and mouse. Our results revealed higher gene turnover and faster evolution of trans-membrane proteins in NK cells compared to other immune cell types, and especially T cells, but similar conservation of nuclear and cytoplasmic protein coding genes. To validate these findings in a distant vertebrate species, we used single-cell RNA-Sequencing of lck:GFP cells in zebrafish and obtained the first transcriptome of specific immune cell types in a non-mammalian species...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28087713/functional-genomics-reveals-that-tumors-with-activating-phosphoinositide-3-kinase-mutations-are-dependent-on-accelerated-protein-turnover
#5
Teresa Davoli, Kristen E Mengwasser, Jingjing Duan, Ting Chen, Camilla Christensen, Eric C Wooten, Anthony N Anselmo, Mamie Z Li, Kwok-Kin Wong, Kristopher T Kahle, Stephen J Elledge
Activating mutations in the phosphoinositide 3-kinase (PI3K) signaling pathway are frequently identified in cancer. To identify pathways that support PI3K oncogenesis, we performed a genome-wide RNAi screen in isogenic cell lines harboring wild-type or mutant PIK3CA to search for PI3K synthetic-lethal (SL) genes. A combined analysis of these results with a meta-analysis of two other large-scale RNAi screening data sets in PI3K mutant cancer cell lines converged on ribosomal protein translation and proteasomal protein degradation as critical nononcogene dependencies for PI3K-driven tumors...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28087276/drosophila-argonaute2-turnover-is-regulated-by-the-ubiquitin-proteasome-pathway
#6
Madoka Chinen, Elissa P Lei
Argonaute (AGO) proteins play a central role in the RNA interference (RNAi) pathway, which is a cytoplasmic mechanism important for post-transcriptional regulation of gene expression. In Drosophila, AGO2 also functions in the nucleus to regulate chromatin insulator activity and transcription. Although there are a number of studies focused on AGO2 function, the regulation of AGO2 turnover is not well understood. We found that mutation of T1149 or R1158 in the conserved PIWI domain causes AGO2 protein instability, but only T1149 affects RNAi activity...
January 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28081210/mutations-in-hyal2-encoding-hyaluronidase-2-cause-a-syndrome-of-orofacial-clefting-and-cor-triatriatum-sinister-in-humans-and-mice
#7
Martina M A Muggenthaler, Biswajit Chowdhury, S Naimul Hasan, Harold E Cross, Brian Mark, Gaurav V Harlalka, Michael A Patton, Miho Ishida, Elijah R Behr, Sanjay Sharma, Kenneth Zahka, Eissa Faqeih, Brian Blakley, Mike Jackson, Melissa Lees, Vernon Dolinsky, Leroy Cross, Philip Stanier, Claire Salter, Emma L Baple, Fowzan S Alkuraya, Andrew H Crosby, Barbara Triggs-Raine, Barry A Chioza
Orofacial clefting is amongst the most common of birth defects, with both genetic and environmental components. Although numerous studies have been undertaken to investigate the complexities of the genetic etiology of this heterogeneous condition, this factor remains incompletely understood. Here, we describe mutations in the HYAL2 gene as a cause of syndromic orofacial clefting. HYAL2, encoding hyaluronidase 2, degrades extracellular hyaluronan, a critical component of the developing heart and palatal shelf matrix...
January 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28075616/role-of-cxc-chemokine-receptor-type-4-as-a-lactoferrin-receptor
#8
Yoshiharu Takayama, Reiji Aoki, Ryo Uchida, Atsushi Tajima, Ayako Aoki-Yoshida
Lactoferrin exerts its biological activities by interacting with receptors on target cells, including LDL receptor-related protein-1 (LRP-1/CD91), intelectin-1 (omentin-1), and Toll-like receptor 4 (TLR4). However, the effects mediated by these receptors are not sufficient to fully explain the many functions of lactoferrin. C-X-C-motif cytokine receptor 4 (CXCR4) is a ubiquitously expressed G-protein coupled receptor for stromal cell-derived factor-1 (SDF-1/CXCL12). Lactoferrin was found to be as capable as SDF-1 in blocking infection by an HIV variant that uses CXCR4 as a co-receptor (X4-tropic HIV), suggesting that lactoferrin interacts with CXCR4...
October 31, 2016: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/28074857/deubiquitylation-of-hepatitis-b-virus-x-protein-hbx-by-ubiquitin-specific-peptidase-15-usp15-increases-hbx-stability-and-its-transactivation-activity
#9
Zhi-Jun Su, Jia-Shou Cao, Yan-Fang Wu, Wan-Nan Chen, Xinjian Lin, Yun-Li Wu, Xu Lin
Hepatitis B virus X protein (HBx) plays important roles in viral replication and the development of hepatocellular carcinoma. HBx is a rapid turnover protein and ubiquitin-proteasome pathway has been suggested to influence HBx stability as treatment with proteasome inhibitors increases the levels of HBx protein and causes accumulation of the polyubiquitinated forms of HBx. Deubiquitinases (DUBs) are known to act by removing ubiquitin moieties from proteins and thereby reverse their stability and/or activity...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28071722/spict-a-cyst-cell-specific-gene-regulates-starvation-induced-spermatogonial-cell-death-in-the-drosophila-testis
#10
Ason C-Y Chiang, Heiko Yang, Yukiko M Yamashita
Tissues are maintained in a homeostatic state by balancing the constant loss of old cells with the continued production of new cells. Tissue homeostasis can shift between high and low turnover states to cope with environmental changes such as nutrient availability. Recently, we discovered that the elimination of transit-amplifying cells plays a critical role in maintaining the stem cell population during protein starvation in the Drosophila testis. Here, we identify spict, a gene expressed specifically in differentiating cyst cells, as a regulator of spermatogonial death...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070565/activation-of-respiratory-complex-i-from-escherichia-coli-studied-by-fluorescent-probes
#11
Nikolai Belevich, Galina Belevich, Zhiyong Chen, Subhash C Sinha, Marina Verkhovskaya
Respiratory Complex I from E. coli may exist in two interconverting forms: resting (R) and active (A). The R/A transition of purified, solubilized Complex I occurring upon turnover was studied employing two different fluorescent probes, Annine 6+, and NDB-acetogenin. NADH-induced fluorescent changes of both dyes bound to solubilized Complex I from E. coli were characterized as a function of the protein:dye ratio, temperature, ubiquinone redox state and the enzyme activity. Analysis of this data combined with time-resolved optical measurements of Complex I activity and spectral changes indicated two ubiquinone-binding sites; a possibility of reduction of the tightly-bound quinone in the resting state and reduction of the loosely-bound quinone in the active state is discussed...
January 2017: Heliyon
https://www.readbyqxmd.com/read/28068319/fbxo32-suppresses-breast-cancer-tumorigenesis-through-targeting-klf4-to-proteasomal-degradation
#12
H Zhou, Y Liu, R Zhu, F Ding, Y Wan, Y Li, Z Liu
Krüppel-like factor 4 (KLF4, GKLF) is a zinc-finger transcription factor involved in a large variety of cellular processes, including apoptosis, cell cycle progression, as well as stem cell renewal. KLF4 is critical for cell fate decision and has an ambivalent role in tumorigenesis. Emerging data keep reminding us that KLF4 dysregulation either facilitates or impedes tumor progression, making it important to clarify the regulating network of KLF4. Like most transcription factors, KLF4 has a rather short half-life within the cell and its turnover must be carefully orchestrated by ubiquitination and ubiquitin-proteasome system...
January 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28065760/establishment-of-a-suite-of-assays-that-support-the-discovery-of-proteasome-stimulators
#13
Darci J Trader, Scott Simanski, Paige Dickson, Thomas Kodadek
BACKGROUND: The proteasome catalyzes the degradation of many mis-folded proteins, which are otherwise cytotoxic. There is interest in the discovery of proteasome agonists, but previous efforts to do so have been disappointing. METHODS: The cleavage of small fluorogenic peptides is used routinely as an assay to screen for proteasome modulators. We have developed follow-on assays that employ more physiologically relevant substrates. RESULTS: To demonstrate the efficacy of this workflow, the NIH Clinical Collection (NCC) was screened...
January 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28065575/multiparametric-analysis-of-cell-shape-demonstrates-that-%C3%AE-pix-directly-couples-yap-activation-to-extracellular-matrix-adhesion
#14
Julia E Sero, Chris Bakal
Mechanical signals from the extracellular matrix (ECM) and cellular geometry regulate the nuclear translocation of transcriptional regulators such as Yes-associated protein (YAP). Elucidating how physical signals control the activity of mechanosensitive proteins poses a technical challenge, because perturbations that affect cell shape may also affect protein localization indirectly. Here, we present an approach that mitigates confounding effects of cell-shape changes, allowing us to identify direct regulators of YAP localization...
January 2, 2017: Cell Systems
https://www.readbyqxmd.com/read/28063985/revealing-the-three-dimensional-architecture-of-focal-adhesion-components-to-explain-ca-2-mediated-turnover-of-focal-adhesions
#15
Shu-Jing Chang, Ying-Chi Chen, Chi-Hsun Yang, Soon-Cen Huang, Ho-Kai Huang, Chun-Chun Li, Hans I-Chen Harn, Wen-Tai Chiu
BACKGROUND: Focal adhesions (FAs) are large, dynamic protein complexes located close to the plasma membrane, which serve as the mechanical linkages and a biochemical signaling hub of cells. The coordinated and dynamic regulation of focal adhesion is required for cell migration. Degradation, or turnover, of FAs is a major event at the trailing edge of a migratory cell, and is mediated by Ca(2+)/calpain-dependent proteolysis and disassembly. Here, we investigated how Ca(2+) influx induces cascades of FA turnover in living cells...
January 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28061504/dub3-deubiquitylating-enzymes-regulate-hippo-pathway-activity-by-regulating-the-stability-of-itch-lats-and-amot-proteins
#16
Hung Thanh Nguyen, Jan-Michael Kugler, Stephen M Cohen
The YAP and TAZ transcriptional coactivators promote oncogenic transformation. Elevated YAP/TAZ activity has been documented in human tumors. YAP and TAZ are negatively regulated by the Hippo tumor suppressor pathway. The activity and stability of several Hippo pathway components, including YAP/TAZ, is regulated by ubiquitin mediated protein turnover and several ubiquitin ligase complexes have been implicated in human cancer. However, little is known about the deubiquitylating enzymes that counteract these ubiquitin ligases in regulation of the Hippo pathway...
2017: PloS One
https://www.readbyqxmd.com/read/28059716/a-sumo-ubiquitin-relay-recruits-proteasomes-to-chromosome-axes-to-regulate-meiotic-recombination
#17
H B D Prasada Rao, Huanyu Qiao, Shubhang K Bhatt, Logan R J Bailey, Hung D Tran, Sarah L Bourne, Wendy Qiu, Anusha Deshpande, Ajay N Sharma, Connor J Beebout, Roberto J Pezza, Neil Hunter
Meiosis produces haploid gametes through a succession of chromosomal events including pairing, synapsis and recombination. Mechanisms that orchestrate these events remain poorly understood. We found that the SUMO-modification and ubiquitin-proteasome systems regulate the major events of meiotic prophase in mouse. Interdependent localization of SUMO, ubiquitin and proteasomes along chromosome axes was mediated largely by RNF212 and HEI10, two E3 ligases that are also essential for crossover recombination. RNF212-dependent SUMO conjugation effected a checkpoint-like process that stalls recombination by rendering the turnover of a subset of recombination factors dependent on HEI10-mediated ubiquitylation...
January 5, 2017: Science
https://www.readbyqxmd.com/read/28057869/leptin-stimulates-bone-formation-in-ob-ob-mice-at-doses-having-minimal-impact-on-energy-metabolism
#18
Kenneth A Philbrick, Carmen P Wong, Adam J Branscum, Russell T Turner, Urszula T Iwaniec
Leptin, the protein product of the ob gene, is essential for normal bone growth, maturation, and turnover. Peripheral actions of leptin occur at lower serum levels of the hormone than central actions because entry of leptin into the central nervous system (CNS) is limited due to its saturable transport across the blood brain barrier (BBB). We performed a study in mice to model the impact of leptin production associated with different levels of adiposity on bone formation and compared the response with well-established centrally-mediated actions of the hormone on energy metabolism...
January 5, 2017: Journal of Endocrinology
https://www.readbyqxmd.com/read/28056778/structural-prediction-of-the-interaction-of-the-tumor-suppressor-p27-kip1-with-cyclin-a-cdk2-identifies-a-novel-catalytically-relevant-determinant
#19
Jinyu Li, Jörg Vervoorts, Paolo Carloni, Giulia Rossetti, Bernhard Lüscher
BACKGROUND: The cyclin-dependent kinase 2 (CDK2) together with its cyclin E and A partners is a central regulator of cell growth and division. Deregulation of CDK2 activity is associated with diseases such as cancer. The analysis of substrates identified S/T-P-X-R/K/H as the CDK2 consensus sequence. The crystal structure of cyclin A/CDK2 with a short model peptide supports this sequence and identifies key interactions. However, CDKs use additional determinants to recognize substrates, including the RXL motif that is read by the cyclin subunits...
January 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28056744/nucleotide-second-messenger-signaling-as-a-target-for-the-control-of-bacterial-biofilm-formation
#20
Alberto J Martín-Rodríguez, Ute Römling
Bacterial biofilm formation and associated phenotypes are the major cause of chronic infection in humans. The major regulator of biofilm formation in Gram-negative and Gram-positive bacteria are nucleotide-based second messenger signaling pathways. Nucleotide-based signaling is a ubiquitous signal transduction mechanism in all domains of life that relay changes in the extracellular or intracellular milieu to protein or RNA effectors, leading to adaptive physiological responses. To date, six bona fide nucleotide signaling pathways, (p)ppGpp, cAMP, cGMP, c-di-AMP, c-di-GMP and cGAMP, have been characterized with respect to basic pathway modules and phenotypic and physiological output...
January 5, 2017: Current Topics in Medicinal Chemistry
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