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transcription Cap binding protein

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https://www.readbyqxmd.com/read/28522457/structure-of-eif4e-in-transcriptional-complex-with-an-eif4g-peptide-supports-a-universal-bipartite-binding-mode-for-protein-translation
#1
Manuel Miras, Veronica Truniger, Cristina Silva, Nuria Verdaguer, Miguel A Aranda, Jordi Querol
The association-dissociation of the cap-binding protein eIF4E with eIF4G is a key control step in eukaryotic translation. The paradigm on the eIF4E-eIF4G interaction states that eIF4G binds to the dorsal surface of eIF4E through a single canonical alpha-helical motif, while metazoan 4E-BPs (m4E-BPs) advantageously compete against eIF4G thanks to a bi-modal binding onto the canonical but additionally to a non-canonical motif in the lateral eIF4E surface thus inhibiting translation. Very recently, it has been shown that metazoan eIF4Gs share this extended binding interface with m4E-BPs, with significant implications on the understanding of translation regulation and the design of therapeutic molecules...
May 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28515298/crimean-congo-hemorrhagic-fever-virus-nucleocapsid-protein-augments-mrna-translation
#2
Subbiah Jeeva, Erdong Cheng, Safder S Ganaie, Mohammad A Mir
Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne nairovirus of the Bunyaviridae family, causing severe illness with high mortality rates in humans. Here we demonstrate that CCHFV nucleocapsid protein (CCHFV-NP) augments mRNA translation. CCHFV-NP binds to the viral mRNA 5' UTR with high affinity. It facilitates the translation of reporter mRNA both in vivo and in vitro with the assistance of viral mRNA 5' UTR. CCHFV-NP equally favors the translation of both capped and uncapped mRNAs, demonstrating the independence of this translation strategy on the 5' cap...
May 17, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28507282/p53-suppresses-ribonucleotide-reductase-via-inhibiting-mtorc1
#3
Zhengfu He, Xing Hu, Weijin Liu, Adrienne Dorrance, Ramiro Garzon, Peter J Houghton, Changxian Shen
Balanced deoxyribonucleotides pools are essential for cell survival and genome stability. Ribonucleotide reductase is the rate-limiting enzyme for the production of deoxyribonucleotides. We report here that p53 suppresses ribonucleotide reductase subunit 1 (RRM1) and 2 (RRM2) via inhibiting mammalian target of rapamycin complex 1 (mTORC1). In vitro, cancer cell lines and mouse embryonic fibroblast cells were treated with different concentrations of pharmacological inhibitors for different times. In vivo, rhabdomyosarcoma Rh30 cell tumor-bearing mice were treated with rapamycin or AZD8055...
April 26, 2017: Oncotarget
https://www.readbyqxmd.com/read/28454255/mir-219-5p-suppresses-the-proliferation-and-invasion-of-colorectal-cancer-cells-by-targeting-calcyphosin
#4
Quhui Wang, Lirong Zhu, Yasu Jiang, Junfei Xu, Feiran Wang, Zhixian He
MicroRNAs (miRNAs) are small non-coding RNAs involved in an array of biological processes, and their dysregulation is associated with tumor development and progression. One such miRNA, miR-219-5p, is abnormally expressed in patients with colorectal cancer (CRC). In the present study, reverse transcription-quantitative polymerase chain reaction was performed to measure miR-219-5p expression in cells from both CRC tumors, and surrounding healthy tissue. MTT and invasion assays were used to determine the role of miR-219-5p in regulating CRC cell proliferation and invasion, respectively...
March 2017: Oncology Letters
https://www.readbyqxmd.com/read/28378569/porcine-circovirus-type-2-capsid-protein-induces-unfolded-protein-response-with-subsequent-activation-of-apoptosis
#5
Ying-Shan Zhou, Yuan-Xing Gu, Bao-Zhu Qi, Yi-Kai Zhang, Xiao-Liang Li, Wei-Huan Fang
Porcine circovirus type 2 (PCV2) has recently been reported to elicit the unfolded protein response (UPR) via activation of the PERK/eIF2α (RNA-activated protein kinase-like endoplasmic reticulum (ER) kinase/eukaryotic initiation factor 2α) pathway. This study attempted to examine which viral protein might be involved in inducing UPR and whether this cellular event would lead to apoptosis of the cells expressing the viral protein. By transient expression, we found that both replicase (Rep) and capsid (Cap) proteins of PCV2 could induce ER stress as shown by increased phosphorylation of PERK with subsequent activation of the eIF2α-ATF4 (activating transcription factor 4)-CHOP (CCAAT/enhancer-binding protein homologous protein) axis...
2017: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/28329686/demethylated-hsatii-dna-and-hsatii-rna-foci-sequester-prc1-and-mecp2-into-cancer-specific-nuclear-bodies
#6
Lisa L Hall, Meg Byron, Dawn M Carone, Troy W Whitfield, Gayle P Pouliot, Andrew Fischer, Peter Jones, Jeanne B Lawrence
This study reveals that high-copy satellite II (HSATII) sequences in the human genome can bind and impact distribution of chromatin regulatory proteins and that this goes awry in cancer. In many cancers, master regulatory proteins form two types of cancer-specific nuclear bodies, caused by locus-specific deregulation of HSATII. DNA demethylation at the 1q12 mega-satellite, common in cancer, causes PRC1 aggregation into prominent Cancer-Associated Polycomb (CAP) bodies. These loci remain silent, whereas HSATII loci with reduced PRC1 become derepressed, reflecting imbalanced distribution of UbH2A on these and other PcG-regulated loci...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28325843/a-biochemical-framework-for-eif4e-dependent-mrna-export-and-nuclear-re-cycling-of-the-export-machinery
#7
Laurent Volpon, Biljana Culjkovic-Kraljacic, Hye Seon Sohn, Alexis Blanchett-Cohen, Michael J Osborne, Katherine L B Borden
The eukaryotic translation initiation factor eIF4E acts in the nuclear export and translation of a subset of mRNAs. Both of these functions contribute to its oncogenic potential. While the biochemical mechanisms that underlie translation are relatively well understood, the molecular basis for eIF4E's role in mRNA export remains largely unexplored. To date over 3000 transcripts, many encoding oncoproteins, were identified as potential nuclear eIF4E export targets. These target RNAs typically contain a ~50 nucleotide eIF4E sensitivity element (4ESE) in the 3' UTR and a 7-methylguanosine cap on the 5' end...
March 21, 2017: RNA
https://www.readbyqxmd.com/read/28297668/mutually-exclusive-cbc-containing-complexes-contribute-to-rna-fate
#8
Simone Giacometti, Nour El Houda Benbahouche, Michal Domanski, Marie-Cécile Robert, Nicola Meola, Michal Lubas, Jakob Bukenborg, Jens S Andersen, Wiebke M Schulze, Celine Verheggen, Grzegorz Kudla, Torben Heick Jensen, Edouard Bertrand
The nuclear cap-binding complex (CBC) stimulates processing reactions of capped RNAs, including their splicing, 3'-end formation, degradation, and transport. CBC effects are particular for individual RNA families, but how such selectivity is achieved remains elusive. Here, we analyze three main CBC partners known to impact different RNA species. ARS2 stimulates 3'-end formation/transcription termination of several transcript types, ZC3H18 stimulates degradation of a diverse set of RNAs, and PHAX functions in pre-small nuclear RNA/small nucleolar RNA (pre-snRNA/snoRNA) transport...
March 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28287067/translational-control-of-mrnas-by-3-untranslated-region-binding-proteins
#9
Akio Yamashita, Osamu Takeuchi
Eukaryotic gene expression is precisely regulated at all points between transcription and translation. In this review, we focus on translational control mediated by the 3'-untranslated regions (UTRs) of mRNAs. mRNA 3'-UTRs contain cis-acting elements that function in the regulation of protein translation or mRNA decay. Each RNA binding protein that binds to these cis-acting elements regulates mRNA translation via various mechanisms targeting the mRNA cap structure, the eukaryotic initiation factor 4E (eIF4E)-eIF4G complex, ribosomes, and the poly (A) tail...
April 2017: BMB Reports
https://www.readbyqxmd.com/read/28282132/quantifying-allosteric-communication-via-both-concerted-structural-changes-and-conformational-disorder-with-cards
#10
Sukrit Singh, Gregory R Bowman
Allosteric (i.e., long-range) communication within proteins is crucial for many biological processes, such as the activation of signaling cascades in response to specific stimuli. However, the physical basis for this communication remains unclear. Existing computational methods for identifying allostery focus on the role of concerted structural changes, but recent experimental work demonstrates that disorder is also an important factor. Here, we introduce the Correlation of All Rotameric and Dynamical States (CARDS) framework for quantifying correlations between both the structure and disorder of different regions of a protein...
March 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28220845/heterogeneous-nuclear-ribonucleoprotein-a1-regulates-rhythmic-synthesis-of-mouse-nfil3-protein-via-ires-mediated-translation
#11
Hyo-Jin Kim, Hwa-Rim Lee, Ji-Young Seo, Hye Guk Ryu, Kyung-Ha Lee, Do-Yeon Kim, Kyong-Tai Kim
Nuclear factor, interleukin 3, regulated (Nfil3, also known as E4 Promoter-Binding Protein 4 (E4BP4)) protein is a transcription factor that binds to DNA and generally represses target gene expression. In the circadian clock system, Nfil3 binds to a D-box element residing in the promoter of clock genes and contributes to their robust oscillation. Here, we show that the 5'-untranslated region (5'-UTR) of Nfil3 mRNA contains an internal ribosome entry site (IRES) and that IRES-mediated translation occurs in a phase-dependent manner...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211915/structure-of-the-shr-scr-heterodimer-bound-to-the-bird-idd-transcriptional-factor-jkd
#12
Yoshinori Hirano, Masahiro Nakagawa, Tomoe Suyama, Kohji Murase, Maya Shirakawa, Seiji Takayama, Tai-Ping Sun, Toshio Hakoshima
The plant-specific GAI, RGA and SCR (GRAS) family proteins play critical roles in plant development and signalling. Two GRAS proteins, SHORT-ROOT (SHR) and SCARECROW (SCR), cooperatively direct asymmetric cell division and the patterning of root cell types by transcriptional control in conjunction with BIRD/INDETERMINATE DOMAIN (IDD) transcription factors, although precise details of these specific interactions and actions remain unknown. Here, we present the crystal structures of the SHR-SCR binary and JACKDAW (JKD)/IDD10-SHR-SCR ternary complexes...
February 17, 2017: Nature Plants
https://www.readbyqxmd.com/read/28179391/the-nuclear-cap-binding-complex-mediates-meiotic-silencing-by-unpaired-dna
#13
Logan M Decker, Hua Xiao, Erin C Boone, Michael M Vierling, Benjamin S Shanker, Shanika L Kingston, Shannon F Boone, Jackson B Haynes, Patrick K T Shiu
In the filamentous fungus Neurospora crassa, cross walls between individual cells are normally incomplete, making the entire fungal network vulnerable to attack by viruses and selfish DNAs. Accordingly, several genome surveillance mechanisms are maintained to help the fungus combat these repetitive elements. One of these defense mechanisms is called meiotic silencing by unpaired DNA (MSUD), which identifies and silences unpaired genes during meiosis. Utilizing common RNA interference (RNAi) proteins, such as Dicer and Argonaute, MSUD targets mRNAs homologous to the unpaired sequence to achieve silencing...
April 3, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28177284/cap-proximal-nucleotides-via-differential-eif4e-binding-and-alternative-promoter-usage-mediate-translational-response-to-energy-stress
#14
Ana Tamarkin-Ben-Harush, Jean-Jacques Vasseur, Françoise Debart, Igor Ulitsky, Rivka Dikstein
Transcription start-site (TSS) selection and alternative promoter (AP) usage contribute to gene expression complexity but little is known about their impact on translation. Here we performed TSS mapping of the translatome following energy stress. Assessing the contribution of cap-proximal TSS nucleotides, we found dramatic effect on translation only upon stress. As eIF4E levels were reduced, we determined its binding to capped-RNAs with different initiating nucleotides and found the lowest affinity to 5'cytidine in correlation with the translational stress-response...
February 8, 2017: ELife
https://www.readbyqxmd.com/read/28093273/identification-of-fhit-as-a-post-transcriptional-effector-of-thymidine-kinase-1-expression
#15
Daniel L Kiss, Catherine E Waters, Iman M Ouda, Joshua C Saldivar, Jenna R Karras, Zaynab A Amin, Seham Mahrous, Teresa Druck, Ralf A Bundschuh, Daniel R Schoenberg, Kay Huebner
FHIT is a genome caretaker gene that is silenced in >50% of cancers. Loss of Fhit protein expression promotes accumulation of DNA damage, affects apoptosis and epithelial-mesenchymal transition, though molecular mechanisms underlying these alterations have not been fully elucidated. Initiation of genome instability directly follows Fhit loss and the associated reduced Thymidine Kinase 1 (TK1) protein expression. The effects on TK1 of Fhit knockdown and Fhit induction in the current study confirmed the role of Fhit in regulating TK1 expression...
March 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28093067/capza1-modulates-emt-by-regulating-actin-cytoskeleton-remodelling-in-hepatocellular-carcinoma
#16
Deng Huang, Li Cao, Shuguo Zheng
BACKGROUND: Epithelial-mesenchymal transition (EMT) elicits dramatic changes, including cytoskeleton remodelling as well as changes in gene expression and cellular phenotypes. During this process, actin filament assembly plays an important role in maintaining the morphology and movement of tumour cells. Capping protein, a protein complex referred to as CapZ, is an actin-binding complex that can regulate actin cytoskeleton remodelling. CAPZA1 is the α1 subunit of this complex, and we hypothesized that CAPZA1 regulates EMT through the regulation of actin filaments assembly, thus reducing the metastatic ability of hepatocellular carcinoma (HCC) cells...
January 16, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28064320/-interactions-of-the-trex-2-complex-with-mrnp-particle-of-%C3%AE-tubulin-56d-gene
#17
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/28039930/interacting-protein-partners-of-arabidopsis-rna-binding-protein-atrbp45b
#18
M Muthuramalingam, Y Wang, Y Li, R Mahalingam
RNA binding proteins, important players in post-transcriptional gene regulation, usually exist in ribonuclear complexes. However, even in model systems like Arabidopsis characterisation of RBP associated proteins is limited. In this study, we investigated the interacting proteins of the Arabidopsis AtRBP45b, which is involved in stress signalling. In vivo localisation of AtRBP45b was conducted using 35S-GFP. FLAG-tagged AtRBP45b under control of the 35S promoter in the Atrbp45b-1 mutant background was used to pull down AtRBP45b interacting proteins...
December 31, 2016: Plant Biology
https://www.readbyqxmd.com/read/28003464/nat1-promotes-translation-of-specific-proteins-that-induce-differentiation-of-mouse-embryonic-stem-cells
#19
Hayami Sugiyama, Kazutoshi Takahashi, Takuya Yamamoto, Mio Iwasaki, Megumi Narita, Masahiro Nakamura, Tim A Rand, Masato Nakagawa, Akira Watanabe, Shinya Yamanaka
Novel APOBEC1 target 1 (Nat1) (also known as "p97," "Dap5," and "Eif4g2") is a ubiquitously expressed cytoplasmic protein that is homologous to the C-terminal two thirds of eukaryotic translation initiation factor 4G (Eif4g1). We previously showed that Nat1-null mouse embryonic stem cells (mES cells) are resistant to differentiation. In the current study, we found that NAT1 and eIF4G1 share many binding proteins, such as the eukaryotic translation initiation factors eIF3 and eIF4A and ribosomal proteins. However, NAT1 did not bind to eIF4E or poly(A)-binding proteins, which are critical for cap-dependent translation initiation...
January 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27994090/a-common-class-of-transcripts-with-5-intron-depletion-distinct-early-coding-sequence-features-and-n-1-methyladenosine-modification
#20
Can Cenik, Hon Nian Chua, Guramrit Singh, Abdalla Akef, Michael P Snyder, Alexander F Palazzo, Melissa J Moore, Frederick P Roth
Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: Genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with >80% accuracy using only sequence features in the early coding region...
March 2017: RNA
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