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upstream open reading frame

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https://www.readbyqxmd.com/read/28445614/two-common-human-cldn5-alleles-encode-different-open-reading-frames-but-produce-one-protein-isoform
#1
Ronald M Cornely, Barbara Schlingmann, Whitney S Shepherd, Joshua D Chandler, David C Neujahr, Michael Koval
Claudins provide tight junction barrier selectivity. The human CLDN5 gene contains a high-frequency single-nucleotide polymorphism (rs885985), where the G allele codes for glutamine (Q) and the A allele codes for an amber stop codon. Thus, these different CLDN5 alleles define nested open reading frames (ORFs) encoding claudin-5 proteins that are 303 or 218 amino acids in length. Interestingly, human claudin-16 and claudin-23 also have long ORFs. The long form of claudin-5 contrasts with the majority of claudin-5 proteins in the National Center for Biotechnology Information protein database, which are less than 220 amino acids in length...
April 26, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28420619/analysis-of-variants-in-upstream-open-reading-frames-of-human-globin-related-genes
#2
Ye Yuhua, Zhang Qianqian, Zhong Jianmei, Li Yihong, Zhang Li, Yu Qiuxia, Xu Xiangmin
β-thalassemia is an autosomal recessive monogenic disease that is caused by defects in the production of β-like globin chains. Activation of γ-globin gene and the increase in fetal hemoglobin expression have been demonstrated as one of the most important factors to ameliorate the clinical outcome of β-thalassemia patients. In this study, 202 genes or miRNAs associated with human hemoglobin gene expression from 1802 β-thalassemia patients were analyzed with target capture and next generation sequencing strategies in terms of functional variants that might affect hemoglobin gene expression...
March 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28414973/regulation-of-antibiotic-resistance-by-non-coding-rnas-in-bacteria
#3
REVIEW
Daniel Dar, Rotem Sorek
Antibiotic resistance genes are commonly regulated by sophisticated mechanisms that activate gene expression in response to antibiotic exposure. Growing evidence suggest that cis-acting non-coding RNAs play a major role in regulating the expression of many resistance genes, specifically those which counteract the effects of translation-inhibiting antibiotics. These ncRNAs reside in the 5'UTR of the regulated gene, and sense the presence of the antibiotics by recruiting translating ribosomes onto short upstream open reading frames (uORFs) embedded in the ncRNA...
April 14, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28369621/critical-23s-rrna-interactions-for-macrolide-dependent-ribosome-stalling-on-the-ermcl-nascent-peptide-chain
#4
Miriam Koch, Jessica Willi, Ugo Pradère, Jonathan Hall, Norbert Polacek
The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading frame in the presence of an exit tunnel-bound macrolide antibiotic. The molecular basis for this translation arrest is still not fully understood. Here, we used a nucleotide analog interference approach to unravel important functional groups on 23S rRNA residues in the ribosomal exit tunnel for ribosome stalling on the ErmC leader peptide...
March 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28368337/crispr-cas9-mediated-gene-silencing-of-the-mutant-huntingtin-gene-in-an-in-vitro-model-of-huntington-s-disease
#5
Nivya Kolli, Ming Lu, Panchanan Maiti, Julien Rossignol, Gray L Dunbar
Huntington's disease (HD) is a fatal neurodegenerative genetic disease characterized by a loss of neurons in the striatum. It is caused by a mutation in the Huntingtin gene (HTT) that codes for the protein huntingtin (HTT). The mutant Huntingtin gene (mHTT) contains extra poly-glutamine (CAG) repeats from which the translated mutant huntingtin proteins (mHTT) undergo inappropriate post-translational modifications, conferring a toxic gain of function, in addition to its non-functional property. In order to curb the production of the mHTT, we have constructed two CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR associate protein) plasmids, among which one nicks the DNA at untranslated region upstream to the open reading frame (uORF), and the other nicks the DNA at exon1-intron boundary...
April 2, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28366877/translational-effects-and-coding-potential-of-an-upstream-open-reading-frame-associated-with-dopa-responsive-dystonia
#6
Lataisia Jones, Lacy Goode, Eduardo Davila, Amber Brown, Deirdre M McCarthy, Nutan Sharma, Pradeep G Bhide, Ioanna A Armata
Upstream open reading frames (uORFs) have emerged as major post-transcriptional regulatory elements in eukaryotic species. In general, uORFs are initiated by a translation start codon within the 5' untranslated region of a gene (upstream ATG; uATG), and they are negatively correlated with translational efficiency. In addition to their translational regulatory role, some uORFs can code for biologically active short peptides. The importance of uATGs/uORFs is further underscored by human diseases associated with single nucleotide polymorphisms (SNPs), which disrupt existing uORFs or introduce novel uORFs...
March 30, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28358924/processing-and-targeting-of-proteins-derived-from-polyprotein-with-2a-and-lp4-2a-as-peptide-linkers-in-a-maize-expression-system
#7
He Sun, Ni Zhou, Hai Wang, Dafang Huang, Zhihong Lang
In the transformation of multiple genes, gene fusion is an attractive alternative to other methods, including sexual crossing, re-transformation, and co-transformation, among others. The 2A peptide from the foot-and-mouth disease virus (FMDV) causes the co-translational "cleavage" of polyprotein and operates in a wide variety of eukaryotic cells. LP4, a linker peptide that originates from a natural polyprotein occurring in the seed of Impatiens balsamina, can be split between the first and second amino acids in post-translational processing...
2017: PloS One
https://www.readbyqxmd.com/read/28358031/serine-protease-sp105-activates-prophenoloxidase-in-asian-corn-borer-melanization-and-is-regulated-by-serpin-3
#8
Yuan Chu, Fang Hong, Qizhi Liu, Chunju An
Melanization reaction, resulting from the activation of prophenoloxidase, is a vital immune response in insects for encapsulating and killing the invasive organisms. Prophenoloxidase needs to be proteolytically activated by its upstream prophenoloxidase-activating protease (PAP) in melanization. Identification and characterization of PAPs facilitates the understanding of the molecular mechanisms involved in insect immunity. We here cloned a full-length cDNA for a serine protease, named as SP105, from Asian corn borer, Ostrinia furnacalis (Guenée)...
March 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28356522/the-minute-virus-of-canines-mvc-np1-protein-governs-the-expression-of-a-subset-of-essential-ns-proteins-via-its-role-in-rna-processing
#9
Olufemi O Fasina, Stephanie Stupps, Wanda Figueroa-Cuilan, David J Pintel
Parvoviruses use a variety of means to control the expression of their compact genomes. The Bocaparvovirus Minute Virus of Canines (MVC) encodes a small, genus-specific protein, NP1, which governs access to the viral capsid gene via its role in alternative polyadenylation and alternative splicing of the single MVC pre-mRNA. In addition to NP1, MVC encodes five additional non-structural proteins (NS) that share an initiation codon at the left end of the genome and which are individually encoded by alternative multiply-spliced mRNAs...
March 29, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28343578/untranslated-regions-utrs-orchestrate-translation-reprogramming-in-cellular-stress-responses
#10
REVIEW
Basavaraj Sajjanar, Rajib Deb, Susheel Kumar Raina, Sachin Pawar, Manoj P Brahmane, Avinash V Nirmale, Nitin P Kurade, Gundallahalli B Manjunathareddy, Santanu Kumar Bal, Narendra Pratap Singh
Stress is the result of an organism's interaction with environmental challenges. Regulations of gene expression including translation modulations are critical for adaptation and survival under stress. Untranslated regions (UTRs) of the transcripts play significant roles in translation regulation and continue to raise many intriguing questions in our understanding of cellular stress physiology. IRES (Internal ribosome entry site) and uORF (upstream open reading frame) mediated alternative translation initiations are emerging as unique mechanisms...
April 2017: Journal of Thermal Biology
https://www.readbyqxmd.com/read/28332641/the-sample-of-choice-for-detecting-middle-east-respiratory-syndrome-coronavirus-in-asymptomatic-dromedary-camels-using-real-time-reversetranscription-polymerase-chain-reaction
#11
K A Mohran, E A B Farag, C B E Reusken, V S Raj, M M Lamers, S D Pas, J Voermans, S L Smits, M M Alhajri, F Alhajri, H E Al-Romaihi, H Ghobashy, M M El-Maghraby, S H S Al Dhahiry, N Al-Mawlawi, A M El-Sayed, M Al-Thani, S A Al-Marri, B L Haagmans, M P G Koopmans
The newly identified Middle East respiratory syndrome coronavirus (MERS-CoV), which causes severe respiratory disease, particularly in people with comorbidities, requires further investigation. Studies in Qatar and elsewhere have provided evidence that dromedary camels are a reservoir for the virus, but the exact modes of transmission of MERS-CoV to humans remain unclear. In February 2014, an assessment was made of the suitability and sensitivity of different types of sample for the detection of MERSCoV by real-time reverse-transcription polymerase chain reaction (RT-PCR) for three gene targets: UpE (upstream of the E gene), the N (nucleocapsid) gene and open reading frame (ORF) 1a...
December 2016: Revue Scientifique et Technique
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
#12
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 18, 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
#13
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
#14
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
#15
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
#16
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
#17
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...
May 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
#18
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
#19
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
#20
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
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