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FEBS Journal

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https://www.readbyqxmd.com/read/30443986/the-intrinsically-disordered-nature-of-the-peroxisomal-protein-translocation-machinery
#1
Aurora Barros-Barbosa, Tony A Rodrigues, Maria J Ferreira, Ana G Pedrosa, Nélson R Teixeira, Tânia Francisco, Jorge E Azevedo
Despite having a membrane that is impermeable to all but the smallest of metabolites, peroxisomes acquire their newly synthesized (cytosolic) matrix proteins in an already folded conformation. In some cases, even oligomeric proteins have been reported to translocate the organelle membrane. The protein sorting machinery that accomplishes this feat must be rather flexible and, unsurprisingly, several of its key components have large intrinsically disordered domains. Here, we provide an overview on these domains and their interactions trying to infer their functional roles in this protein sorting pathway...
November 16, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30431240/fancd2-protects-genome-stability-by-recruiting-rna-processing-enzymes-to-resolve-r-loops-during-mild-replication-stress
#2
Yusuke Okamoto, Masako Abe, Akiko Itaya, Junya Tomida, Masamichi Ishiai, Akifumi Takaori-Kondo, Masato Taoka, Toshiaki Isobe, Minoru Takata
R-loops, which consist of DNA:RNA hybrids and displaced single-strand DNA, are a major threat to genome stability. We have previously reported that a key Fanconi anemia protein, FANCD2, accumulates on large fragile genes during mild replication stress in a manner depending on R-loops. In this study, we found that FANCD2 suppresses R-loop levels. Furthermore, we identified FANCD2 interactions with RNA processing factors, including hnRNP U and DDX47. Our data suggest that FANCD2, which accumulates with R-loops in chromatin, recruits these factors and thereby promotes efficient processing of long RNA transcripts...
November 15, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30430741/discovery-and-analysis-of-a-novel-type-serine-biosynthetic-enzyme-phosphoserine-phosphatase-in-thermus-thermophilus
#3
Yoko Chiba, Ayako Yoshida, Shigeru Shimamura, Masafumi Kameya, Takeo Tomita, Makoto Nishiyama, Ken Takai
Studying the diversity of extant metabolisms and enzymes, especially those involved in the biosynthesis of primary metabolites including amino acids, is important to shed light on the evolution of life. Many organisms synthesize serine from phosphoserine via a reaction catalyzed by phosphoserine phosphatase (PSP). Two types of PSPs, belonging to distinct protein superfamilies, have been reported. Genomic analyses have revealed that the thermophilic bacterium Thermus thermophilus lacks both homologs while still having the ability to synthesize serine...
November 15, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30430736/cooperativity-in-proton-sensing-by-pip-aquaporins
#4
Victoria Vitali, Cintia Jozefkowicz, Agustina Canessa Fortuna, Gabriela Soto, F Luis Gonzalez Flecha, Karina Alleva
One of the most intriguing properties of PIP aquaporins is their ability to modulate water transport by sensing different levels of intracellular pH through the assembly of homo- and heterotetrameric molecular species in the plasma membrane. In this work, using a phenomenological modeling approach, we demonstrate that cooperativity in PIP biological response cannot be directly attributed to a cooperative proton binding, as it is usually considered, since it could also be the consequence of a cooperative conformation transition between open and closed states of the channel...
November 15, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30430732/phosphomimetic-mediated-in-vitro-rescue-of-hypertrophic-cardiomyopathy-linked-to-r58q-mutation-in-myosin-regulatory-light-chain
#5
Sunil Yadav, Katarzyna Kazmierczak, Jingsheng Liang, Yoel H Sitbon, Danuta Szczesna-Cordary
Myosin regulatory light chain (RLC) phosphorylation is important for cardiac muscle mechanics/function as well as for the Ca2+ -troponin/tropomyosin regulation of muscle contraction. This study focuses on the arginine to glutamine (R58Q) substitution in the human ventricular RLC (MYL2 gene), linked to malignant hypertrophic cardiomyopathy in humans and causing severe functional abnormalities in transgenic R58Q mice, including inhibition of cardiac RLC phosphorylation. Using a phosphomimic recombinant RLC variant where the phosphorylation site Ser-15 was substituted with an aspartic acid (S15D) and placed in the background of R58Q, we aimed to assess whether we could rescue/mitigate R58Q-induced structural/functional abnormalities in vitro...
November 15, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30430727/crystal-structures-of-vim-1-complexes-explain-active-site-heterogeneity-in-vim-class-metallo-%C3%AE-lactamases
#6
Ramya Salimraj, Philip Hinchliffe, Magda Kosmopoulou, Jonathan M Tyrrell, Jürgen Brem, Sander S van Berkel, Anil Verma, Raymond J Owens, Michael A McDonough, Timothy R Walsh, Christopher J Schofield, James Spencer
Metallo-β-Lactamases (MBLs) protect bacteria from almost all β-lactam antibiotics. VIM enzymes are among the most clinically important MBLs, with VIM-1 increasing in carbapenem-resistant Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae) that are amongst the hardest bacterial pathogens to treat. VIM enzymes display sequence variation at residues (224 and 228) that in related MBLs are conserved and participate in substrate binding. How they accommodate this variability, while retaining catalytic efficiency against a broad substrate range, has remained unclear...
November 15, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30422398/structural-basis-for-protein-phosphatase-1-recruitment-by-glycogen-targeting-subunits
#7
Jun Yu, Tingting Deng, Song Xiang
The rate-limiting enzymes in glycogen metabolism are subject to regulation by reversible phosphorylation. The glycogen-targeted protein phosphatase 1 (PP1) holo-enzyme catalyzes their dephosphorylation. It is composed of a catalytic subunit (PP1C) and a glycogen-targeting subunit (G subunit). To date, seven G subunits have been identified. They all contain an RVxF PP1C-binding motif. The interactions between this motif in the skeletal muscle-specific GM and PP1C have been revealed by structural studies. However, whether elements outside of this motif contribute to the interaction with PP1C is not clear...
November 13, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30422384/propeptide-glycosylation-and-galectin-3-binding-decrease-proteolytic-activation-of-human-prommp-9-progelatinase-b
#8
Lise Boon, Estefania Ugarte-Berzal, Erik Martens, Jennifer Vandooren, Vasily Rybakin, Didier Colau, Monica Gordon-Alonso, Pierre van der Bruggen, Walter Stöcker, Christoph Becker-Pauly, Peter Witters, Eva Morava-Kozics, Jaak Jaeken, Paul Proost, Ghislain Opdenakker
Matrix metalloproteinases (MMPs) are secreted as proenzymes, containing propeptides that interact with the catalytic zinc, thereby controlling MMP activation. The MMP-9 propeptide is unique in the MMP family because of its posttranslational modification with an N-linked oligosaccharide. ProMMP-9 activation by MMP-3 occurs stepwise by cleavage of the propeptide in an aminoterminal (pro-AT) and carboxyterminal (pro-CT) peptide. We chemically synthesized aglycosyl pro-AT and pro-CT and purified recombinant glycosylated pro-ATS f-9 ...
November 13, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30414318/membrane-topologies-of-pex13-and-pex14-provide-new-insights-on-the-mechanism-of-protein-import-into-peroxisomes
#9
Aurora Barros-Barbosa, Maria J Ferreira, Tony A Rodrigues, Ana G Pedrosa, Cláudia P Grou, Manuel P Pinto, Marc Fransen, Tânia Francisco, Jorge E Azevedo
PEX13 and PEX14 are two core components of the so-called peroxisomal docking/translocation module, the transmembrane hydrophilic channel through which newly synthesized peroxisomal proteins are translocated into the organelle matrix. The two proteins interact with each other and with PEX5, the peroxisomal matrix protein shuttling receptor, through relatively well characterized domains. However, the topologies of these membrane proteins are still poorly defined. Here, we subjected proteoliposomes containing PEX13 or PEX14 and purified rat liver peroxisomes to protease-protection assays and analyzed the protected protein fragments by mass spectrometry, Edman degradation and Western blotting using antibodies directed to specific domains of the proteins...
November 10, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30414312/nanodsf-as-screening-tool-for-enzyme-libraries-and-biotechnology-development
#10
Anders O Magnusson, Anna Szekrenyi, Henk-Jan Joosten, James Finnigan, Simon Charnock, Wolf-Dieter Fessner
Enzymes are attractive tools for synthetic applications. To be viable for industrial use enzymes need sufficient stability towards the desired reaction conditions such as high substrate and cosolvent concentration, non-neutral pH and elevated temperatures. Thermal stability is an attractive feature not only because it allows for protein purification by thermal treatment and higher process temperatures, but also due to the associated higher stability against other destabilising factors. Therefore, high-throughput screening methods are desirable for the identification of thermostable biocatalysts by discovery from nature or by protein engineering but current methods have low throughput and require time-demanding purification of protein samples...
November 10, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30390414/from-single-cells-to-tissue-self-organization
#11
REVIEW
Aline Xavier da Silveira Dos Santos, Prisca Liberali
Self-organization is a process by which interacting cells organize and arrange themselves in higher order structures and patterns. To achieve this, cells must have molecular mechanisms to sense their complex local environment and interpret it in order to respond accordingly. A combination of cell-intrinsic and cell-extrinsic cues are decoded by the single cells dictating their behaviour, their differentiation and symmetry-breaking potential driving development, tissue remodelling and regenerative processes...
November 3, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30390412/-inside-out-a-dialogue-between-mitochondria-and-bacteria
#12
REVIEW
Bing Han, Chih-Chun Janet Lin, Guo Hu, Meng C Wang
Mitochondria play crucial roles in regulating metabolism and longevity. A body of recent evidences reveals that the gut microbiome can also exert significant effects on these activities in the host. Here, by summarizing the currently known mechanisms underlying these regulations, and by comparing mitochondrial fission-fusion dynamics with bacterial interactions such as quorum sensing, we hypothesize that the microbiome impacts the host by communicating with their intracellular relatives, mitochondria. We highlight recent discoveries supporting this model, and these new findings reveal that metabolite molecules derived from bacteria can fine-tune mitochondrial dynamics in intestinal cells and hence influence host metabolic fitness and longevity...
November 3, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30390411/the-biology-of-the-cell-insights-from-mass-cytometry
#13
REVIEW
Petter Brodin
In single-cell biology there is an ongoing push towards more and more comprehensive measurements made in individual cells. By combining measurements of proteins, mRNA, genetic and epigenetic traits, in contexts of cell stimulation or drug treatment, novel single-cell analyses will help understand the determinants of cellular identity, differentiation decisions, and regulatory mechanisms governing cellular function in health and disease. Mass cytometry is a flexible methodology developed towards this aim, allowing analyses of cells in suspension such as blood, but also extended for the analyses of tissue sections...
November 3, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30387556/secreted-d-aspartate-oxidase-functions-in-c-elegans-reproduction-and-development
#14
Yasuaki Saitoh, Masumi Katane, Tetsuya Miyamoto, Masae Sekine, Taro Sakamoto, Hirotaka Imai, Hiroshi Homma
d-Aspartate oxidase (DDO) is a degradative enzyme that acts stereospecifically on free acidic D-amino acids such as d-aspartate and d-glutamate. d-Aspartate plays an important role in regulating neurotransmission, developmental processes, hormone secretion, and reproductive functions in mammals. In contrast, the physiological role of d-glutamate in mammals remains unclear. In Caenorhabditis elegans, the enzyme responsible for in vivo metabolism of d-glutamate is DDO-3, one of the three DDO isoforms, which is also required for normal self-fertility, hatching, and lifespan...
November 2, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30387554/novel-flavagline-like-compounds-with-potent-fli-1-inhibitory-activity-suppress-diverse-types-of-leukemia
#15
Jialei Song, Chunmao Yuan, Jue Yang, Tangjingjun Liu, Yao Yao, Xiao Xiao, Babu Gajendran, Dahai Xu, You-Jun Li, Chunlin Wang, Wuling Liu, Min Wen, David Spaner, Jorge Filmus, Eldad Zacksenhaus, Yiguo Zhang, Xiaojiang Hao, Yaacov Ben-David
E26 transformation-specific (ETS) gene family contains a common DNA binding domain, the ETS domain, responsible for sequence-specific DNA recognition on target promoters. The Fli-1 oncogene, a member of ETS gene family, plays a critical role in hematopoiesis and is overexpressed in diverse hematological malignancies. This ETS transcription factor regulates genes controlling several hallmarks of cancer and thus represents an excellent target for cancer therapy. Through screening compounds isolated from the medicinal plant Dysoxylum binectariferum in China, we identified two chemically related flavagline-like compounds including 4'-demethoxy-3',4'-methylenedioxyrocaglaol and rocaglaol that strongly inhibited Fli-1 transactivation ability...
November 2, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30387551/the-golgi-casein-kinase-fam20c-is-a-genuine-phosvitin-kinase-and-phosphorylates-polyserine-stretches-devoid-of-the-canonical-consensus
#16
Giorgio Cozza, Enrico Moro, Miles Black, Oriano Marin, Mauro Salvi, Andrea Venerando, Vincent S Tagliabracci, Lorenzo A Pinna
Egg yolk phosvitins, generated through the fragmentation of vitellogenins, are among the most heavily phosphorylated proteins ever described. Despite the early discovery in 1900 that chicken phosvitin is a phosphoprotein and its subsequent employment as an artificial substrate for a number of protein kinases, the identity of the enzyme(s) responsible for its phosphorylation remained a matter of conjecture until present. Here we provide evidence that phosvitin phosphorylation is catalyzed by Fam20C, an atypical protein kinase recently identified as the genuine casein kinase and responsible for the phosphorylation of many other secreted proteins at residues specified by the S-x-E/pS consensus...
November 2, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30387270/the-structure-of-pghl-hydrolase-bound-to-its-substrate-poly-%C3%AE-glutamate
#17
Sneha Ramaswamy, Masooma Rasheed, Carlo F Morelli, Cinzia Calvio, Brian J Sutton, Annalisa Pastore
The identification of new strategies to fight bacterial infections in view of the spread of multiple resistance to antibiotics has become mandatory. It has been demonstrated that several bacteria develop poly-γ-glutamic acid (γ-PGA) capsules as a protection from external insults and/or host defence systems. Among the pathogens that shield themselves in these capsules are B. anthracis, F. tularensis and several Staphylococcus strains. These are important pathogens with a profound influence on human health...
November 2, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30375744/2-deoxy-d-glucose-has-distinct-and-cell-line-specific-effects-on-the-survival-of-different-cancer-cells-upon-antitumor-drug-treatment
#18
Polina Maximchik, Alibek Abdrakhmanov, Evgeniya Inozemtseva, Pyotr A Tyurin-Kuzmin, Boris Zhivotovsky, Vladimir Gogvadze
The dependence of tumors on glycolysis for ATP generation offers a rationale for therapeutic strategies aimed at selective inhibition of the glycolytic pathway. Analysis of tumor cell responses to anticancer drugs revealed that inhibition of glycolysis by 2-deoxy-D-glucose (2-DG) generally augmented the apoptotic response; however, in HCT116 human colon carcinoma cells, apoptosis was suppressed. A comparison of neuroblastoma SK-N-BE(2) and HCT116 cells revealed, that in contrast to HCT116, in SK-N-BE(2) cells 2-DG alone was able to induce cell death...
October 30, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30369053/ancestral-diterpene-cyclases-show-increased-thermostability-and-substrate-acceptance
#19
Natalie M Hendrikse, Gwenaëlle Charpentier, Erik Nordling, Per-Olof Syrén
Bacterial diterpene cyclases are receiving increasing attention in biocatalysis and synthetic biology for the sustainable generation of complex multicyclic building blocks. Herein we explore the potential of ancestral sequence reconstruction to generate remodeled cyclases with enhanced stability, activity, and promiscuity. Putative ancestors of spiroviolene synthase, a bacterial class I diterpene cyclase, display an increased yield of soluble protein of up to fourfold upon expression in the model organism Escherichia coli...
October 28, 2018: FEBS Journal
https://www.readbyqxmd.com/read/30369031/crystal-structure-of-afifavidin-reveals-common-features-of-molecular-assemblage-in-the-bacterial-dimeric-avidins
#20
Orly Avraham, Edward A Bayer, Oded Livnah
The subfamily of bacterial dimeric avidins is being extended through discovery of additional members originating from diverse sources. All of these newly discovered dimeric avidin forms exhibit high affinity towards biotin, despite their lack of the critical Trp in the classical tetrameric forms. The common feature of forming cylinder-like multimers (hexamers and octamers) seems to be more than a random occurrence, which generally characterizes their apo forms in the crystalline state and also in some cases in solution...
October 28, 2018: FEBS Journal
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