keyword
MENU ▼
Read by QxMD icon Read
search

upstream open reading frame

keyword
https://www.readbyqxmd.com/read/28521011/translation-initiation-events-on-structured-eukaryotic-mrnas-generate-gene-expression-noise
#1
Estelle Dacheux, Naglis Malys, Xiang Meng, Vinoy Ramachandran, Pedro Mendes, John Eg McCarthy
Gene expression stochasticity plays a major role in biology, creating non-genetic cellular individuality and influencing multiple processes, including differentiation and stress responses. We have addressed the lack of knowledge about posttranscriptional contributions to noise by determining cell-to-cell variations in the abundance of mRNA and reporter protein in yeast. Two types of structural element, a stem-loop and a poly(G) motif, not only inhibit translation initiation when inserted into an mRNA 5΄ untranslated region, but also generate noise...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28514448/uorf-mediated-translation-allows-engineered-plant-disease-resistance-without-fitness-costs
#2
Guoyong Xu, Meng Yuan, Chaoren Ai, Lijing Liu, Edward Zhuang, Sargis Karapetyan, Shiping Wang, Xinnian Dong
Controlling plant disease has been a struggle for humankind since the advent of agriculture. Studies of plant immune mechanisms have led to strategies of engineering resistant crops through ectopic transcription of plants' own defence genes, such as the master immune regulatory gene NPR1 (ref. 1). However, enhanced resistance obtained through such strategies is often associated with substantial penalties to fitness, making the resulting products undesirable for agricultural applications. To remedy this problem, we sought more stringent mechanisms of expressing defence proteins...
May 17, 2017: Nature
https://www.readbyqxmd.com/read/28494858/mtorc1-balances-cellular-amino-acid-supply-with-demand-for-protein-synthesis-through-post-transcriptional-control-of-atf4
#3
Yeonwoo Park, Andrea Reyna-Neyra, Lucas Philippe, Carson C Thoreen
The mammalian target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth that is commonly deregulated in human diseases. Here we find that mTORC1 controls a transcriptional program encoding amino acid transporters and metabolic enzymes through a mechanism also used to regulate protein synthesis. Bioinformatic analysis of mTORC1-responsive mRNAs identified a promoter element recognized by activating transcription factor 4 (ATF4), a key effector of the integrated stress response. ATF4 translation is normally induced by the phosphorylation of eukaryotic initiation factor 2 alpha (eIF2α) through a mechanism that requires upstream open reading frames (uORFs) in the ATF4 5' UTR...
May 9, 2017: Cell Reports
https://www.readbyqxmd.com/read/28484048/novel-translation-initiation-regulation-mechanism-in-escherichia-coli-ptrb-mediated-by-a-5-terminal-aug
#4
Heather J Beck, Gary R Janssen
Alternative translation initiation mechanisms, distinct from the Shine-Dalgarno (SD) sequence-dependent mechanism, are more prevalent in bacteria than once anticipated. Translation of Escherichia coliptrB instead requires an AUG triplet at the 5'-terminus of its messenger RNA (mRNA). The 5'-terminal AUG (5'-uAUG) acts as a ribosomal recognition signal to attract ribosomes to the ptrB mRNA rather than functioning as an initiation codon to support translation of an upstream open reading frame. ptrB expression exhibits a stronger dependence on the 5'-uAUG than the predicted SD sequence; however, strengthening the predicted ptrB SD sequence relieves the necessity for the 5'-uAUG...
May 8, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28481333/regulation-of-pfemp1-var2csa-translation-by-a-plasmodium-translation-enhancing-factor
#5
Sherwin Chan, Alejandra Frasch, Chandra Sekhar Mandava, Jun-Hong Ch'ng, Maria Del Pilar Quintana, Mattias Vesterlund, Mehdi Ghorbal, Nicolas Joannin, Oscar Franzén, Jose-Juan Lopez-Rubio, Sonia Barbieri, Antonio Lanzavecchia, Suparna Sanyal, Mats Wahlgren
Pregnancy-associated malaria commonly involves the binding of Plasmodium falciparum-infected erythrocytes to placental chondroitin sulfate A (CSA) through the PfEMP1-VAR2CSA protein. VAR2CSA is translationally repressed by an upstream open reading frame. In this study, we report that the P. falciparum translation enhancing factor (PTEF) relieves upstream open reading frame repression and thereby facilitates VAR2CSA translation. VAR2CSA protein levels in var2csa-transcribing parasites are dependent on the expression level of PTEF, and the alleviation of upstream open reading frame repression requires the proteolytic processing of PTEF by PfCalpain...
May 8, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28461717/molecular-cloning-and-characterization-of-s-adenosylmethionine-decarboxylase-gene-in-rubber-tree-hevea-brasiliensis
#6
Manman Zhao, Hui Liu, Zhi Deng, Jiangshu Chen, Hong Yang, Huiping Li, Zhihui Xia, Dejun Li
S-Adenosylmethionine decarboxylase (SAMDC) is a key rate-limiting enzyme involved in polyamines biosynthesis, and it plays important roles in plant growth, development and stresses response. However, no SAMDC gene was reported in rubber tree. Here we report characteristics of an SAMDC gene (HbSAMDC1) in rubber tree. HbSAMDC1 contains a 1080 bp open reading frame (ORF) encoding 359 amino acids. Quantitative real-time PCR analyses revealed that HbSAMDC1 exhibited distinct expression patterns in different tissues and was regulated by various stresses, including drought, cold, salt, wounding, and H2O2 treatments...
April 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/28461625/transcript-specific-characteristics-determine-the-contribution-of-endo-and-exonucleolytic-decay-pathways-during-the-degradation-of-nonsense-mediated-decay-substrates
#7
Franziska Ottens, Volker Boehm, Christopher R Sibley, Jernej Ule, Niels H Gehring
Nonsense-mediated mRNA decay (NMD) controls gene expression by eliminating mRNAs with premature or aberrant translation termination. Degradation of NMD substrates is initiated by the central NMD factor UPF1, which recruits the endonuclease SMG6 and the deadenylation-promoting SMG5/7 complex. The extent to which SMG5/7 and SMG6 contribute to the degradation of individual substrates and their regulation by UPF1 remain elusive. Here we map transcriptome-wide sites of SMG6-mediated endocleavage via 3' fragment capture and degradome sequencing...
May 1, 2017: RNA
https://www.readbyqxmd.com/read/28459876/alternative-oxidase-aox-constitutes-a-small-family-of-proteins-in-citrus-clementina-and-citrus-sinensis-l-osb
#8
Jacqueline Araújo Castro, Monique Drielle Gomes Ferreira, Raner José Santana Silva, Bruno Silva Andrade, Fabienne Micheli
The alternative oxidase (AOX) protein is present in plants, fungi, protozoa and some invertebrates. It is involved in the mitochondrial respiratory chain, providing an alternative route for the transport of electrons, leading to the reduction of oxygen to form water. The present study aimed to characterize the family of AOX genes in mandarin (Citrus clementina) and sweet orange (Citrus sinensis) at nucleotide and protein levels, including promoter analysis, phylogenetic analysis and C. sinensis gene expression...
2017: PloS One
https://www.readbyqxmd.com/read/28450857/the-functional-roles-of-the-cis-acting-elements-in-bamboo-mosaic-virus-rna-genome
#9
REVIEW
I-Hsuan Chen, Ying-Wen Huang, Ching-Hsiu Tsai
Bamboo mosaic virus (BaMV), which belongs to the genus Potexvirus in the family Alphaflexiviridae, has a single-stranded positive-sense RNA genome that is approximately 6400 nucleotides (nts) in length. Positive-sense RNA viruses can use genomic RNA as a template for translation and replication after entering a suitable host cell. Furthermore, such viral RNA is recognized by capsid protein for packaging and by viral movement protein(s) or the movement protein complex for cell-to-cell and systemic movement. Hence, viral RNA must contain signals for different functions to complete the viral infection cycle...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28445614/two-common-human-cldn5-alleles-encode-different-open-reading-frames-but-produce-one-protein-isoform
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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 31, 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
#16
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
#17
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
#18
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
#19
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
#20
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
keyword
keyword
95619
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"