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upstream open reading frame

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https://www.readbyqxmd.com/read/29339760/biochemical-and-genetic-characterization-of-a-novel-metallo-%C3%AE-lactamase-from-marine-bacterium-erythrobacter-litoralis-htcc-2594
#1
Xia-Wei Jiang, Hong Cheng, Ying-Yi Huo, Lin Xu, Yue-Hong Wu, Wen-Hong Liu, Fang-Fang Tao, Xin-Jie Cui, Bei-Wen Zheng
Metallo-β-lactamases (MBLs) are a group of enzymes that can inactivate most commonly used β-lactam-based antibiotics. Among MBLs, New Delhi metallo-β-lactamase-1 (NDM-1) constitutes an urgent threat to public health as evidenced by its success in rapidly disseminating worldwide since its first discovery. Here we report the biochemical and genetic characteristics of a novel MBL, ElBla2, from the marine bacterium Erythrobacter litoralis HTCC 2594. This enzyme has a higher amino acid sequence similarity to NDM-1 (56%) than any previously reported MBL...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29323119/cug-initiation-and-frameshifting-enable-production-of-dipeptide-repeat-proteins-from-als-ftd-c9orf72-transcripts
#2
Ricardos Tabet, Laure Schaeffer, Fernande Freyermuth, Melanie Jambeau, Michael Workman, Chao-Zong Lee, Chun-Chia Lin, Jie Jiang, Karen Jansen-West, Hussein Abou-Hamdan, Laurent Désaubry, Tania Gendron, Leonard Petrucelli, Franck Martin, Clotilde Lagier-Tourenne
Expansion of G4C2 repeats in the C9ORF72 gene is the most prevalent inherited form of amyotrophic lateral sclerosis and frontotemporal dementia. Expanded transcripts undergo repeat-associated non-AUG (RAN) translation producing dipeptide repeat proteins from all reading frames. We determined cis-factors and trans-factors influencing translation of the human C9ORF72 transcripts. G4C2 translation operates through a 5'-3' cap-dependent scanning mechanism, requiring a CUG codon located upstream of the repeats and an initiator Met-tRNAMeti...
January 11, 2018: Nature Communications
https://www.readbyqxmd.com/read/29295906/using-multisite-lr-cloning-to-generate-a-destination-clone
#3
John S Reece-Hoyes, Albertha J M Walhout
This protocol describes using the Gateway recombinatorial cloning system to simultaneously transfer a promoter and an open reading frame (ORF) from two different Entry clones into the same Destination vector using LR enzymes. A multisite cloning reaction transfers the inserts from multiple Entry clones into a single Destination vector. This type of recombination is much less efficient than transferring a single DNA fragment; however, the variety of Destination clones that can be generated in this manner is vast...
January 2, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29281982/polyamines-in-the-life-of-arabidopsis-profiling-the-expression-of-s-adenosylmethionine-decarboxylase-samdc-gene-family-during-its-life-cycle
#4
Rajtilak Majumdar, Lin Shao, Swathi A Turlapati, Subhash C Minocha
BACKGROUND: Arabidopsis has 5 paralogs of the S-adenosylmethionine decarboxylase (SAMDC) gene. Neither their specific role in development nor the role of positive/purifying selection in genetic divergence of this gene family is known. While some data are available on organ-specific expression of AtSAMDC1, AtSAMDC2, AtSAMDC3 and AtSAMDC4, not much is known about their promoters including AtSAMDC5, which is believed to be non-functional. RESULTS: (1) Phylogenetic analysis of the five AtSAMDC genes shows similar divergence pattern for promoters and coding sequences (CDSs), whereas, genetic divergence of 5'UTRs and 3'UTRs was independent of the promoters and CDSs; (2) while AtSAMDC1 and AtSAMDC4 promoters exhibit high activity (constitutive in the former), promoter activities of AtSAMDC2, AtSAMDC3 and AtSAMDC5 are moderate to low in seedlings (depending upon translational or transcriptional fusions), and are localized mainly in the vascular tissues and reproductive organs in mature plants; (3) based on promoter activity, it appears that AtSAMDC5 is both transcriptionally and translationally active, but based on it's coding sequence it seems to produce a non-functional protein; (4) though 5'-UTR based regulation of AtSAMDC expression through upstream open reading frames (uORFs) in the 5'UTR is well known, no such uORFs are present in AtSAMDC4 and AtSAMDC5; (5) the promoter regions of all five AtSAMDC genes contain common stress-responsive elements and hormone-responsive elements; (6) at the organ level, the activity of AtSAMDC enzyme does not correlate with the expression of specific AtSAMDC genes or with the contents of spermidine and spermine...
December 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29281028/translation-reinitiation-in-microbes-and-higher-eukaryotes
#5
Stanislava Gunišová, Vladislava Hronová, Mahabub Pasha Mohammad, Alan G Hinnebusch, Leoš Shivaya Valášek
Protein production must be strictly controlled at its beginning and end to synthesize a polypeptide that faithfully copies genetic information carried in the encoding mRNA. In contrast to viruses and prokaryotes, the majority of mRNAs in eukaryotes contain only one coding sequence, resulting in production of a single protein. There are, however, many exceptional mRNAs that either carry short open reading frames upstream of the main coding sequence (uORFs) or even contain multiple long ORFs. A wide variety of mechanisms has evolved in microbes and higher eukaryotes to prevent recycling of some or all translational components upon termination of the first translated ORF in such mRNAs and thereby enable subsequent translation of the next uORF or downstream coding sequence...
December 21, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/29232504/a-genetic-toolbox-for-modulating-the-expression-of-heterologous-genes-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#6
Bo Wang, Carrie Eckert, Pin-Ching Maness, Jianping Yu
Cyanobacteria, genetic models for photosynthesis research for decades, have recently become attractive hosts for producing renewable fuels and chemicals, owing to their genetic tractability, relatively fast growth, and their ability to utilize sunlight, fix carbon dioxide and, in some cases, fix nitrogen. Despite significant advances, there is still an urgent demand for synthetic biology tools in order to effectively manipulate genetic circuits in cyanobacteria. In this study, we have compared a total of 17 natural and chimeric promoters, focusing on expression of the ethylene-forming enzyme (EFE) in the cyanobacterium Synechocystis sp...
December 12, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29228904/comparative-ribosome-profiling-uncovers-a-dominant-role-for-translational-control-in-toxoplasma-gondii
#7
Musa A Hassan, Juan J Vasquez, Chew Guo-Liang, Markus Meissner, T Nicolai Siegel
BACKGROUND: The lytic cycle of the protozoan parasite Toxoplasma gondii, which involves a brief sojourn in the extracellular space, is characterized by defined transcriptional profiles. For an obligate intracellular parasite that is shielded from the cytosolic host immune factors by a parasitophorous vacuole, the brief entry into the extracellular space is likely to exert enormous stress. Due to its role in cellular stress response, we hypothesize that translational control plays an important role in regulating gene expression in Toxoplasma during the lytic cycle...
December 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29211764/identification-expression-and-functional-characterization-of-m4l-a-muscarinic-acetylcholine-m4-receptor-splice-variant
#8
Douglas A Schober, Carrie H Croy, Cara L Ruble, Ran Tao, Christian C Felder
Rodent genomic alignment sequences support a 2-exon model for muscarinic M4 receptor. Using this model a novel N-terminal extension was discovered in the human muscarinic acetylcholine M4 receptor. An open reading frame was discovered in the human, mouse and rat with a common ATG (methionine start codon) that extended the N-terminus of the muscarinic acetylcholine M4 receptor subtype by 155 amino acids resulting in a longer variant. Transcriptional evidence for this splice variant was confirmed by RNA-Seq and RT-PCR experiments performed from human donor brain prefrontal cortices...
2017: PloS One
https://www.readbyqxmd.com/read/29208497/molecular-cloning-expression-promoter-analysis-and-functional-characterization-of-a-new-crustin-from-litopenaeus-vannamei
#9
Ming Li, Chunxia Ma, Haoyang Li, Jinxia Peng, Digang Zeng, Xiaohan Chen, Chaozheng Li
Antimicrobial peptides (AMPs) are the most important players in the innate immune system, providing a principal first-line of defense against the invading pathogens. Crustin, a type of whey acidic protein (WAP) domain-containing and cationic cysteine-rich AMP, can function in a protease inhibition or an effector molecule manner. In the present study, a new Crustin was cloned and identified from Pacific white shrimp Litopenaeus vannamei and designated as LvCrustinA. The full-length cDNA of LvCrustinA was 687 bp, with a 519 bp open reading frame (ORF) that encoded a peptide of 172 amino acids...
December 5, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29163393/the-5bsl3-2-functional-rna-domain-connects-distant-regions-in-the-hepatitis-c-virus-genome
#10
REVIEW
Cristina Romero-López, Alfredo Berzal-Herranz
Viral genomes are complexly folded entities that carry all the information required for the infective cycle. The nucleotide sequence of the RNA virus genome encodes proteins and functional information contained in discrete, highly conserved structural units. These so-called functional RNA domains play essential roles in the progression of infection, which requires their preservation from one generation to the next. Numerous functional RNA domains exist in the genome of the hepatitis C virus (HCV). Among them, the 5BSL3...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29162641/discovery-of-non-canonical-translation-initiation-sites-through-mass-spectrometric-analysis-of-protein-n-termini
#11
Chan Hyun Na, Mustafa Barbhuiya, Min-Sik Kim, Steven Verbruggen, Stephen Eacker, Olga Pletnikova, Juan Troncoso, Marc Halushka, Gerben Menschaert, Christopher Overall, Akhilesh Pandey
Translation initiation generally occurs at AUG codons in eukaryotes although it has been shown that non-AUG or non-canonical translation initiation can also occur. However, the evidence for non-canonical translation initiation sites (TISs) is largely indirect and based on ribosome profiling studies. Here, using a strategy specifically designed to enrich N-termini of proteins, we demonstrate that many human proteins are translated at non-canonical TISs. The large majority of TISs that mapped to 5' untranslated regions were non-canonical and led to N-terminal extension of annotated proteins or translation of upstream small open reading frames (uORF)...
November 21, 2017: Genome Research
https://www.readbyqxmd.com/read/29155138/hpv16-e5-is-produced-from-an-hpv16-early-mrna-spliced-from-sd226-to-sa3358
#12
Kersti Nilsson, Christopher Norberg, Ann-Kristin Mossberg, Stefan Schwartz
The HPV16 E5 open reading frame (ORF) is present on the majority of all alternatively spliced HPV16 mRNAs, but it is currently unknown how well it is translated into E5 protein. To identify HPV16 mRNAs that are efficiently translated into E5, we have generated cDNA plasmids expressing individual, alternatively spliced HPV16 mRNAs with the potential to produce E5. By replacing the E5 ORF with sLuc, we could quantitate sLuc and determine how well each cDNA was translated. Our results showed that the upstream E1 and E7 AUGs inhibited translation of the E5 ORF and revealed that only one HPV16 mRNA produced high levels of E5...
November 16, 2017: Virus Research
https://www.readbyqxmd.com/read/29146899/alternative-transcription-start-site-selection-in-mr-opy2-controls-lifestyle-transitions-in-the-fungus-metarhizium-robertsii
#13
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
#14
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
#15
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...
December 2017: Genome Research
https://www.readbyqxmd.com/read/29089381/drosophila-sister-of-sex-lethal-is-a-repressor-of-translation
#16
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
#17
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
#18
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
#19
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 18, 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
#20
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
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