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upstream open reading frame

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https://www.readbyqxmd.com/read/28322871/recurrent-emergence-of-structural-variants-of-ltr-retrotransposon-csrn1-evolving-novel-expression-strategy-and-their-selective-expansion-in-a-carcinogenic-liver-fluke-clonorchis-sinensis
#1
Seon-Hee Kim, Yoon Kong, Young-An Bae
Autonomous retrotransposons, in which replication and transcription are coupled, encode the essential gag and pol genes as a fusion or separate overlapping form(s) that are expressed in single transcripts regulated by a common upstream promoter. The element-specific expression strategies have driven development of relevant translational recoding mechanisms including ribosomal frameshifting to satisfy the protein stoichiometry critical for the assembly of infectious virus-like particles. Retrotransposons with different recoding strategies exhibit a mosaic distribution pattern across the diverse families of reverse transcribing elements, even though their respective distributions are substantially skewed towards certain family groups...
March 16, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28322766/characterization-of-a-molt-related-myostatin-gene-fmmstn-from-the-banana-shrimp-fenneropenaeus-merguiensis
#2
Rui Qun Zhuo, Ting Ting Zhou, Shi Ping Yang, Siuming Francis Chan
Myostatin is an important member of the Transforming Growth Factor (TGF) family that functions to regulate muscle growth in animals. In this study, the myostatin gene (FmMstn) and two slightly different (short and long forms) cDNAs of the banana shrimp Fenneropenaeus merguiensis were cloned and characterized. Similar to Mstn gene of the scallop, fish and mammal, FmMstn gene consists of 3 exons and 2 introns. The 2 kb upstream promoter region of the FmMstn gene consists of putative response elements for myocyte enhancing factor (MEF2) and E-box factors...
March 17, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28279185/constitutively-stressed-yeast-strains-are-high-yielding-for-recombinant-fps1-implications-for-the-translational-regulation-of-an-aquaporin
#3
Stephanie P Cartwright, Richard A J Darby, Debasmita Sarkar, Nicklas Bonander, Stephane R Gross, Mark P Ashe, Roslyn M Bill
BACKGROUND: We previously selected four strains of Saccharomyces cerevisiae for their ability to produce the aquaporin Fps1 in sufficient yield for further study. Yields from the yeast strains spt3Δ, srb5Δ, gcn5Δ and yTHCBMS1 (supplemented with 0.5 μg/mL doxycycline) that had been transformed with an expression plasmid containing 249 base pairs of 5' untranslated region (UTR) in addition to the primary FPS1 open reading frame (ORF) were 10-80 times higher than yields from wild-type cells expressing the same plasmid...
March 9, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28276452/de-novo-computational-identification-of-stress-related-sequence-motifs-and-microrna-target-sites-in-untranslated-regions-of-a-plant-translatome
#4
Prabhakaran Munusamy, Yevgen Zolotarov, Louis-Valentin Meteignier, Peter Moffett, Martina V Strömvik
Gene regulation at the transcriptional and translational level leads to diversity in phenotypes and function in organisms. Regulatory DNA or RNA sequence motifs adjacent to the gene coding sequence act as binding sites for proteins that in turn enable or disable expression of the gene. Whereas the known DNA and RNA binding proteins range in the thousands, only a few motifs have been examined. In this study, we have predicted putative regulatory motifs in groups of untranslated regions from genes regulated at the translational level in Arabidopsis thaliana under normal and stressed conditions...
March 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28274720/functional-analysis-of-a-novel-repressor-luxr-in-comamonas-testosteroni
#5
Ye Ji, Tianyuan Pan, Yang Zhang, Guangming Xiong, Yuanhua Yu
Comamonas testosteroni (C. testosteroni) ATCC11996 is a gram negative bacterium which can use steroid as a carbon and energy source. 3,17β-hydroxysteroid dehydrogenase (3,17β-HSD) is a key enzyme for the degradation of steroid hormones in C. testosteroni. The LuxR regulation family is a group of regulatory proteins which play important role in gram negative bacterium. The luxr gene is located on 58 kb upstream of 3,17β-HSD gene with the opposite transcription orientation in the chromosomal DNA of C. testosteroni...
March 6, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28260621/differential-regulation-of-hepatitis-b-virus-core-protein-expression-and-genome-replication-by-a-small-upstream-open-reading-frame-and-naturally-occurring-mutations-in-the-precore-region
#6
Li Zong, Yanli Qin, Haodi Jia, Lei Ye, Yongxiang Wang, Jiming Zhang, Jack R Wands, Shuping Tong, Jisu Li
Hepatitis B virus (HBV) transcribes two subsets of 3.5-kb RNAs: precore RNA for hepatitis B e antigen (HBeAg) expression, and pregenomic RNA for core and P protein translation as well as genome replication. HBeAg expression could be prevented by mutations in the precore region, while an upstream open reading frame (uORF) has been proposed as a negative regulator of core protein translation. We employed replication competent HBV DNA constructs and transient transfection experiments in Huh7 cells to verify the uORF effect and to explore the alternative function of precore RNA...
March 2, 2017: Virology
https://www.readbyqxmd.com/read/28259047/the-tripartite-leader-sequence-is-required-for-ectopic-expression-of-hadv-b-and-hadv-e-e3-cr1-genes
#7
Camden R Bair, Poornima Kotha Lakshmi Narayan, Adriana E Kajon
The unique repertoire of genes that characterizes the early region 3 (E3) of the different species of human adenovirus (HAdV) likely contributes to their distinct pathogenic traits. The function of many E3 CR1 proteins remains unknown possibly due to unidentified intrinsic properties that make them difficult to express ectopically. This study shows that the species HAdV-B- and HAdV-E-specific E3 CR1 genes can be expressed from vectors carrying the HAdV tripartite leader (TPL) sequence but not from traditional mammalian expression vectors...
March 1, 2017: Virology
https://www.readbyqxmd.com/read/28198412/a-screening-strategy-for-the-discovery-of-drugs-that-reduce-c-ebp%C3%AE-lip-translation-with-potential-calorie-restriction-mimetic-properties
#8
Mohamad A Zaini, Christine Müller, Tobias Ackermann, Jeanette Reinshagen, Gertrud Kortman, Ole Pless, Cornelis F Calkhoven
An important part of the beneficial effects of calorie restriction (CR) on healthspan and lifespan is mediated through regulation of protein synthesis that is under control of the mechanistic target of rapamycin complex 1 (mTORC1). As one of its activities, mTORC1 stimulates translation into the metabolic transcription factor CCAAT/Enhancer Binding Protein β (C/EBPβ) isoform Liver-specific Inhibitory Protein (LIP). Regulation of LIP expression strictly depends on a translation re-initiation event that requires a conserved cis-regulatory upstream open reading frame (uORF) in the C/EBPβ-mRNA...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28195124/pervasive-translational-regulation-of-the-cell-signalling-circuitry-underlies-mammalian-development
#9
Kotaro Fujii, Zhen Shi, Olena Zhulyn, Nicolas Denans, Maria Barna
The degree and dynamics of translational control during mammalian development remain poorly understood. Here we monitored translation of the mammalian genome as cells become specified and organize into tissues in vivo. This identified unexpected and pervasive translational regulation of most of the core signalling circuitry including Shh, Wnt, Hippo, PI3K and MAPK pathways. We further identify and functionally characterize a complex landscape of upstream open reading frames (uORFs) across 5'-untranslated regions (UTRs) of key signalling components...
February 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28191331/development-of-dual-taqman-based-one-step-rrt-pcr-assay-panel-for-rapid-and-accurate-diagnostic-test-of-mers-cov-a-novel-human-coronavirus-ahead-of-hajj-pilgrimage
#10
Mohammad Sadegh Hashemzadeh, Rahimeh Rasouli, Bentolhoda Zahraei, Morteza Izadi, Mahdi Tat, Seyed Hassan Saadat, Mohammad Najarasl, Behzad Khansari Nejad, Ruhollah Dorostkar
BACKGROUND: Coronaviruses (CoVs) are large ribonucleic acid (RNA) viruses causing primarily respiratory disease in humans. A novel human coronavirus, subsequently named middle east respiratory syndrome coronavirus (MERS-CoV), was first reported in Saudi Arabia in September of 2012. With increasing numbers of infections and deaths from MERS-CoV, development of a rapid and reliable kit was crucial to prevent further spread of MERS-CoV. OBJECTIVES: In this study, we present two real-time reverse-transcription polymerase chain reaction (rRT-PCR) assays for in-house rapid and sensitive diagnostic testing of MERS-CoV, detecting the regions upstream of the envelope gene (upE) and open reading frame (ORF) 1b, respectively, for initial screening and final confirmation of MERS-CoV infection, as recommended by the world health organization (WHO)...
November 2016: Iranian Red Crescent Medical Journal
https://www.readbyqxmd.com/read/28190998/quantitative-nucleotide-level-analysis-of-regulation-of-translation-in-response-to-depolarization-of-cultured-neural-cells
#11
Jasbir S Dalal, Chengran Yang, Darshan Sapkota, Allison M Lake, David R O'Brien, Joseph D Dougherty
Studies on regulation of gene expression have contributed substantially to understanding mechanisms for the long-term activity-dependent alterations in neural connectivity that are thought to mediate learning and memory. Most of these studies, however, have focused on the regulation of mRNA transcription. Here, we utilized high-throughput sequencing coupled with ribosome footprinting to globally characterize the regulation of translation in primary mixed neuronal-glial cultures in response to sustained depolarization...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28187409/pgminer-reloaded-fully-automated-proteogenomic-annotation-tool-linking-genomes-to-proteomes
#12
Canan Has, Sergey A Lashin, Alexey V Kochetov, Jens Allmer
Improvements in genome sequencing technology increased the availability of full genomes and transcriptomes of many organisms. However, the major benefit of massive parallel sequencing is to better understand the organization and function of genes which then lead to understanding of phenotypes. In order to interpret genomic data with automated gene annotation studies, several tools are currently available. Even though the accuracy of computational gene annotation is increasing, a combination of multiple lines of experimental evidences should be gathered...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28092655/circadian-and-upr-dependent-control-of-cpeb4-mediates-a-translational-response-to-counteract-hepatic-steatosis-under-er-stress
#13
Carlos Maillo, Judit Martín, David Sebastián, Maribel Hernández-Alvarez, Mar García-Rocha, Oscar Reina, Antonio Zorzano, Mercedes Fernandez, Raúl Méndez
The cytoplasmic polyadenylation element-binding (CPEB) proteins regulate pre-mRNA processing and translation of CPE-containing mRNAs in early embryonic development and synaptic activity. However, specific functions in adult organisms are poorly understood. Here we show that CPEB4 is required for adaptation to high-fat-diet- and ageing-induced endoplasmic reticulum (ER) stress, and subsequent hepatosteatosis. Stress-activated liver CPEB4 expression is dual-mode regulated. First, Cpeb4 mRNA transcription is controlled by the circadian clock, and then its translation is regulated by the unfolded protein response (UPR) through upstream open reading frames within the 5'UTR...
February 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28057705/translational-control-of-lipogenic-enzymes-in-the-cell-cycle-of-synchronous-growing-yeast-cells
#14
Heidi M Blank, Ricardo Perez, Chong He, Nairita Maitra, Richard Metz, Joshua Hill, Yuhong Lin, Charles D Johnson, Vytas A Bankaitis, Brian K Kennedy, Rodolfo Aramayo, Michael Polymenis
Translational control during cell division determines when cells start a new cell cycle, how fast they complete it, the number of successive divisions, and how cells coordinate proliferation with available nutrients. The translational efficiencies of mRNAs in cells progressing synchronously through the mitotic cell cycle, while preserving the coupling of cell division with cell growth, remain uninvestigated. We now report comprehensive ribosome profiling of a yeast cell size series from the time of cell birth, to identify mRNAs under periodic translational control...
January 5, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28045577/thermospermine-enhances-translation-of-sac51-and-sacl1-in-arabidopsis
#15
Mai Yamamoto, Taku Takahashi
The excessive xylem phenotype of acaulis5 (acl5), an Arabidopsis mutant defective in the synthesis of thermospermine, indicates that thermospermine is required for negative regulation of xylem differentiation. SAC51 was identified from a dominant suppressor of acl5, sac51-d, and encodes a basic helix-loop-helix (bHLH) protein. sac51-d has a premature termination codon in one of upstream open-reading frames (uORFs) of the SAC51 mRNA that is conserved among the SAC51 family members. Thermospermine may act to bypass the inhibitory effect of the uORF on main ORF translation...
January 2, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28017601/identification-and-characterization-of-the-sulfazecin-monobactam-biosynthetic-gene-cluster
#16
Rongfeng Li, Ryan A Oliver, Craig A Townsend
The monobactams, exemplified by the natural product sulfazecin, are the only class of β-lactam antibiotics not inactivated by metallo-β-lactamases, which confer bacteria with extended-spectrum β-lactam resistance. We screened a transposon mutagenesis library from Pseudomonas acidophila ATCC 31363 and isolated a sulfazecin-deficient mutant that revealed a gene cluster encoding two non-ribosomal peptide synthetases (NRPSs), a methyltransferase, a sulfotransferase, and a dioxygenase. Three modules and an aberrant C-terminal thioesterase (TE) domain are distributed across the two NRPSs...
January 19, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/27990012/characterization-of-the-traf3ip1-gene-in-yesso-scallop-patinopecten-yessoensis-and-its-expression-in-response-to-bacterial-challenge
#17
Jie Cheng, Jing Wang, Shuyue Wang, Ruojiao Li, Xianhui Ning, Qiang Xing, Xiaoli Ma, Lingling Zhang, Shi Wang, Xiaoli Hu, Zhenmin Bao
Tumor necrosis factor receptor-associated factor 3 (TRAF3) is an important adaptor that transmits upstream activation signals to induce innate immune responses. TRAF3 interacting protein 1 (TRAF3IP1) interacts specifically with TRAF3, but its function in innate immunity remains unclear, especially in marine invertebrates. In this study, to better understand the functions of TRAFs in innate immune responses, we identified and characterized the first bivalve TRAF3IP1 gene, PyTRAF3IP1, from Yesso scallop (Patinopecten yessoensis), one of the most important mollusk species for aquaculture...
December 19, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27966655/the-5-utr-variant-of-ercc5-fails-to-influence-outcomes-in-ovarian-and-lung-cancer-patients-undergoing-treatment-with-platinum-based-drugs
#18
Eliana Rulli, Federica Guffanti, Elisa Caiola, Monica Ganzinelli, Giovanna Damia, Marina C Garassino, Sheila Piva, Lorenzo Ceppi, Massimo Broggini, Mirko Marabese
The common polymorphic variant in the 5' untranslated region of the excision repair cross-complementation group 5 (ERCC5) gene was described to generate an upstream open reading frame that regulates both the basal ERCC5 expression and its ability to be synthesized following DNA damage. This variant was reported to affect response to platinum therapy in a cohort of patients with pediatric ependymoma. The role of this variant was investigated in two cohorts of cancer patients, specifically in non-small-cell lung cancer (NSCLC) patients (N = 137) and in epithelial ovarian carcinoma (EOC) patients (N = 240), treated in first-line with platinum-based compounds...
December 14, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27956492/screening-for-novel-genes-of-saccharomyces-cerevisiae-involved-in-recombinant-antibody-production
#19
Jorg C de Ruijter, German Jurgens, Alexander D Frey
Cost-effective manufacturing of biopharmaceuticals in non-mammalian hosts still requires tremendous efforts in strain development. In order to expedite identification of novel leads for strain engineering, we used a transposon-mutagenized yeast genomic DNA library to create a collection of Saccharomyces cerevisiae deletion strains expressing a full-length IgG antibody. Using a high-throughput screening, transformants with either significantly higher or lower IgG expression were selected. The integration site of the transposon in three of the selected strains was located by DNA sequencing...
December 11, 2016: FEMS Yeast Research
https://www.readbyqxmd.com/read/27935038/extensive-translational-regulation-during-seed-germination-revealed-by-polysomal-profiling
#20
Bing Bai, Alessia Peviani, Sjors van der Horst, Magdalena Gamm, Berend Snel, Leónie Bentsink, Johannes Hanson
This work investigates the extent of translational regulation during seed germination. The polysome occupancy of each gene is determined by genome-wide profiling of total mRNA and polysome-associated mRNA. This reveals extensive translational regulation during Arabidopsis thaliana seed germination. The polysome occupancy of thousands of individual mRNAs changes to a large extent during the germination process. Intriguingly, these changes are restricted to two temporal phases (shifts) during germination, seed hydration and germination...
April 2017: New Phytologist
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