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upstream open reading frame

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https://www.readbyqxmd.com/read/29146899/alternative-transcription-start-site-selection-in-mr-opy2-controls-lifestyle-transitions-in-the-fungus-metarhizium-robertsii
#1
Na Guo, Ying Qian, Qiangqiang Zhang, Xiaoxuan Chen, Guohong Zeng, Xing Zhang, Wubing Mi, Chuan Xu, Raymond J St Leger, Weiguo Fang
Metarhizium robertsii is a versatile fungus with saprophytic, plant symbiotic and insect pathogenic lifestyle options. Here we show that M. robertsii mediates the saprophyte-to-insect pathogen transition through modulation of the expression of a membrane protein, Mr-OPY2. Abundant Mr-OPY2 protein initiates appressorium formation, a prerequisite for infection, whereas reduced production of Mr-OPY2 elicits saprophytic growth and conidiation. The precise regulation of Mr-OPY2 protein production is achieved via alternative transcription start sites...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29114030/near-cognate-codons-contribute-complexity-to-translation-regulation
#2
N Louise Glass
The interplay between translation initiation, modification of translation initiation factors, and selection of start sites on mRNA for protein synthesis can play a regulatory role in the cellular response to stress, development, and cell fate in eukaryotic species by shaping the proteome. As shown by Ivanov et al. (mBio 8:e00844-17, 2017, https://doi.org/10.1128/mBio.00844-17), in the filamentous fungus Neurospora crassa, both upstream open reading frames (uORFs) and near-cognate start codons negatively or positively regulate the translation of the transcription factor CPC1 and production of CPC1 isoforms, which mediate the cellular response to amino acid starvation...
November 7, 2017: MBio
https://www.readbyqxmd.com/read/29097404/deep-learning-of-the-regulatory-grammar-of-yeast-5-untranslated-regions-from-500-000-random-sequences
#3
Josh T Cuperus, Benjamin Groves, Anna Kuchina, Alexander B Rosenberg, Nebojsa Jojic, Stanley Fields, Georg Seelig
Our ability to predict protein expression from DNA sequence alone remains poor, reflecting our limited understanding of cis-regulatory grammar and hampering the design of engineered genes for synthetic biology applications. Here, we generate a model that predicts the protein expression of the 5' untranslated region (UTR) of mRNAs in the yeast Saccharomyces cerevisiae. We constructed a library of half a million 50-nucleotide-long random 5' UTRs and assayed their activity in a massively parallel growth selection experiment...
November 2, 2017: Genome Research
https://www.readbyqxmd.com/read/29089381/drosophila-sister-of-sex-lethal-is-a-repressor-of-translation
#4
Rebecca Moschall, Daniela Strauss, Marina Garcia-Bayert, Fatima Gebauer, Jan Medenbach
The RNA-binding protein Sex Lethal (Sxl) is an important post-transcriptional regulator of gene expression in female Drosophila To prevent the assembly of the dosage compensation complex in female flies, Sxl acts as a repressor of msl-2 mRNA translation. It employs two distinct and mutually reinforcing blocks to translation that operate on the 5' and 3' untranslated regions (UTRs) of msl-2 mRNA, respectively. While 5' UTR-mediated translational control involves an upstream open reading frame, 3' UTR-mediated regulation strictly requires the co-repressor protein Upstream of N-ras (Unr) which is recruited to the msl-2 mRNA by Sxl...
October 31, 2017: RNA
https://www.readbyqxmd.com/read/29080154/thermospermine-an-evolutionarily-ancient-but-functionally-new-compound-in-plants
#5
Taku Takahashi
Themospermine is a structural isomer of spermine and is present in some bacteria and most of plants. An Arabidopsis mutant, acaulis5 (acl5), that is defective in the biosynthesis of thermospermine displays excessive proliferation of xylem vessels with dwarfed growth. Recent studies using acl5 and its suppressor mutants that recover the growth without thermospermine have revealed that thermospermine plays a key role in the negative control of the proliferation of xylem vessels through enhancing translation of specific mRNAs that contain a conserved upstream open-reading-frame (uORF) in the 5' leader region...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29065505/kinases-of-eif2a-switch-translation-of-mrna-subset-during-neuronal-plasticity
#6
REVIEW
Ekaterina Chesnokova, Natalia Bal, Peter Kolosov
Compared to other types of cells, neurons express the largest number of diverse mRNAs, including neuron-specific ones. This mRNA diversity is required for neuronal function, memory storage, maintenance and retrieval. Regulation of translation in neurons is very complicated and involves various proteins. Some proteins, implementing translational control in other cell types, are used by neurons for synaptic plasticity. In this review, we discuss the neuron-specific activity of four kinases: protein kinase R (PKR), PKR-like endoplasmic reticulum kinase (PERK), general control nonderepressible 2 kinase (GCN2), and heme-reguated eIF2α kinase (HRI), the substrate for which is α-subunit of eukaryotic initiation factor 2 (eIF2α)...
October 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29054828/cloning-and-expression-study-of-an-irf4a-gene-and-its-two-transcript-variants-in-turbot-scophthalmus-maximus
#7
Song Li, Guobin Hu, Zhipeng Chen, Lianfei Song, Guanjie Wang, Dahai Liu, Qiuming Liu
Interferon regulatory factor 4 (IRF4) is known to be involved in antiviral response as well as regulation of functional and developmental processes in lymphomyeloid cell lineages in mammals. In this study, the gene of IRF4a and its two transcript variants (named IRF4a1 and -2) were cloned from turbot, Scophthalmus maximus, the tissue distributions and in vivo immune responsive expression patterns of the two transcripts were subsequently examined. The Scophthalmus maximus (Sm)IRF4a gene is 8367 nucleotide (nt) in length, consisting of eight exons and seven introns...
October 17, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29045794/allosteric-modulation-of-the-faecalibacterium-prausnitzii-hepatitis-delta-virus-like-ribozyme-by-glucosamine-6-phosphate-the-substrate-of-the-adjacent-gene-product
#8
Luiz F M Passalacqua, Randi M Jimenez, Jennifer Y Fong, Andrej Lupták
Self-cleaving ribozymes were discovered 30 years ago and have been found throughout nature, from bacteria to animals, but little is known about their biological functions and regulation, particularly how cofactors and metabolites alter their activity. A hepatitis delta virus-like self-cleaving ribozyme maps upstream of a phosphoglucosamine mutase (glmM) open reading frame in the genome of the human gut bacterium Faecalibacterium prausnitzii. The presence of a ribozyme in the untranslated region of glmM suggests a regulation mechanism of gene expression...
November 3, 2017: Biochemistry
https://www.readbyqxmd.com/read/28986213/characterization-of-nuclear-factor-of-activated-t-cells-c3-nfatc3-and-gene-expression-of-upstream-downstream-signaling-molecules-in-response-to-immunostimulants-in-pacific-red-snapper-cells
#9
Carlos Angulo, Erika Alamillo, Felipe Ascencio, Martha Reyes-Becerril
The nuclear factor of activated T cells (NFAT) proteins have crucial roles in the development and function of the immune system since they not only regulate activation of T cells but are also involved in the control of thymocyte development and T-cell differentiation. In this study, NFATc3 was characterized from the Pacific red snapper, Lutjanus peru. LpNFAtc3, which contains an open reading of 3300 bp frame coding for a protein of 1100 aa with a predicted molecular weight of 118.52 kDa. The predicted protein showed a conserved NFAT family structure with signature motifs and domains, sharing high identity (up to 76%) compared to other fish sequences...
October 3, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28971534/the-zap1-transcriptional-activator-negatively-regulates-translation-of-the-rtc4-mrna-through-the-use-of-alternative-5-transcript-leaders
#10
Amanda J Bird, Simon Labbé
The zinc-responsive transcription activator Zap1 plays a central role in zinc homeostasis in the budding yeast Saccharomyces cerevisiae. In zinc-deficient cells, Zap1 binds to zinc responsive elements in target gene promoters and activates gene expression. In most cases, Zap1-dependent gene activation results in increased levels of mRNAs and proteins. However, Zap1-dependent activation of RTC4 results in increased levels of the RTC4 mRNA and decreased levels of the Rtc4 protein. This atypical regulation results from Zap1-mediated changes in the transcriptional start site for RTC4 and the production of a RTC4 transcript with a longer 5' leader...
October 3, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28963784/zap1-dependent-transcription-from-an-alternative-upstream-promoter-controls-translation-of-rtc4-mrna-in-zinc-deficient-saccharomyces-cerevisiae
#11
Janet Taggart, Colin W MacDiarmid, Spencer Haws, David J Eide
Maintaining zinc homeostasis is an important property of all organisms. In the yeast Saccharomyces cerevisiae, the Zap1 transcriptional activator is a central player in this process. In response to zinc deficiency, Zap1 activates transcription of many genes and consequently increases accumulation of their encoded proteins. In this report, we describe a new mechanism of Zap1-mediated regulation whereby increased transcription of certain target genes results in reduced protein expression. Transcription of the Zap1-responsive genes RTC4 and RAD27 increases markedly in zinc-deficient cells but, surprisingly, their protein levels decrease...
September 30, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28956754/a-uorf-represses-the-transcription-factor-athb1-in-aerial-tissues-to-avoid-a-deleterious-phenotype
#12
Pamela A Ribone, Matías Capella, Agustín L Arce, Raquel L Chan
AtHB1 is an Arabidopsis (Arabidopsis thaliana) homeodomain-leucine zipper transcription factor that participates in hypocotyl elongation under short-day conditions. Here, we show that its expression is posttranscriptionally regulated by an upstream open reading frame (uORF) located in its 5' untranslated region. This uORF encodes a highly conserved peptide (CPuORF) that is present in varied monocot and dicot species. The Arabidopsis uORF and its maize (Zea mays) homolog repressed the translation of the main open reading frame in cis, independent of the sequence of the latter...
November 2017: Plant Physiology
https://www.readbyqxmd.com/read/28941630/a-novel-transposon-tn6306-mediates-the-spread-of-blaimi-in-enterobacteriaceae-in-hospitals
#13
Fangfang Zhang, Xiaoli Wang, Lianyan Xie, Qiuyue Zheng, Xiaokui Guo, Lizhong Han, Jingyong Sun
The increasing incidence of carbapenem-resistant Enterobacteriaceae has become a challenge for clinical therapy. In our study, we analysed the molecular characteristics of imipenem-hydrolyzing β-lactamase (IMI) in Enterobacteriaceae isolates. Two reported clinical isolates, the IMI-3-producing Raoultella ornithinolytica RJ46C and the IMI-2-producing Escherichia coli RJ18 were identified in our retrospective review of isolates collected from June 2010 to June 2013, both isolates were resistant to carbapenem but sensitive to expanded-spectrum cephalosporins...
September 21, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28940803/the-torradovirus-specific-rna2-orf1-protein-is-necessary-for-plant-systemic-infection
#14
I Ferriol, M Vallino, M Ciuffo, J C Nigg, E J Zamora-Macorra, B W Falk, M Turina
Tomato apex necrosis virus (species Tomato marchitez virus, genus Torradovirus, family Secoviridae) causes a severe tomato disease in Mexico. One distinctive feature of torradoviruses compared to other members of the family Secoviridae is the presence of an additional open reading frame (ORF) in genomic RNA2 (denominated RNA2-ORF1), located upstream of ORF2. RNA2-ORF2 encodes a polyprotein that is processed into a putative movement protein and three capsid proteins (CPs). The RNA2-ORF1 protein has homologues only among other torradoviruses, and so far, no function has been associated to it...
September 21, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28935601/ctenopharyngodon-idella-perk-eif2ak3-decreases-cell-viability-by-phosphorylating-eif2%C3%AE-under-er-stress
#15
Tao Zhang, Dongming Li, Lijuan Wan, Xin Chen, Xiangqin Wang, Bin Zhong, Zhen Wu, Huiling Mao, Chengyu Hu
As an upstream kinase of eIF2α, protein kinase RNA-like ER (endoplasmic reticulum) kinase (PERK) is a type I transmembrane protein located in ER in eukaryotic cells. PERK is mainly composed of two domains, the intracavitary domain for BIP protein combination and the dissociative C-terminal region containing a typical serine/threonine kinase domain which promotes the phosphorylation of eIF2α. In this study, we cloned a PERK (also known as EIF2AK3) gene from grass carp (Ctenopharyngodon idella). The full-length cDNA of grass carp PERK (CiPERK) is 5192 bp including a 176 bp of 5' untranslated region, a 1719 bp of 3' untranslated region and a 3297 bp of the longest open reading frame (ORF) encoding 1098 amino acids...
September 19, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28934489/antisense-oligonucleotides-targeting-translation-inhibitory-elements-in-5-utrs-can-selectively-increase-protein-levels
#16
Xue-Hai Liang, Hong Sun, Wen Shen, Shiyu Wang, Joyee Yao, Michael T Migawa, Huynh-Hoa Bui, Sagar S Damle, Stan Riney, Mark J Graham, Rosanne M Crooke, Stanley T Crooke
A variety of diseases are caused by deficiencies in amounts or activity of key proteins. An approach that increases the amount of a specific protein might be of therapeutic benefit. We reasoned that translation could be specifically enhanced using trans-acting agents that counter the function of negative regulatory elements present in the 5' UTRs of some mRNAs. We recently showed that translation can be enhanced by antisense oligonucleotides (ASOs) that target upstream open reading frames. Here we report the amount of a protein can also be selectively increased using ASOs designed to hybridize to other translation inhibitory elements in 5' UTRs...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28924029/circuitry-linking-the-global-csr-and-%C3%AF-e-dependent-cell-envelope-stress-response-systems
#17
Helen Yakhnin, Robert Aichele, Sarah E Ades, Tony Romeo, Paul Babitzke
CsrA of Escherichia coli is an RNA-binding protein that globally regulates a wide variety of cellular processes and behaviors including carbon metabolism, motility, biofilm formation, and the stringent response. CsrB and CsrC are sRNAs that sequester CsrA, thereby preventing CsrA-mRNA interaction. RpoE (σ(E)) is the extracytoplasmic stress response sigma factor of E. coli Previous RNA-seq studies identified rpoE mRNA as a CsrA target. Here we explored the regulation of rpoE by CsrA and found that CsrA represses rpoE translation...
September 18, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28917040/studying-selenoprotein-mrna-translation-using-rna-seq-and-ribosome-profiling
#18
Brian K Dalley, Lisa Baird, Michael T Howard
Deep sequencing of ribosome protected mRNA footprints, also called ribosome profiling or Ribo-Seq, is a relatively new methodology well suited to address questions regarding the mechanisms and efficiency of protein expression. Specifically, the ability of this technique to quantify ribosome abundance with codon resolution enables experiments aimed at studying many aspects of translation, including gene-specific translational efficiency, translation of regulatory upstream short open reading frames, sites of ribosome pausing, and most importantly for selenoproteins, the efficiency by which UGA codons are redefined to encode selenocysteine...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28881981/titer-predicting-translation-initiation-sites-by-deep-learning
#19
Sai Zhang, Hailin Hu, Tao Jiang, Lei Zhang, Jianyang Zeng
Motivation: Translation initiation is a key step in the regulation of gene expression. In addition to the annotated translation initiation sites (TISs), the translation process may also start at multiple alternative TISs (including both AUG and non-AUG codons), which makes it challenging to predict TISs and study the underlying regulatory mechanisms. Meanwhile, the advent of several high-throughput sequencing techniques for profiling initiating ribosomes at single-nucleotide resolution, e...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28851853/translational-repression-of-the-rpos-antiadapter-irad-by-csra-is-mediated-via-translational-coupling-to-a-short-upstream-open-reading-frame
#20
Hongmarn Park, Louise C McGibbon, Anastasia H Potts, Helen Yakhnin, Tony Romeo, Paul Babitzke
CsrA is a global regulatory RNA binding protein that has important roles in regulating carbon metabolism, motility, biofilm formation, and numerous other cellular processes. IraD functions as an antiadapter protein that inhibits RssB-mediated degradation of RpoS, the general stress response and stationary-phase sigma factor of Escherichia coli Here we identified a novel mechanism in which CsrA represses iraD translation via translational coupling. Expression studies with quantitative reverse transcriptase PCR, Western blotting, and lacZ fusions demonstrated that CsrA represses iraD expression...
August 29, 2017: MBio
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