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https://www.readbyqxmd.com/read/28334829/structure-of-the-sac3-rna-binding-m-region-in-the-saccharomyces-cerevisiae-trex-2-complex
#1
James M B Gordon, Shintaro Aibara, Murray Stewart
Transcription-export complex 2 (TREX-2, or THSC) facilitates localization of actively transcribing genes such as GAL1 to the nuclear periphery, contributes to the generation of export-competent mRNPs and influences gene expression through interactions with Mediator. TREX-2 is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31 and Sus1 bind and consists of three modules: the N-region (Sac3∼1-100), which binds mRNA export factor Mex67:Mtr2; the M-region, in which Thp1 and Sem1 bind to Sac3∼100-550; and the CID region in which Cdc31 and two Sus1 chains bind to Sac3∼720-805...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28064320/-interactions-of-the-trex-2-complex-with-mrnp-particle-of-%C3%AE-tubulin-56d-gene
#2
V V Popova, A A Glukhova, S G Georgieva, G P Georgiev, D V Kopytova
mRNA transport from the nucleus to the cytoplasm is an essential step of eukaryotic gene expression. A pre-mRNA molecule undergoes modification, such as 5'-capping, splicing, and 3'-end processing, in the nucleus. The molecule being modified interacts with a large number of proteins and, thus, mRNP particles are formed. The binding of factors involved in nuclear export also occurs during transcription and mRNA processing. We have shown that the functioning of TREX-2, an mRNA export complex, is restricted to the nucleus...
November 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28004241/the-arabidopsis-tho-trex-component-tex1-functionally-interacts-with-mos11-and-modulates-mrna-export-and-alternative-splicing-events
#3
Brian B Sørensen, Hans F Ehrnsberger, Silvia Esposito, Alexander Pfab, Astrid Bruckmann, Judith Hauptmann, Gunter Meister, Rainer Merkl, Thomas Schubert, Gernot Längst, Michael Melzer, Marion Grasser, Klaus D Grasser
We identify proteins that associate with the THO core complex, and show that the TEX1 and MOS11 components functionally interact, affecting mRNA export and splicing as well as plant development. TREX (TRanscription-EXport) is a multiprotein complex that plays a central role in the coordination of synthesis, processing and nuclear export of mRNAs. Using targeted proteomics, we identified proteins that associate with the THO core complex of Arabidopsis TREX. In addition to the RNA helicase UAP56 and the mRNA export factors ALY2-4 and MOS11 we detected interactions with the mRNA export complex TREX-2 and multiple spliceosomal components...
February 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/27933408/twelve-weeks-progressive-resistance-training-combined-with-protein-supplementation-beyond-habitual-intakes-increases-upper-leg-lean-tissue-mass-muscle-strength-and-extended-gait-speed-in-healthy-older-women
#4
Peter Francis, William Mc Cormack, Clodagh Toomey, Catherine Norton, Jean Saunders, Emmet Kerin, Mark Lyons, Philip Jakeman
The age-related decline in functional capability is preceded by a reduction in muscle quality. The purpose of this study was to assess the combined effects of progressive resistance training (PRT) and protein supplementation beyond habitual intakes on upper leg lean tissue mass (LTM), muscle quality and functional capability in healthy 50-70 years women. In a single-blinded, randomized, controlled design, 57 healthy older women (age 61.1 ± 5.1 years, 1.61 ± 0.65 m, 65.3 ± 15.3 kg) consumed 0.33 g/kg body mass of a milk-based protein matrix (PRO) for 12 weeks...
December 8, 2016: Biogerontology
https://www.readbyqxmd.com/read/27900689/novel-tools-for-the-functional-expression-of-metagenomic-dna
#5
Nadine Katzke, Andreas Knapp, Anita Loeschcke, Thomas Drepper, Karl-Erich Jaeger
Functional expression of genes from metagenomic libraries is limited by various factors including inefficient transcription and/or translation of target genes as well as improper folding and assembly of the corresponding proteins caused by the lack of appropriate chaperones and cofactors. It is now well accepted that the use of different expression hosts of distinct phylogeny and physiology can dramatically increase the rate of success. In the following chapter, we therefore describe tools and protocols allowing for the comparative heterologous expression of genes in five bacterial expression hosts, namely Escherichia coli, Pseudomonas putida, Bacillus subtilis, Burkholderia glumae, and Rhodobacter capsulatus...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27884288/trex-through-cutaneous-health%C3%A2-and%C3%A2-disease
#6
Alicia R Mathers
TREX1 and 2 are exonucleases that repair and degrade DNA. Degradation of DNA is involved in maintaining the integrity of the epidermis. The importance of these enzymes to cutaneous integrity is observed when TREX1 and TREX2 pathways become aberrant, and autoimmune or cancerous diseases ensue. Manils et al. have now shown that overexpression of TREX2 may play a role in potentiating psoriasis. Thus, these pathways are likely targets for novel therapeutics.
December 2016: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/27863845/macular-atrophy-in-neovascular-age-related-macular-degeneration-with-monthly-versus-treat-and-extend-ranibizumab-findings-from-the-trex-amd-trial
#7
Nizar S Abdelfattah, Mayss Al-Sheikh, Sean Pitetta, Ahmed Mousa, SriniVas R Sadda, Charles C Wykoff
PURPOSE: To compare the enlargement rate of macular atrophy (ERMA) in eyes treated with ranibizumab monthly or using a treat-and-extend (TREX) regimen for neovascular age-related macular degeneration (AMD) or fellow control eyes, as well as analyze risk factors for macular atrophy (MA) development and progression. DESIGN: Eighteen-month, multicenter, randomized, controlled clinical trial. PARTICIPANTS: Sixty patients with treatment-naïve neovascular AMD in 1 eye randomized 1:2 to monthly or TREX ranibizumab...
February 2017: Ophthalmology
https://www.readbyqxmd.com/read/27836430/randomized-trial-of-treat-and-extend-ranibizumab-with-and-without-navigated-laser-for-diabetic-macular-edema-trex-dme-1-year-outcomes
#8
John F Payne, Charles C Wykoff, W Lloyd Clark, Beau B Bruce, David S Boyer, David M Brown
PURPOSE: To compare monthly dosing with a treat and extend algorithm using ranibizumab 0.3 mg with and without angiography-guided macular laser photocoagulation for center-involving diabetic macular edema (DME). DESIGN: Multicenter, prospective, randomized clinical trial. PARTICIPANTS: A total of 150 eyes from 116 subjects were randomized into 3 cohorts: Monthly (n = 30), TReat and EXtend without macular laser photocoagulation (TREX; n = 60), and treat and extend with angiography-GuIded macular LAser photocoagulation (GILA; n = 60)...
January 2017: Ophthalmology
https://www.readbyqxmd.com/read/27825215/comparing-generalized-ensemble-methods-for-sampling-of-systems-with-many-degrees-of-freedom
#9
James Lincoff, Sukanya Sasmal, Teresa Head-Gordon
We compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchange (TREx) method...
November 7, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27780949/alterations-in-acetylation-of-histone-h4-lysine-8-and-trimethylation-of-lysine-20-associated-with-lytic-gene-promoters-during-kaposi-s-sarcoma-associated-herpesvirus-reactivation
#10
Sora Lim, Seho Cha, Jun Hyeong Jang, Dahye Yang, Joonho Choe, Taegun Seo
Kaposi's sarcoma-associated herpesvirus (KSHV) is associated with formation of Kaposi's sarcoma, multicentric Castleman's disease and primary effusion lymphoma. Replication and transcription activator (RTA) genes are expressed upon reactivation of KSHV, which displays a biphasic life cycle consisting of latent and lytic replication phases. RTA protein expression results in KSHV genome amplification and successive viral lytic gene expression. Transcriptional activity of viral lytic genes is regulated through epigenetic modifications...
October 25, 2016: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27698495/the-oncoprotein-brd4-nut-generates-aberrant-histone-modification-patterns
#11
Barry M Zee, Amy B Dibona, Artyom A Alekseyenko, Christopher A French, Mitzi I Kuroda
Defects in chromatin proteins frequently manifest in diseases. A striking case of a chromatin-centric disease is NUT-midline carcinoma (NMC), which is characterized by expression of NUT as a fusion partner most frequently with BRD4. ChIP-sequencing studies from NMC patients revealed that BRD4-NUT (B4N) covers large genomic regions and elevates transcription within these domains. To investigate how B4N modulates chromatin, we performed affinity purification of B4N when ectopically expressed in 293-TREx cells and quantified the associated histone posttranslational modifications (PTM) using proteomics...
2016: PloS One
https://www.readbyqxmd.com/read/27679854/the-role-of-trex-in-gene-expression-and-disease
#12
REVIEW
Catherine G Heath, Nicolas Viphakone, Stuart A Wilson
TRanscription and EXport (TREX) is a conserved multisubunit complex essential for embryogenesis, organogenesis and cellular differentiation throughout life. By linking transcription, mRNA processing and export together, it exerts a physiologically vital role in the gene expression pathway. In addition, this complex prevents DNA damage and regulates the cell cycle by ensuring optimal gene expression. As the extent of TREX activity in viral infections, amyotrophic lateral sclerosis and cancer emerges, the need for a greater understanding of TREX function becomes evident...
October 1, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27672037/sac3b-a-central-component-of-the-mrna-export-complex-trex-2-is-required-for-prevention-of-epigenetic-gene-silencing-in-arabidopsis
#13
Yu Yang, Honggui La, Kai Tang, Daisuke Miki, Lan Yang, Bangshing Wang, Cheng-Guo Duan, Wenfeng Nie, Xingang Wang, Siwen Wang, Yufeng Pan, Elizabeth J Tran, Lizhe An, Huiming Zhang, Jian-Kang Zhu
Epigenetic regulation is important for organismal development and response to the environment. Alteration in epigenetic status has been known mostly from the perspective of enzymatic actions of DNA methylation and/or histone modifications. In a genetic screen for cellular factors involved in preventing epigenetic silencing, we isolated an Arabidopsis mutant defective in SAC3B, a component of the conserved TREX-2 complex that couples mRNA transcription with nuleo-cytoplasmic export. Arabidopsis SAC3B dysfunction causes gene silencing at transgenic and endogenous loci, accompanied by elevation in the repressive histone mark H3K9me2 and by reduction in RNA polymerase Pol II occupancy...
January 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27575477/quassinoids-viral-protein-r-inhibitors-from-picrasma-javanica-bark-collected-in-myanmar-for-hiv-infection
#14
Nwet Nwet Win, Takuya Ito, Yi Yi Win, Hla Ngwe, Takeshi Kodama, Ikuro Abe, Hiroyuki Morita
Viral protein R (Vpr) is an accessory protein that plays important roles in the viral pathogenesis of Human Immunodeficiency Virus-1 (HIV-1). An assay for anti-Vpr activity, using TREx-HeLa-Vpr cells, is a promising strategy to discover Vpr inhibitors. The anti-Vpr assay revealed that the CHCl3-soluble extract of Picrasma javanica bark possesses potent anti-Vpr activity. Furthermore, studies of quassinoids (1-15) previously isolated from the extract demonstrated that all of the tested quassinoids exhibit anti-Vpr activity...
October 1, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27542978/uap56-is-a-conserved-crucial-component-of-a-divergent-mrna-export-pathway-in-toxoplasma-gondii
#15
Mariana Serpeloni, Elena Jiménez-Ruiz, Newton Medeiros Vidal, Constanze Kroeber, Nicole Andenmatten, Leandro Lemgruber, Patricia Mörking, Gurman S Pall, Markus Meissner, Andréa R Ávila
Nucleo-cytoplasmic RNA export is an essential post-transcriptional step to control gene expression in eukaryotic cells and is poorly understood in apicomplexan parasites. With the exception of UAP56, a component of TREX (Transcription Export) complex, other components of mRNA export machinery are not well conserved in divergent supergroups. Here, we use Toxoplasma gondii as a model system to functionally characterize TgUAP56 and its potential interaction factors. We demonstrate that TgUAP56 is crucial for mRNA export and that functional interference leads to significant accumulation of mRNA in the nucleus...
November 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27509857/hiv-1-uses-dynamic-capsid-pores-to-import-nucleotides-and-fuel-encapsidated-dna-synthesis
#16
David A Jacques, William A McEwan, Laura Hilditch, Amanda J Price, Greg J Towers, Leo C James
During the early stages of infection, the HIV-1 capsid protects viral components from cytosolic sensors and nucleases such as cGAS and TREX, respectively, while allowing access to nucleotides for efficient reverse transcription. Here we show that each capsid hexamer has a size-selective pore bound by a ring of six arginine residues and a 'molecular iris' formed by the amino-terminal β-hairpin. The arginine ring creates a strongly positively charged channel that recruits the four nucleotides with on-rates that approach diffusion limits...
August 18, 2016: Nature
https://www.readbyqxmd.com/read/27466416/nuclear-innate-immune-dna-sensor-ifi16-is-degraded-during-lytic-reactivation-of-kaposi-s-sarcoma-associated-herpesvirus-kshv-role-of-ifi16-in-maintenance-of-kshv-latency
#17
Arunava Roy, Dipanjan Dutta, Jawed Iqbal, Gina Pisano, Olsi Gjyshi, Mairaj Ahmed Ansari, Binod Kumar, Bala Chandran
UNLABELLED: IFI16 (interferon gamma-inducible protein 16) recognizes nuclear episomal herpesvirus (Kaposi's sarcoma-associated herpesvirus [KSHV], Epstein-Barr virus [EBV], and herpes simplex virus 1 [HSV-1]) genomes and induces the inflammasome and interferon beta responses. It also acts as a lytic replication restriction factor and inhibits viral DNA replication (human cytomegalovirus [HCMV] and human papillomavirus [HPV]) and transcription (HSV-1, HCMV, and HPV) through epigenetic modifications of the viral genomes...
October 1, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27422657/the-sac3-tpr-like-region-in-the-saccharomyces-cerevisiae-trex-2-complex-is-more-extensive-but-independent-of-the-cid-region
#18
Shintaro Aibara, Xiao-Chen Bai, Murray Stewart
UNLABELLED: Transcription-export complex 2 (TREX-2 complex) facilitates the localization of actively transcribing genes to the nuclear periphery and also functions to contribute to the generation of export-competent mRNPs through interactions with the general mRNA nuclear export factor Mex67:Mtr2. The TREX-2 complex is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31, and Sus1 bind. TREX-2 can be subdivided into two modules: one, in which Thp1 and Sem1 bind to the Sac3(M) region (residues ∼100-551), and the other in which Cdc31 and two Sus1 chains bind to the Sac3(CID) region (residues ∼710-805)...
September 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27417714/ctcf-and-sgfl1-proteins-form-alternative-complexes-with-eny2-proteins
#19
A N Bonchuk, P G Georgiev, O G Maksimenko
ENY2 is a multifunctional protein, a component of the SAGA complex (protein complex involved in the regulation of transcription, possessing histone-acetyltransferase and H2B-histone-deubiquitinylating activities [1]) and TREX-2 (complex involved in the mRNA nuclear export [2]). Besides this, the interactions of ENY2 with DNA-binding insulator proteins Su(Hw) and dCTCF have been described as essential for the barrier activity of corresponding insulators [3, 4]. In this study, we described the formation of mutually exclusive complexes of ENY2 with insulator proteins and Sgfl1-a component of the SAGA complex, direct binding partner for ENY2...
May 2016: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/27348862/icp35-is-a-trex-like-protein-identified-in-white-spot-syndrome-virus
#20
Panapat Phairoh, Thana Suthibatpong, Triwit Rattanarojpong, Nujarin Jongruja, Saengchan Senapin, Kiattawee Choowongkomon, Pongsak Khunrae
ICP35 is a non-structural protein from White spot syndrome virus believed to be important in viral replication. Since ICP35 was found to localize in the host nucleus, it has been speculated that the function of ICP35 might be involved in the interaction of DNA. In this study, we overexpressed, purified and characterized ICP35. The thioredoxin-fused ICP35 (thio-ICP35) was strongly expressed in E. coli and be able to form itself into dimers. Investigation of the interaction between ICP35 and DNA revealed that ICP35 can perform DNase activity...
2016: PloS One
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