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https://www.readbyqxmd.com/read/29150446/biogenesis-of-the-bacterial-cbb3-cytochrome-c-oxidase-active-subcomplexes-support-a-sequential-assembly-model
#1
Anne Durand, Marie-Line Bourbon, Anne-Soisig Steunou, Bahia Khalfaoui-Hassani, Camille Legrand, Audrey Guitton, Chantal Astier, Soufian Ouchane
The cbb3 oxidase has a high affinity for oxygen and is required for growth of bacteria, including pathogens, in oxygen-limited environments. However, the assembly of this oxidase is poorly understood. Most cbb3 are composed of four subunits: the catalytic CcoN subunit, the two cytochromes c subunits (CcoO and CcoP) involved in electron transfer and the small CcoQ subunit with an unclear function. Here, we address the role of these four subunits in cbb3 biogenesis in the purple bacterium Rubrivivax gelatinosus Analyses of membrane proteins from different mutants revealed the presence of active CcoNQO and CcoNO subcomplexes and also showed that the CcoP subunit is not essential for their assembly...
November 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29149347/signal-recognition-particle-binds-to-translating-ribosomes-before-emergence-of-a-signal-anchor-sequence
#2
Evan Mercier, Wolf Holtkamp, Marina V Rodnina, Wolfgang Wintermeyer
The bacterial signal recognition particle (SRP) is part of the machinery that targets ribosomes synthesizing membrane proteins to membrane-embedded translocons co-translationally. Recognition of nascent membrane proteins occurs by virtue of a hydrophobic signal-anchor sequence (SAS) contained in the nascent chain, usually at the N terminus. Here we use fluorescence-based stopped-flow to monitor SRP-ribosome interactions with actively translating ribosomes while an SRP substrate is synthesized and emerges from the peptide exit tunnel...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29149285/draft-genome-analysis-provides-insights-into-the-fiber-yield-crude-protein-biosynthesis-and-vegetative-growth-of-domesticated-ramie-boehmeria-nivea-l-gaud
#3
Chan Liu, Liangbin Zeng, Siyuan Zhu, Lingqing Wu, Yanzhou Wang, Shouwei Tang, Hongwu Wang, Xia Zheng, Jian Zhao, Xiaorong Chen, Qiuzhong Dai, Touming Liu
Plentiful bast fiber, a high crude protein content, and vigorous vegetative growth make ramie a popular fiber and forage crop. Here, we report the draft genome of ramie, along with a genomic comparison and evolutionary analysis. The draft genome contained a sequence of approximately 335.6 Mb with 42,463 predicted genes. A high-density genetic map with 4,338 single nucleotide polymorphisms (SNPs) was developed and used to anchor the genome sequence, thus, creating an integrated genetic and physical map containing a 58...
November 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29147710/step-by-step-build-up-of-covalent-poly-ethylene-oxide-nanogel-films
#4
S Zahouani, L Hurman, M De Giorgi, C Vigier-Carrière, F Boulmedais, B Senger, B Frisch, P Schaaf, P Lavalle, L Jierry
Hydrogels based on poly(ethylene glycol) (PEG) are commonly used for studies related to cell fate and tissue engineering. Here we present a new covalent layer-by-layer build-up process leading to PEG coatings of nanometer size called "nanogel films". Compared to macroscopic hydrogels, such nanogels should provide a fine control over the structure and the thickness of the coating. Alternated deposition of bifunctional and tetra functional PEG molecules reacting through thiol/maleimide click chemistry is evaluated by quartz crystal microbalance...
November 17, 2017: Nanoscale
https://www.readbyqxmd.com/read/29145811/genome-wide-analysis-of-the-auxin-indoleacetic-acid-aux-iaa-gene-family-in-allotetraploid-rapeseed-brassica-napus-l
#5
Haitao Li, Bo Wang, Qinghua Zhang, Jing Wang, Graham J King, Kede Liu
BACKGROUND: Auxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development. Although the Aux/IAA gene family has been identified in many plants, within allotetraploid Brassica napus little is known. RESULTS: In this study, a total of 119 Aux/IAA genes were found in the genome of B. napus. They were distributed non-randomly across all 19 chromosomes and other non-anchored random scaffolds, with a symmetric distribution in the A and C subgenomes...
November 16, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29145196/aqp2-abundance-is-regulated-by-the-e3-ligase-chip-via-hsp70
#6
Mariangela Centrone, Marianna Ranieri, Annarita Di Mise, Sante Princiero Berlingerio, Annamaria Russo, Peter M T Deen, Olivier Staub, Giovanna Valenti, Grazia Tamma
BACKGROUND/AIMS: AQP2 expression is mainly controlled by vasopressin-dependent changes in protein abundance which is in turn regulated by AQP2 ubiquitylation and degradation, however the proteins involved in these processes are largely unknown. Here, we investigated the potential role of the CHIP E3 ligase in AQP2 regulation. METHODS: MCD4 cells and kidney slices were used to study the involvement of the E3 ligase CHIP on AQP2 protein abundance by cell homogenization and immunoprecipitation followed by immunoblotting...
November 17, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29144135/parameterization-of-palmitoylated-cysteine-farnesylated-cysteine-geranylgeranylated-cysteine-and-myristoylated-glycine-for-the-martini-force-field
#7
Yoav Atsmon-Raz, D Peter Tieleman
Peripheral membrane proteins go through various post-translational modifications that covalently bind fatty acid tails to specific amino acids. These post translational modifications significantly alter the lipophilicity of the modified proteins and allow them to anchor to biological membranes. Over 1000 different proteins have been identified to date that require such membrane-protein interactions in order to carry out their biological functions, including members of the Src and Ras superfamilies that play key roles in cell signaling and carcinogenesis...
November 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29140585/timap-the-versatile-protein-phosphatase-1-regulator-in-endothelial-cells
#8
REVIEW
Anita Boratkó, Csilla Csortos
Transforming growth factor (TGF)-β inhibited membrane associated protein, TIMAP, is the member of the myosin phosphatase targeting protein (MYPT) family of protein phosphatase 1 (PP1) regulatory subunits. The N-terminal part of TIMAP has a typical MYPT family structure with a sequence element called MyPhone (myosin phosphatase N-terminal element), a putative bipartite nuclear localization signal, a PP1 catalytic subunit binding motif, and five ankyrin repeats. The C-terminal half of TIMAP is intrinsically disordered, but ends with a functional CAAX box for lipid modification which allows localization of TIMAP at the plasma membrane...
November 15, 2017: IUBMB Life
https://www.readbyqxmd.com/read/29138828/identification-of-risk-genes-associated-with-myocardial-infarction-based-on-the-recursive-feature-elimination-algorithm-and-support-vector-machine-classifier
#9
Xiaoqiang Yang
The aim of the present study was to identify risk genes in myocardial infarction. Microarray data GSE34198, containing data from the peripheral blood of 49 myocardial infarction samples and 48 corresponding control samples, were downloaded from the Gene Expression Omnibus database to screen the differentially expressed genes (DEGs). The DEGs were used to construct a protein‑protein interaction (PPI) network of patient samples, from which the feature genes were identified using the neighboring score method...
November 14, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29138354/efficient-er-fusion-requires-a-dimerization-and-c-terminal-tail-mediated-membrane-anchoring-of-rhd3
#10
Jiaqi Sun, Huanquan Zheng
The endoplasmic reticulum (ER) is a network of tubules and sheets stretching throughout the eukaryotic cells. The formation of the ER requires homotypic membrane fusion, which is mediated by a family of Dynamin-like GTPase proteins. The Arabidopsis member ROOT HAIR DEFECTIVE3 (RHD3) has been demonstrated to mediate ER membrane fusion, but how exactly RHD3 is involved in the process is still unknown. Here we conducted systemic structure-function analyses of roles of different RHD3 domains in mediating ER fusion...
November 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29138001/pdz-ligand-binding-induced-conformational-coupling-of-the-pdz-sh3-gk-tandems-in-psd-95-family-maguks
#11
Menglong Zeng, Fei Ye, Jia Xu, Mingjie Zhang
DLG MAGUKs are abundantly expressed in glutamatergic synapses, crucial for synaptic transmission and plasticity by anchoring various postsynaptic components including glutamate receptors, downstream scaffold proteins and signaling enzymes. Different DLG members have shared structures and functions, but also contain unique features. How DLG family proteins function individually and cooperatively are largely unknown. Here, we report that PSD-95 PDZ3 directly couples with SH3-GK tandem in a PDZ ligand binding-dependent manner, and the coupling can promote PSD-95 dimerization and multimerization...
November 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29137293/identification-of-novel-genetic-regulations-associated-with-airway-epithelial-homeostasis-using-next-generation-sequencing-data-and-bioinformatics-approaches
#12
Chau-Chyun Sheu, Ming-Ju Tsai, Feng-Wei Chen, Kuo-Feng Chang, Wei-An Chang, Inn-Wen Chong, Po-Lin Kuo, Ya-Ling Hsu
Airway epithelial cells play important roles in airway remodeling. Understanding gene regulations in airway epithelial homeostasis may provide new insights into pathogenesis and treatment of asthma. This study aimed to combine gene expression (GE) microarray, next generation sequencing (NGS), and bioinformatics to explore genetic regulations associated with airway epithelial homeostasis. We analyzed expression profiles of mRNAs (GE microarray) and microRNAs (NGS) in normal and asthmatic bronchial epithelial cells, and identified 9 genes with potential microRNA-mRNA interactions...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137139/deduction-of-novel-genes-potentially-involved-in-osteoblasts-of-rheumatoid-arthritis-using-next-generation-sequencing-and-bioinformatic-approaches
#13
Yi-Jen Chen, Wei-An Chang, Ya-Ling Hsu, Chia-Hsin Chen, Po-Lin Kuo
The role of osteoblasts in peri-articular bone loss and bone erosion in rheumatoid arthritis (RA) has gained much attention, and microRNAs are hypothesized to play critical roles in the regulation of osteoblast function in RA. The aim of this study is to explore novel microRNAs differentially expressed in RA osteoblasts and to identify genes potentially involved in the dysregulated bone homeostasis in RA. RNAs were extracted from cultured normal and RA osteoblasts for sequencing. Using the next generation sequencing and bioinformatics approaches, we identified 35 differentially expressed microRNAs and 13 differentially expressed genes with potential microRNA-mRNA interactions in RA osteoblasts...
November 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29134801/adsorbed-polyzwitterion-copolymer-layers-designed-for-protein-repellency-and-interfacial-retention
#14
S Kalasin, R A Letteri, T Emrick, M M Santore
Poly(2-methacryloyloxyethyl phosphorylcholine) (pMPC), when end-tethered to surfaces by the adsorption of copolymeric cationic segments, forms adsorbed layers that substantially reduce protein adsorption. This study examined variations in the molecular architecture of copolymers containing cationic poly(trimethylammonium ethyl methacrylate (pTMAEMA) anchor blocks that adsorbed strongly to negative surfaces. With appropriate copolymer design, the pTMAEMA blocks were shielded, by pMPC tethers, from solution-phase proteins...
November 14, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29131610/real-time-imaging-of-single-molecule-enzyme-cascade-using-a-dna-origami-raft
#15
Lele Sun, Yanjing Gao, Yan Xu, Jie Chao, Huajie Liu, Lianhui Wang, Di Li, Chunhai Fan
The dynamics of enzymes are directly associated with their functions in various biological processes. Nevertheless, the ability to image motions of single enzymes in a highly parallel fashion remains a challenge. Here, we develop a DNA origami raft-based platform for in-situ real-time imaging of enzyme cascade at the single-molecule level. The motions of enzymes are rationally controlled via different tethering modes on a two-dimensional (2D) supported lipid bilayer (SLB). We construct an enzyme cascade by anchoring catalase on cholesterol-labeled double stranded (ds) DNA, and glucose oxidase on cholesterol-labeled origami rafts...
November 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29131302/highly-active-spore-biocatalyst-by-self-assembly-of-co-expressed-anchoring-scaffoldin-and-multimeric-enzyme
#16
Long Chen, Megan Holmes, Elise Schaefer, Ashok Mulchandani, Xin Ge
We report a spore-based biocatalysis platform capable of producing and self-assembling active multimeric enzymes on a spore surface with a high loading density. This was achieved by co-expressing both a spore surface-anchoring scaffoldin protein containing multiple cohesin domains and a dockerin-tagged enzyme of interest in the mother cell compartment during Bacillus subtilis sporulation. Using this method, tetrameric β-galactosidase was successfully displayed on the spore surface with a loading density of 1...
November 13, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29127429/a-high-density-consensus-linkage-map-of-white-lupin-highlights-synteny-with-narrow-leafed-lupin-and-provides-markers-tagging-key-agronomic-traits
#17
Michał Książkiewicz, Nelson Nazzicari, Hua'an Yang, Matthew N Nelson, Daniel Renshaw, Sandra Rychel, Barbara Ferrari, Maria Carelli, Magdalena Tomaszewska, Stanisław Stawiński, Barbara Naganowska, Bogdan Wolko, Paolo Annicchiarico
White lupin (Lupinus albus L.) is a valuable source of seed protein, carbohydrates and oil, but requires genetic improvement to attain its agronomic potential. This study aimed to (i) develop a new high-density consensus linkage map based on new, transcriptome-anchored markers; (ii) map four important agronomic traits, namely, vernalization requirement, seed alkaloid content, and resistance to anthracnose and Phomopsis stem blight; and, (iii) define regions of synteny between the L. albus and narrow-leafed lupin (L...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29127190/vesicle-mediated-secretion-of-misfolded-prion-protein-molecules-from-cyclosporin-a-treated-cells
#18
Ieshita Pan, Noa Roitenberg, Ehud Cohen
Loss of protein homeostasis is a hazardous situation that jeopardizes cellular functionality and viability. Cells have developed mechanisms that supervise protein integrity and direct misfolded molecules for degradation. Nevertheless, subsets of aggregation-prone proteins escape degradation and form aggregates that can underlie the development of neurodegenerative disorders. In some cases, cells deposit hazardous protein aggregates in designated sites, like aggresomes, or secrete them with vesicles. The prion protein (PrP) is an aggregation-prone, membrane-anchored glycoprotein, whose aggregation causes familial and sporadic, fatal, neurodegenerative diseases...
November 10, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29126905/failure-of-active-targeting-by-a-cholesterol-anchored-ligand-and-improvement-by-altering-the-lipid-composition-to-prevent-ligand-desorption
#19
Shoshiro Yamamoto, Yu Sakurai, Hideyoshi Harashima
Although anti-angiogenic therapy is predicted to be an effective therapy for treating cancer, selectively targeting tumor endothelial cells (TECs), and not normal endothelial cells, remains a major obstacle. Modifying a drug carrier with a targeting ligand is a popular strategy for developing an active-targeting type drug delivery system (DDS). We previously reported that a cyclo(Arg-Gly-Asp-D-Phe-Lys) (cRGD)-equipped liposome that contains encapsulated siRNA (RGD-MEND) achieved an efficient therapeutic outcome in a murine cancer model...
November 7, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/29126902/identification-and-characterization-of-the-mitochondrial-membrane-sorting-signals-in-phosphatidylserine-decarboxylase-1-from-saccharomyces-cerevisiae
#20
Ariane Wagner, Francesca Di Bartolomeo, Isabella Klein, Claudia Hrastnik, Kim Nguyen Doan, Thomas Becker, Günther Daum
Phosphatidylserine decarboxylase 1 (Psd1p) catalyzes the formation of the majority of phosphatidylethanolamine (PE) in the yeast Saccharomyces cerevisiae. Psd1p is localized to mitochondria, anchored to the inner mitochondrial membrane (IMM) through membrane spanning domains and oriented towards the mitochondrial intermembrane space. We found that Psd1p harbors at least two inner membrane-associated domains, which we named IM1 and IM2. IM1 is important for proper orientation of Psd1p within the IMM (Horvath et al...
November 7, 2017: Biochimica et Biophysica Acta
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