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Biomolecules

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https://www.readbyqxmd.com/read/28230817/common%C3%A2-chemical%C3%A2-inductors%C3%A2-of%C3%A2-replication%C3%A2-stress-%C3%A2-focus%C3%A2-on%C3%A2-cell-based%C3%A2-studies
#1
REVIEW
Eva Vesela, Katarina Chroma, Zsofia Turi, Martin Mistrik
DNA replication is a highly demanding process regarding the energy and material supply and must be precisely regulated, involving multiple cellular feedbacks. The slowing down or stalling of DNA synthesis and/or replication forks is referred to as replication stress (RS). Owing to the complexity and requirements of replication, a plethora of factors may interfere and challenge the genome stability, cell survival or affect the whole organism. This review outlines chemical compounds that are known inducers of RS and commonly used in laboratory research...
February 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28230814/m1a%C3%A2-post-transcriptional%C3%A2-modification%C3%A2-in%C3%A2-trnas
#2
REVIEW
Stephanie Oerum, Clément Dégut, Pierre Barraud, Carine Tisné
To date, about 90 post-transcriptional modifications have been reported in tRNA expanding their chemical and functional diversity. Methylation is the most frequent post-transcriptional tRNA modification that can occur on almost all nitrogen sites of the nucleobases, on the C5 atom of pyrimidines, on the C2 and C8 atoms of adenosine and, additionally, on the oxygen of the ribose 2'-OH. The methylation on the N1 atom of adenosine to form 1-methyladenosine (m1A) has been identified at nucleotide position 9, 14, 22, 57, and 58 in different tRNAs...
February 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28230807/effect-of-reduction-of-redox-modifications-of-cys-residues-in-the-na-k-atpase-%C3%AE-1-subunit-on-its-activity
#3
Elena A Dergousova, Irina Yu Petrushanko, Elizaveta A Klimanova, Vladimir A Mitkevich, Rustam H Ziganshin, Olga D Lopina, Alexander A Makarov
Sodium-potassium adenosine triphosphatase (Na,K-ATPase) creates a gradient of sodium and potassium ions necessary for the viability of animal cells, and it is extremely sensitive to intracellular redox status. Earlier we found that regulatory glutathionylation determines Na,K-ATPase redox sensitivity but the role of basal glutathionylation and other redox modifications of cysteine residues is not clear. The purpose of this study was to detect oxidized, nitrosylated, or glutathionylated cysteine residues in Na,K-ATPase, evaluate the possibility of removing these modifications and assess their influence on the enzyme activity...
February 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28218716/sulfur-modifications-of-the-wobble-u34-in-trnas-and-their-intracellular-localization-in-eukaryotic-cells
#4
REVIEW
Yumi Nakai, Masato Nakai, Takato Yano
The wobble uridine (U34) of transfer RNAs (tRNAs) for two-box codon recognition, i.e., tRNA(Lys)UUU, tRNA(Glu)UUC, and tRNA(Gln)UUG, harbor a sulfur- (thio-) and a methyl-derivative structure at the second and fifth positions of U34, respectively. Both modifications are necessary to construct the proper anticodon loop structure and to enable them to exert their functions in translation. Thio-modification of U34 (s²U34) is found in both cytosolic tRNAs (cy-tRNAs) and mitochondrial tRNAs (mt-tRNAs). Although l-cysteine desulfurase is required in both cases, subsequent sulfur transfer pathways to cy-tRNAs and mt-tRNAs are different due to their distinct intracellular locations...
February 18, 2017: Biomolecules
https://www.readbyqxmd.com/read/28212318/alcohol-%C3%A2-adipose%C3%A2-tissue%C3%A2-and%C3%A2-lipid%C3%A2-dysregulation
#5
Jennifer L Steiner, Charles H Lang
Chronic alcohol consumption perturbs lipid metabolism as it increases adipose tissue lipolysis and leads to ectopic fat deposition within the liver and the development of alcoholic fatty liver disease. In addition to the recognition of the role of adipose tissue derived fatty acids in liver steatosis, alcohol also impacts other functions of adipose tissue and lipid metabolism. Lipid balance in response to long-term alcohol intake favors adipose tissue loss and fatty acid efflux as lipolysis is upregulated and lipogenesis is either slightly decreased or unchanged...
February 16, 2017: Biomolecules
https://www.readbyqxmd.com/read/28216563/the-genomic-impact-of-dna-cpg-methylation-on-gene-expression-relationships-in-prostate-cancer
#6
REVIEW
Mark D Long, Dominic J Smiraglia, Moray J Campbell
The process of DNA CpG methylation has been extensively investigated for over 50 years and revealed associations between changing methylation status of CpG islands and gene expression. As a result, DNA CpG methylation is implicated in the control of gene expression in developmental and homeostasis processes, as well as being a cancer-driver mechanism. The development of genome-wide technologies and sophisticated statistical analytical approaches has ushered in an era of widespread analyses, for example in the cancer arena, of the relationships between altered DNA CpG methylation, gene expression, and tumor status...
February 14, 2017: Biomolecules
https://www.readbyqxmd.com/read/28208632/cross-talk-between-dnmt2-dependent-trna-methylation-and-queuosine-modification
#7
REVIEW
Ann E Ehrenhofer-Murray
Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA) methyltransferases for cytosine-5 methylation, foremost C38 (m5C38) of tRNAAsp. The second unanticipated finding was our recent discovery of a nutritional regulation of Dnmt2 in the fission yeast Schizosaccharomyces pombe. Significantly, the presence of the nucleotide queuosine in tRNAAsp strongly stimulates Dnmt2 activity both in vivo and in vitro in S...
February 10, 2017: Biomolecules
https://www.readbyqxmd.com/read/28208788/next-generation%C3%A2-sequencing-based%C3%A2-ribomethseq%C3%A2-protocol%C3%A2-for%C3%A2-analysis%C3%A2-of%C3%A2-trna%C3%A2-2-o-methylation
#8
Virginie Marchand, Florian Pichot, Kathrin Thüring, Lilia Ayadi, Isabel Freund, Alexander Dalpke, Mark Helm, Yuri Motorin
Analysis of RNA modifications by traditional physico-chemical approaches is labor  intensive,  requires  substantial  amounts  of  input  material  and  only  allows  site-by-site  measurements.  The  recent  development  of  qualitative  and  quantitative  approaches  based  on   next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA  species.  The  Illumina  sequencing-based  RiboMethSeq  protocol  was  initially  developed  and  successfully applied for mapping of ribosomal RNA (rRNA) 2'-O-methylations...
February 9, 2017: Biomolecules
https://www.readbyqxmd.com/read/28208705/the-escherichia-coli-cog1738-member-yhhq-is-involved-in-7-cyanodeazaguanine-preq%C3%A2-transport
#9
Rémi Zallot, Yifeng Yuan, Valérie de Crécy-Lagard
Queuosine (Q) is a complex modification of the wobble base in tRNAs with GUN anticodons. The full Q biosynthesis pathway has been elucidated in Escherichia coli. FolE, QueD, QueE and QueC are involved in the conversion of guanosine triphosphate (GTP) to 7-cyano-7-deazaguanine (preQ₀), an intermediate of increasing interest for its central role in tRNA and DNA modification and secondary metabolism. QueF then reduces preQ₀ to 7-aminomethyl-7-deazaguanine (preQ₁). PreQ₁ is inserted into tRNAs by tRNA guanine(34) transglycosylase (TGT)...
February 8, 2017: Biomolecules
https://www.readbyqxmd.com/read/28208700/role-of-protein-quality-control-failure-in-alcoholic-hepatitis-pathogenesis
#10
REVIEW
Samuel W French, Maryam Masouminia, Sara Samadzadeh, Brittany C Tillman, Alejandro Mendoza, Barbara A French
: The mechanisms of protein quality control in hepatocytes in cases of alcoholic hepatitis (AH) including ufmylation, FAT10ylation, metacaspase 1 (Mca1), ERAD (endoplasmic reticulum-associated degradation), JUNQ (juxta nuclear quality control), IPOD (insoluble protein deposit) autophagocytosis, and ER stress are reviewed. The Mallory-Denk body (MDB) formation develops in the hepatocytes in alcoholic hepatitis as a consequence of the failure of these protein quality control mechanisms to remove misfolded and damaged proteins and to prevent MDB aggresome formation within the cytoplasm of hepatocytes...
February 8, 2017: Biomolecules
https://www.readbyqxmd.com/read/28146121/a-novel-diterpene-glycoside-with-nine-glucose-units-from-stevia-rebaudiana-bertoni
#11
Indra Prakash, Gil Ma, Cynthia Bunders, Romila D Charan, Catherine Ramirez, Krishna P Devkota, Tara M Snyder
Following our interest in new diterpene glycosides with better taste profiles than that of Rebaudioside M, we have recently isolated and characterized Rebaudioside IX-a novel steviol glycoside-from a commercially-supplied extract of Stevia rebaudiana Bertoni. This molecule contains a hexasaccharide group attached at C-13 of the central diterpene core, and contains three additional glucose units when compared with Rebaudioside M. Here we report the complete structure elucidation-based on extensive Nuclear Magnetic Resonance (NMR) analysis (1H, 13C, Correlation Spectroscopy (COSY), Heteronuclear Single Quantum Coherence-Distortionless Enhancement Polarization Transfer (HSQC-DEPT), Heteronuclear Multiple Bond Correlation (HMBC), 1D Total Correlation Spectroscopy (TOCSY), Nuclear Overhauser Effect Spectroscopy (NOESY)) and mass spectral data-of this novel diterpene glycoside with nine sugar moieties and containing a relatively rare 16 α-linked glycoside...
January 31, 2017: Biomolecules
https://www.readbyqxmd.com/read/28134813/key%C3%A2-events%C3%A2-participating%C3%A2-in%C3%A2-the%C3%A2-pathogenesis%C3%A2-of%C3%A2-alcoholic%C3%A2-liver%C3%A2-disease
#12
REVIEW
Fernando Magdaleno, Chuck C Blajszczak, Natalia Nieto
Alcoholic liver disease (ALD) is a leading cause of morbidity and mortality worldwide. It ranges from fatty liver to steatohepatitis, fibrosis, cirrhosis and hepatocellular carcinoma.The most prevalent forms of ALD are alcoholic fatty liver, alcoholic hepatitis (AH) and alcoholic cirrhosis, which frequently progress as people continue drinking. ALD refers to a number of symptoms/deficits that contribute to liver injury. These include steatosis, inflammation, fibrosis and cirrhosis, which, when taken together, sequentially or simultaneously lead to significant disease progression...
January 27, 2017: Biomolecules
https://www.readbyqxmd.com/read/28134793/trm112-a-protein-activator-of-methyltransferases-modifying-actors-of-the-eukaryotic-translational-apparatus
#13
REVIEW
Gabrielle Bourgeois, Juliette Létoquart, Nhan van Tran, Marc Graille
Post-transcriptional and post-translational modifications are very important for the control and optimal efficiency of messenger RNA (mRNA) translation. Among these, methylation is the most widespread modification, as it is found in all domains of life. These methyl groups can be grafted either on nucleic acids (transfer RNA (tRNA), ribosomal RNA (rRNA), mRNA, etc.) or on protein translation factors. This review focuses on Trm112, a small protein interacting with and activating at least four different eukaryotic methyltransferase (MTase) enzymes modifying factors involved in translation...
January 27, 2017: Biomolecules
https://www.readbyqxmd.com/read/28134782/role-of-pseudouridine-formation-by-deg1-for-functionality-of-two-glutamine-isoacceptor-trnas
#14
Roland Klassen, Raffael Schaffrath
Loss of Deg1/Pus3 and concomitant elimination of pseudouridine in tRNA at positions 38 and 39 (ψ38/39) was shown to specifically impair the function of tRNA(Gln)UUG under conditions of temperature-induced down-regulation of wobble uridine thiolation in budding yeast and is linked to intellectual disability in humans. To further characterize the differential importance of the frequent ψ38/39 modification for tRNAs in yeast, we analyzed the in vivo function of non-sense suppressor tRNAs SUP4 and sup70-65 in the absence of the modifier...
January 26, 2017: Biomolecules
https://www.readbyqxmd.com/read/28117687/critical-minireview-the-fate-of-trna-cys-during-oxidative-stress-in-bacillus-subtilis
#15
REVIEW
Juan Campos Guillen, George H Jones, Carlos Saldaña Gutiérrez, José Luis Hernández-Flores, Julio Alfonso Cruz Medina, José Humberto Valenzuela Soto, Sergio Pacheco Hernández, Sergio Romero Gómez, Verónica Morales Tlalpan
Oxidative stress occurs when cells are exposed to elevated levels of reactive oxygen species that can damage biological molecules. One bacterial response to oxidative stress involves disulfide bond formation either between protein thiols or between protein thiols and low-molecular-weight (LMW) thiols. Bacillithiol was recently identified as a major low-molecular-weight thiol in Bacillus subtilis and related Firmicutes. Four genes (bshA, bshB1, bshB2, and bshC) are involved in bacillithiol biosynthesis. The bshA and bshB1 genes are part of a seven-gene operon (ypjD), which includes the essential gene cca, encoding CCA-tRNA nucleotidyltransferase...
January 20, 2017: Biomolecules
https://www.readbyqxmd.com/read/28098827/shared-sulfur-mobilization-routes-for-trna-thiolation-and-molybdenum-cofactor-biosynthesis-in-prokaryotes-and-eukaryotes
#16
REVIEW
Silke Leimkühler, Martin Bühning, Lena Beilschmidt
Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm⁵s²U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure...
January 14, 2017: Biomolecules
https://www.readbyqxmd.com/read/28085093/acknowledgement-to-reviewers-of-biomolecules-in-2016
#17
EDITORIAL
Biomolecules Editorial Office
The  editors of  Biomolecules would like  to  express  their sincere  gratitude  to  the  following  reviewers for assessing manuscripts in 2016.[...].
January 12, 2017: Biomolecules
https://www.readbyqxmd.com/read/28067760/dna-methylation-targeting-the-dnmt-hmt-crosstalk-challenge
#18
REVIEW
Omar Castillo-Aguilera, Patrick Depreux, Ludovic Halby, Paola B Arimondo, Laurence Goossens
Chromatin can adopt a decondensed state linked to gene transcription (euchromatin) and a condensed state linked to transcriptional repression (heterochromatin). These states are controlled by epigenetic modulators that are active on either the DNA or the histones and are tightly associated to each other. Methylation of both DNA and histones is involved in either the activation or silencing of genes and their crosstalk. Since DNA/histone methylation patterns are altered in cancers, molecules that target these modifications are interesting therapeutic tools...
January 5, 2017: Biomolecules
https://www.readbyqxmd.com/read/28054978/hemoglobin-based-blood-substitutes-and-the-treatment-of-sickle-cell-disease-more-harm-than-help
#19
REVIEW
Abdu I Alayash
Intense efforts have been made by both industry and academia over the last three decades to produce viable hemoglobin (Hb)-based oxygen carriers (HBOCs), also known as "blood substitutes". Human trials conducted so far by several manufactures in a variety of clinical indications, including trauma, and elective surgeries have failed and no product has gained the Food and Drug Administration approval for human use. Safety concerns due to frequent incidences of hemodynamic, cardiac events, and even death led to the termination of some of these trials...
January 4, 2017: Biomolecules
https://www.readbyqxmd.com/read/28036012/emerging-roles-for-ciz1-in-cell-cycle-regulation-and-as-a-driver-of-tumorigenesis
#20
REVIEW
Tekle Pauzaite, Urvi Thacker, James Tollitt, Nikki A Copeland
Precise duplication of the genome is a prerequisite for the health and longevity of multicellular organisms. The temporal regulation of origin specification, replication licensing, and firing at replication origins is mediated by the cyclin-dependent kinases. Here the role of Cip1 interacting Zinc finger protein 1 (Ciz1) in regulation of cell cycle progression is discussed. Ciz1 contributes to regulation of the G1/S transition in mammalian cells. Ciz1 contacts the pre-replication complex (pre-RC) through cell division cycle 6 (Cdc6) interactions and aids localization of cyclin A- cyclin-dependent kinase 2 (CDK2) activity to chromatin and the nuclear matrix during initiation of DNA replication...
December 27, 2016: Biomolecules
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