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Biochemistry. Biokhimii︠a︡

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https://www.readbyqxmd.com/read/27908248/do-mitochondria-have-an-immune-system
#1
V A Popkov, L D Zorova, I O Korvigo, D N Silachev, S S Jankauskas, V A Babenko, I B Pevzner, T I Danilina, S D Zorov, E Y Plotnikov, D B Zorov
The question if mitochondria have some kind of immune system is not trivial. The basis for raising this question is the fact that bacteria, which are progenitors of mitochondria, do have an immune system. The CRISPR system in bacteria based on the principle of RNA interference serves as an organized mechanism for destroying alien nucleic acids, primarily those of viral origin. We have shown that mitochondria are also a target for viral attacks, probably due to a related organization of genomes in these organelles and bacteria...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908247/knockdown-of-minichromosome-maintenance-proteins-inhibits-foci-forming-of-mediator-of-dna-damage-checkpoint-1-in-response-to-dna-damage-in-human-esophageal-squamous-cell-carcinoma-te-1-cells
#2
Jinzhong Yu, Ruijie Wang, Jinfeng Wu, Zhongqin Dang, Qinsheng Zhang, Bo Li
Esophageal squamous cell carcinoma (ESCC) has a high morbidity in China and its treatment depends greatly on adjuvant chemotherapy. However, DNA damage repair in cancer cells severely affects the outcome of treatment. This study investigated the potential mechanism regarding mediator of DNA-damage checkpoint 1 (MDC1) and minichromosome maintenance proteins (MCMs) during DNA damage in ESCC. Recombinant vectors of MDC1 and MCMs with tags were constructed and transfected into human ESCC cell line TE-1. Immunoprecipitation and mass spectrometry were performed to screen the MCMs interacting with MDC1, and direct interaction was confirmed by glutathione S-transferase (GST) pull-down assay in vitro...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908246/inhibition-of-chaperonin-groel-by-a-monomer-of-ovine-prion-protein-and-its-oligomeric-forms
#3
S S Kudryavtseva, Y Y Stroylova, I A Zanyatkin, T Haertle, V I Muronetz
The possibility of inhibition of chaperonin functional activity by amyloid proteins was studied. It was found that the ovine prion protein PrP as well as its oligomeric and fibrillar forms are capable of binding with the chaperonin GroEL. Besides, GroEL was shown to promote amyloid aggregation of the monomeric and oligomeric PrP as well as PrP fibrils. The monomeric PrP was shown to inhibit the GroEL-assisted reactivation of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The oligomers of PrP decelerate the GroEL-assisted reactivation of GAPDH, and PrP fibrils did not affect this process...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908245/perfect-hemihedral-twinning-in-crystals-of-the-%C3%AE-subunit-of-translation-initiation-factor-2-from-sulfolobus-solfataricus-cause-and-effect
#4
O V Kravchenko, O S Nikonov, N A Nevskaya, E A Stolboushkina, V I Arkhipova, M B Garber, S V Nikonov
The crystal structure of the γ-subunit of translation initiation factor 2 from the archaeon Sulfolobus solfataricus (SsoIF2γ) has been solved based on perfectly hemihedral twinned data. The protein was cocrystallized with the 10-fold molar excess of GTP analog (GDPCP) over protein. However, no nucleotide was found in the structure, and the model demonstrated the apo form of the protein. Two slightly different molecules in the asymmetric unit of the crystal are related by the non-crystallographic 2-fold axis and form a tightly associated dimer...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908244/free-initiation-factors-eif4a-and-eif4b-are-dispensable-for-translation-initiation-on-uncapped-mrnas
#5
P A Sakharov, S Ch Agalarov
The formation of ribosomal 48S initiation complexes at the start AUG codon of uncapped mRNA leader sequences was studied using the methodology of primer extension inhibition (toe-printing). The experiments were performed in the system composed of purified individual components required for translation initiation. The formation of ribosomal 48S initiation complexes at the initiation codon was tested depending on the presence of the initiation factors eIF4F, eIF4A, and eIF4B. Several mRNAs containing short leader sequences lacking the extended secondary structure were studied...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908243/mitochondria-targeted-antioxidant-skqr1-reduces-tnf-induced-endothelial-permeability-in-vitro
#6
I I Galkin, O Yu Pletjushkina, R A Zinovkin, V V Zakharova, B V Chernyak, E N Popova
Prolonged or excessive increase in the circulatory level of proinflammatory tumor necrosis factor (TNF) leads to abnormal activation and subsequent damage to endothelium. TNF at high concentrations causes apoptosis of endothelial cells. Previously, using mitochondria-targeted antioxidants of SkQ family, we have shown that apoptosis of endothelial cells is dependent on the production of reactive oxygen species (ROS) in mitochondria (mito-ROS). Now we have found that TNF at low concentrations does not cause cell death but activates caspase-3 and caspase-dependent increase in endothelial permeability in vitro...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908242/participation-of-two-carbonic-anhydrases-of-the-alpha-family-in-photosynthetic-reactions-in-arabidopsis-thaliana
#7
E M Zhurikova, L K Ignatova, N N Rudenko, V A Mudrik, D V Vetoshkina, B N Ivanov
The expression of genes of two carbonic anhydrases (CA) belonging to the α-family, α-CA2 and α-CA4 (according to the nomenclature in N. Fabre et al. (2007) Plant Cell Environ., 30, 617-629), was studied in arabidopsis (Arabidopsis thaliana, var. Columbia) leaves. The expression of the At2g28210 gene coding α-CA2 decreased under increase in plant illumination, while the expression of the At4g20990 gene coding α-CA4 increased. Under conditions close to optimal for photosynthesis, in plants with gene At2g28210 knockout, the effective quantum yield of photosystem 2 and the light-induced accumulation of hydrogen peroxide in leaves were lower than in wild type plants, while the coefficient of non-photochemical quenching of leaf chlorophyll a fluorescence and the rate of CO2 assimilation in leaves were higher...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908241/molecular-cloning-biochemical-characterization-and-antitumor-properties-of-a-novel-l-asparaginase-from-synechococcus-elongatus-pcc6803
#8
R Kebeish, A El-Sayed, H Fahmy, A Abdel-Ghany
L-asparaginase (EC 3.5.1.1), which catalyzes the deamidation of L-asparagine to L-aspartic acid and ammonia, has been widely used as a key therapeutic tool in the treatment of tumors. The current commercially available L-asparaginases, produced from bacteria, have signs of toxicity and hypersensitivity reactions during the course of tumor therapy. Therefore, searching for L-asparaginases with unique biochemical properties and fewer adverse effects was the objective of this work. In this study, cyanobacterial strain Synechococcus elongatus PCC6803 was found as a novel source of L-asparaginase...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908240/new-fluorescent-macrolide-derivatives-for-studying-interactions-of-antibiotics-and-their-analogs-with-the-ribosomal-exit-tunnel
#9
A G Tereshchenkov, A V Shishkina, V V Karpenko, V A Chertkov, A L Konevega, P S Kasatsky, A A Bogdanov, N V Sumbatyan
Novel fluorescent derivatives of macrolide antibiotics related to tylosin bearing rhodamine, fluorescein, Alexa Fluor 488, BODIPY FL, and nitrobenzoxadiazole (NBD) residues were synthesized. The formation of complexes of these compounds with 70S E. coli ribosomes was studied by measuring the fluorescence polarization depending on the ribosome amount at constant concentration of the fluorescent substance. With the synthesized fluorescent tylosin derivatives, the dissociation constants for ribosome complexes with several known antibiotics and macrolide analogs previously obtained were determined...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908239/protein-transphosphorylation-during-the-mutual-interaction-between-phytochrome-a-and-a-nuclear-isoform-of-nucleoside-diphosphate-kinase-is-regulated-by-red-light
#10
A Hetmann, M Wujak, S Kowalczyk
The nuclear isoform of nucleoside diphosphate kinase isoenzyme NDPK-In undergoes strong catalytic activation upon its interaction with the active form of phytochrome A (Pfr) in red light. The autophosphorylation or intermolecular transphosphorylation of NDPK-In leads to the formation of phosphoester bonds stable in acidic solution. The phosphate residue of the phosphamide bond in the active center of NDPK-In can also be transferred to serine and threonine residues localized in other proteins, including phytochrome A...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908238/thermodynamic-analysis-of-fast-stages-of-specific-lesion-recognition-by-dna-repair-enzymes
#11
REVIEW
N A Kuznetsov, O S Fedorova
The methodology of determination of the thermodynamic parameters of fast stages of recognition and cleavage of DNA substrates is described for the enzymatic processes catalyzed by DNA glycosylases Fpg and hOGG1 and AP endonuclease APE1 during base excision repair (BER) pathway. For this purpose, stopped-flow pre-steady-state kinetic analysis of tryptophan fluorescence intensity changes in proteins and fluorophores in DNA substrates was performed at various temperatures. This approach made it possible to determine the changes of standard Gibbs free energy, enthalpy, and entropy of sequential steps of DNA-substrate binding, as well as activation enthalpy and entropy for the transition complex formation of the catalytic stage...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908237/plant-factories-for-the-production-of-monoclonal-antibodies
#12
REVIEW
E V Sheshukova, T V Komarova, Y L Dorokhov
Like animal cells, plant cells bear mechanisms for protein synthesis and posttranslational modification (glycosylation and phosphorylation) that allow them to be seriously considered as factories for therapeutic proteins, including antibodies, with the development of biotechnology. The plant platform for monoclonal antibody production is an attractive approach due to its flexibility, speed, scalability, low cost of production, and lack of contamination risk from animal-derived pathogens. Contemporary production approaches for therapeutic proteins rely on transgenic plants that are obtained via the stable transformation of plant cells as well as the transient (temporary) expression of foreign proteins...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908236/interaction-between-saccharomyces-cerevisiae-mitochondrial-dna-binding-protein-abf2p-and-cce1p-resolvase
#13
E O Samoilova, I A Krasheninnikov, S A Levitskii
Mitochondrial DNA is susceptible to the action of reactive oxygen species generated by the reactions of oxidative phosphorylation. Homologous recombination is one of the mechanisms providing integrity of the mitochondrial genome. Some proteins that take part in this process in budding yeast mitochondria have been identified. These include Abf2p, the major protein of the mt-nucleoid that specifically binds cruciform DNA, and Cce1p - Holliday junction resolvase. Here we show that Abf2p does not significantly affect either binding of Cce1p to branched DNA or rate and specificity of Holliday junction resolution...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908235/pentatricopeptide-motifs-in-the-n-terminal-extension-domain-of-yeast-mitochondrial-rna-polymerase-rpo41p-are-not-essential-for-its-function
#14
J Kruszewski, P Golik
The core mitochondrial RNA polymerase is a single-subunit enzyme that in yeast Saccharomyces cerevisiae is encoded by the nuclear RPO41 gene. It is an evolutionary descendant of the bacteriophage RNA polymerases, but it includes an additional unconserved N-terminal extension (NTE) domain that is unique to the organellar enzymes. This domain mediates interactions between the polymerase and accessory regulatory factors, such as yeast Sls1p and Nam1p. Previous studies demonstrated that deletion of the entire NTE domain results only in a temperature-dependent respiratory deficiency...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908234/sustained-early-disruption-of-mitochondrial-function-contributes-to-arsenic-induced-prostate-tumorigenesis
#15
B Singh, M Kulawiec, K M Owens, A Singh, K K Singh
Arsenic is a well-known human carcinogen that affects millions of people worldwide, but the underlying mechanisms of carcinogenesis are unclear. Several epidemiological studies have suggested increased prostate cancer incidence and mortality due to exposure to arsenic. Due to lack of an animal model of arsenic-induced carcinogenesis, we used a prostate epithelial cell culture model to identify a role for mitochondria in arsenic-induced prostate cancer. Mitochondrial morphology and membrane potential was impacted within a few hours of arsenic exposure of non-neoplastic prostate epithelial cells...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908233/procedure-for-purification-of-recombinant-premsk1p-from-e-coli-determines-its-properties-as-a-factor-of-trna-import-into-yeast-mitochondria
#16
E V Smirnova, I V Chicherin, M V Baleva, N S Entelis, I A Tarassov, P A Kamenski
Mitochondrial genomes of many eukaryotic organisms do not code for the full tRNA set necessary for organellar translation. Missing tRNA species are imported from the cytosol. In particular, one out of two cytosolic lysine tRNAs of the yeast Saccharomyces cerevisiae is partially internalized by mitochondria. The key protein factor of this process is the precursor of mitochondrial lysyl-tRNA synthetase, preMsk1p. In this work, we show that recombinant preMsk1p purified from E. coli in native conditions, when used in an in vitro tRNA import system, demonstrates some properties different from those shown by the renatured protein purified from E...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908232/iron-sulfur-clusters-in-mitochondrial-metabolism-multifaceted-roles-of-a-simple-cofactor
#17
REVIEW
Johnny Stiban, Minyoung So, Laurie S Kaguni
Iron-sulfur metabolism is essential for cellular function and is a key process in mitochondria. In this review, we focus on the structure and assembly of mitochondrial iron-sulfur clusters and their roles in various metabolic processes that occur in mitochondria. Iron-sulfur clusters are crucial in mitochondrial respiration, in which they are required for the assembly, stability, and function of respiratory complexes I, II, and III. They also serve important functions in the citric acid cycle, DNA metabolism, and apoptosis...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908231/the-mitochondrial-genome-the-nucleoid
#18
REVIEW
A A Kolesnikov
Mitochondrial DNA (mtDNA) in cells is organized in nucleoids containing DNA and various proteins. This review discusses questions of organization and structural dynamics of nucleoids as well as their protein components. The structures of mt-nucleoid from different organisms are compared. The currently accepted model of nucleoid organization is described and questions needing answers for better understanding of the fine mechanisms of the mitochondrial genetic apparatus functioning are discussed.
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908230/dna-import-into-mitochondria
#19
REVIEW
Yu M Konstantinov, A Dietrich, F Weber-Lotfi, N Ibrahim, E S Klimenko, V I Tarasenko, T A Bolotova, M V Koulintchenko
In recent decades, it has become evident that the condition for normal functioning of mitochondria in higher eukaryotes is the presence of membrane transport systems of macromolecules (proteins and nucleic acids). Natural competence of the mitochondria in plants, animals, and yeasts to actively uptake DNA may be directly related to horizontal gene transfer into these organelles occurring at much higher rate compared to the nuclear and chloroplast genomes. However, in contrast with import of proteins and tRNAs, little is known about the biological role and molecular mechanism underlying import of DNA into eukaryotic mitochondria...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908229/localization-of-nuclear-encoded-mrnas-to-mitochondria-outer-surface
#20
REVIEW
A Golani-Armon, Y Arava
The diverse functions of mitochondria depend on hundreds of different proteins. The vast majority of these proteins is encoded in the nucleus, translated in the cytosol, and must be imported into the organelle. Import was shown to occur after complete synthesis of the protein, with the assistance of cytosolic chaperones that maintain it in an unfolded state and target it to the mitochondrial translocase of the outer membrane (TOM complex). Recent studies, however, identified many mRNAs encoding mitochondrial proteins near the outer membrane of mitochondria...
October 2016: Biochemistry. Biokhimii︠a︡
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