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Frameshifting, Ribosomal (0):
Recent article
Frameshifting, Ribosomal
Abstract
We report here an RNA pseudoknot capable of stimulating -1 PRF whose efficiency can be tuned in response to the concentration of S-adenosylhomocysteine (SAH), and the improvement of its frameshifting efficiency by RNA engineering. In addition to providing an alternative approach for small-molecule r...
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PMID: 20435898
PDF is available here.
PDF is available here.
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Journal of Virology (84)3 2010
Abstract
We provide experimental evidence that NS1' is the product of a -1 ribosomal frameshift event that occurs at a conserved slippery heptanucleotide motif located near the beginning of the NS2A gene and is stimulated by a downstream RNA pseudoknot structure. Using site-directed mutagenesis of these sequ...
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PMID: 19906906
PDF is available here.
PDF is available here.
Abstract
We show that Sua5 is critical for normal translation. The loss of SUA5 causes increased leaky scanning through AUG codons, +1 frameshifting, and nonsense suppression. In addition, the loss of SUA5 amplifies the 20S RNA virus found in Saccharomyces cerevisiae, possibly through an internal ribosome en...
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PMID: 19884342
PDF is available here.
PDF is available here.
Virus Research (139)2 2009
Abstract
Programmed ribosomal frameshifting (PRF) is one of the multiple translational recoding processes that fundamentally alters triplet decoding of the messenger RNA by the elongating ribosome. The ability of the ribosome to change translational reading frames in the -1 direction (-1 PRF) is employed by...
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PMID: 18621088
PDF is available here.
PDF is available here.
Abstract
Combating HIV currently remains one of the key public health challenges. While immense effort has been invested in the development of HIV-targeted therapeutic agents, interfering with protein synthesis is a relatively unexplored area. HIV has an absolute requirement for a -1 ribosomal frameshift eve...
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PMID: 19197789
PDF is available here.
PDF is available here.
Journal of Molecular Biology (385)2 2009
Abstract
We have selected mutants of Salmonella typhimurium with alterations in tRNA(cmo5UGG)(Pro) that cause increased frameshifting when present in the ribosomal P-site. In 108 such mutants, two parts of the tRNA molecule are altered: the anticodon stem and the D-arm, including its tertiary interactions wi...
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PMID: 19013179
PDF is available here.
PDF is available here.
Molecular Microbiology (70)3 2008
Abstract
The majority of bacteriophages have a long non-contractile tail (Siphoviridae) that serves as a conduit for viral DNA traffic from the phage capsid to the host cell at the beginning of infection. The 160-nm-long tail tube of Bacillus subtilis bacteriophage SPP1 is shown to be composed of two major t...
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PMID: 18786146
PDF is available here.
PDF is available here.
Abstract
We used Xenopus oocytes as an intracellular system to study ribosomal frameshifting. Microinjection of oocytes with a construct encoding the naturally occurring UUU or AAC codon at the frameshift site demonstrated that the level of frameshifting was similar or lower than found normally in retroviral...
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PMID: 18675785
PDF is available here.
PDF is available here.
Molecular Microbiology (70)3 2008
Abstract
The tail apparatus of the bacteriophage SPP1 is an extraordinary approximately 1600-A-long molecular machine. The tail mediates attachment of the virus to the host surface receptor, as well-as ejection of the viral genome into the host. The distal tip of the tail binds the extracellular ectodomain o...
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PMID: 18826406
PDF is available here.
PDF is available here.
Virus Research (136)1-2 2008
Abstract
The complete nucleotide sequence of polyprotein gene 1 and the assembled full-length genome sequence are presented for turkey coronavirus (TCoV) isolates 540 and ATCC. The TCoV polyprotein gene encoded two open reading frames (ORFs), which are translated into two products, pp1a and pp1ab, the latter...
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PMID: 18514348
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)29 2008
Abstract
We could demonstrate that mutations affecting the stability of the structure reduce both frameshifting and transposition, thus establishing the biological importance of this new type of RNA structure for the control of transposition level....
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PMID: 18474594
PDF is available here.
PDF is available here.
Journal of General Virology (89)Pt 7 2008
Abstract
Since the first report of frameshifting in HCV-1, its sequence has been the paradigm for examining the mechanism that directs alternative translation of the hepatitis C virus (HCV) genome. The region encoding the core protein from this strain contains a cluster of 10 adenines at codons 8-11, which i...
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PMID: 18559926
PDF is available here.
PDF is available here.
Abstract
We show here that the VMV stimulatory RNA is indeed a pseudoknot, conforming closely to the modeled structure, and that the ISE is essential for frameshifting. Pseudoknot function was predictably sensitive to changes in the length of the ISE, yet altering its sequence to alternate pyrimidine/purine...
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PMID: 18495941
PDF is available here.
PDF is available here.
Abstract
We investigated how p27 and p88 were engaged in the replication of RCNMV genomic RNAs by using DNA vectors or in vitro transcribed RNAs in protoplasts and in a cell-free extract of evacuolated BY-2 protoplasts. Our results show a cis-preferential requirement of p88, but not of p27, for the replicati...
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PMID: 18308359
PDF is available here.
PDF is available here.
Abstract
We describe a novel N-RAG-TP transposon identified from the sea slug Aplysia californica that encodes a protein similar to the N-terminal part of RAG1 in vertebrates. This refines the "RAG transposon" hypothesis and allows us to propose a scenario for V(D)J recombination machinery evolution from a r...
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PMID: 18313399
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)9 2008
Abstract
We investigated the molecular regulatory mechanisms of ARFP expression in HCV target cells. Chimeric HCV-luciferase reporter constructs derived from the infectious HCV prototype isolate H77 were transfected into hepatocyte-derived cell lines. Translation initiation was most efficient at the internal...
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PMID: 18400784
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)8 2008
Abstract
We propose three different kinetic models of +1 PRF, incorporating the effects of the ribosomal E-, P- and A-sites toward promoting efficient +1 frameshifting in Escherichia coli. Specifically, the timing of E-site tRNA dissociation is discussed within the context of the kinetic proofreading mechani...
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PMID: 18344525
PDF is available here.
PDF is available here.
Abstract
We used a fluorescent two-reporter system to screen for peptides that reduce HIV-1 frameshift in bacteria, knowing that the frameshift can be reproduced in Escherichia coli. Expression of one reporter, the green fluorescent protein (GFP), requires the HIV-1 frameshift, whereas the second reporter, t...
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PMID: 18367719
PDF is available here.
PDF is available here.
Abstract
We have studied the impact of successive clusters of these rare codons on the accuracy of mRNA translation in E. coli. For this purpose, we have analyzed the expression of an mRNA which contains in its 3' region a triplet and a tandem of AGA codons. This mRNA is derived from the human hepatitis B vi...
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PMID: 18313865
PDF is available here.
PDF is available here.
Abstract
We conducted virtual screening of a chemical database targeting the X-ray crystal structure of RNA pseudoknot complexed with biotin to identify ligands that may regulate an -1RF system containing biotin-aptamer as an RNA pseudoknot component. After docking screening of about 80,000 compounds, 58 hig...
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PMID: 18321712
PDF is available here.
PDF is available here.
Abstract
We substitute it for a new one, in which sets of nucleotide cyclic motifs define RNA structures. This model allows us to unify all base pairing energetic contributions in an effective scoring function to tackle the problem of RNA folding. We show how pipelining two computer algorithms based on nucle...
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PMID: 18322526
PDF is available here.
PDF is available here.
Journal of Molecular Biology (375)2 2008
Abstract
We have used optical tweezers to study the kinetics and thermodynamics of mechanical unfolding and refolding of single RNA molecules. Here we describe the unfolding of the frameshifting pseudoknot from infectious bronchitis virus (IBV), three constituent hairpins, and three mutants of the IBV pseudo...
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PMID: 18021801
PDF is available here.
PDF is available here.
Abstract
We summarize current knowledge and add additional insight regarding the function of the programmed -1 ribosomal frameshift signal in the coronavirus lifecycle....
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PMID: 18508552
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)1 2008
Abstract
We investigated here whether changes in translation initiation caused by TAR affect HIV-1 frameshift efficiency. CD4+ T cells and 293T cells were transfected with a dual-luciferase construct where the firefly luciferase expression depends upon the HIV-1 frameshift. Translation initiation was altered...
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PMID: 17984074
PDF is available here.
PDF is available here.
Extremophiles (12)1 2008
Abstract
We describe the identification of the catalytic residues of the archaeal enzyme, by means of the chemical rescue strategy. The intrinsic stability of the hyperthermophilic enzyme allowed the use of this method, which resulted of general applicability for beta and alpha glycoside hydrolases. In addit...
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PMID: 17687508
PDF is available here.
PDF is available here.
BMC Bioinformatics (9)1 2008
Abstract
We have developed a computer tool, OAF (ODC antizyme finder) for identifying antizyme encoding sequences in spliced or intronless nucleic acid sequenes. OAF utilizes a combination of profile hidden Markov models (HMM) built separately for the products of each open reading frame constituting the enti...
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PMID: 18384676
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
The A. vastus mtDNA consisted of a 17,427 base pair circular molecule containing thirteen protein-coding genes, divergent large and small subunit ribosomal RNAs, and a reduced set of 18 tRNAs. The A. vastus mtDNA showed a typical hexactinellid nucleotide composition and shared a large synteny with t...
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PMID: 18215303
PDF is available here.
PDF is available here.
ChemBioChem (9)1 2008
Abstract
We report the binding of guanidinoneomycin B (GNB) to an RNA helix from the HIV-1 frameshift site. The binding of GNB increases the melting temperature (T(m)) of the frameshift-site RNA by at least 10 degrees C, to a point at which a melting transition is not even observed in 2 M urea. A structure o...
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PMID: 18058789
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
To identify putative -1 PRF signals, sequences are first imported from whole genomes or datasets, e.g. the yeast genome project and mammalian gene collection. They are then filtered through multiple algorithms to identify potential -1 PRF signals as defined by a heptameric slippery site followed by...
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PMID: 18637175
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts.
Abstract
Our method searched human, mouse and rat transcripts in frames +1 and -1 for ORFs which are unusually well conserved at the amino acid level. We name these conserved frameshifted overlapping ORFs 'matreshkas' to reflect their nested character. Select findings of our analysis revealed that the G-prot...
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PMID: 18325113
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)49 2007
Abstract
We study in vivo RF1 and RF2 activity at termination codons in competition with programmed frameshifting and the effect of the Ala-246 --> Thr mutation. PrmC inactivation reduces the specific termination activity of RF1 and RF2(Ala-246) by approximately 3- to 4-fold. The mutation Ala-246 --> Thr in...
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PMID: 17932046
PDF is available here.
PDF is available here.
Abstract
We previously developed a program called FSFinder for predicting -1 and +1 frameshifts for Windows systems. With our new web application and web service called FSFinder2, users can predict frameshifts of any type from any web browser and operating system. We tested it on Shewanella oneidensis MR-1,...
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PMID: 17678640
PDF is available here.
PDF is available here.
Abstract
I explore how coding properties of leading regions may account for their disparate efficiencies. Trinucleotides that form off frame stop codons decrease costs of ribosomal slippages during protein synthesis: protein activity (as a proxy of gene expression, and as measured in experiments using artifi...
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PMID: 17706680
PDF is available here.
PDF is available here.
Abstract
We have tested this model by making a saturating set of single-base mutations of the Ty3 stimulator. The phenotypes of these mutations are inconsistent with the Helix 18 base-pairing model. We discuss the phenotypes of these mutations in light of structural data on the path of the mRNA on the riboso...
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PMID: 17881742
PDF is available here.
PDF is available here.
Journal of Molecular Biology (373)3 2007
Abstract
We report the functional, structural and thermodynamic characterization of the SIV frameshift site RNA. Translational frameshift assays indicate that a stem-loop structure is sufficient to promote efficient frameshifting in vitro. NMR and thermodynamic studies of SIV RNA constructs of varying length...
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PMID: 17868691
PDF is available here.
PDF is available here.
Virus Genes (35)2 2007
Abstract
In the course of sobemovirus gene cloning the complete genome of Ryegrass mottle virus (RGMoV) was sequenced. Sequence analysis revealed differences including missing and extraneous nucleotides in comparison to the previously published sequence (Zhang, Toriyama, Takanashi, J. Gen. Plant Pathol. 67,...
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PMID: 17356908
PDF is available here.
PDF is available here.
Genome Research (17)10 2007
Abstract
We show that viruses with larger genomes tend to have less gene overlap. We provide a numerical model to show how a high mutation rate could lead to gene overlap, and we discuss the factors that might explain the observed relationship between gene overlap and genome size. We also propose a model for...
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PMID: 17785537
PDF is available here.
PDF is available here.
Abstract
Journal of Biological Chemistry (282)36 2007
Abstract
We hypothesized that this modification was needed for -1 frameshifting. Using a reporter system incorporating a SCV-LA yeast virus slippery site for detecting -1 frameshifts in vivo, yeast strains were created that enabled chemical-genetic dissection of the role of different functional groups of wye...
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PMID: 17623669
PDF is available here.
PDF is available here.
Abstract
We describe Korean isolates of Trichomonas vaginalis infected with double-stranded (ds) RNA virus (TVV). One T. vaginalis isolate infected with TVV IH-2 evidenced weak pathogenicity in the mouse assay coupled with the persistent presence of a dsRNA, thereby indicating a hypovirulence effect of dsRNA...
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PMID: 17570970
PDF is available here.
PDF is available here.
Abstract
We report crystal structures of two anticodon stem-loops (ASLs) from tRNAs known to facilitate +1 frameshifting bound to the 30S ribosomal subunit with their cognate mRNAs. ASL(CCCG) and ASL(ACCC) (5'-3' nomenclature) form unpredicted anticodon-codon interactions where the anticodon base 34 at the w...
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PMID: 17416634
PDF is available here.
PDF is available here.
Abstract
Transposable elements (TEs), represent a large fraction of the eukaryotic genome. In Drosophila melanogaster, about 20% of the genome corresponds to such middle repetitive DNA dispersed sequences. A fraction of TEs is composed of elements showing a retrovirus-like structure, the LTR-retrotransposons...
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PMID: 17382490
PDF is available here.
PDF is available here.
Abstract
We show that the efficiency of frameshifting relates to the mechanical strength of the pseudoknot. Two pseudoknots derived from the Infectious Bronchitis Virus were used, differing by one base pair in the first stem. In Escherichia coli, these two pseudoknots caused frameshifting frequencies that di...
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PMID: 17389398
PDF is available here.
PDF is available here.
Abstract
We show that the site is complex, consisting of a heptameric sequence at which the frameshift occurs and a downstream 27-nucleotide stimulator sequence that increases frameshifting eightfold. The stimulator appears to be modular, composed of at least three separable domains. It increases frameshifti...
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PMID: 17329356
PDF is available here.
PDF is available here.
Journal of General Virology (88)Pt 1 2007
Abstract
Expression of the pol-encoded proteins of human immunodeficiency virus type 1 (HIV-1) requires a programmed -1 ribosomal frameshift at the junction of the gag and pol coding sequences. Frameshifting takes place at a heptanucleotide slippery sequence, UUUUUUA, and is enhanced by a stimulatory RNA str...
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PMID: 17170455
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)1 2007
Abstract
In viruses, programmed -1 ribosomal frameshifting (-1 PRF) signals direct the translation of alternative proteins from a single mRNA. Given that many basic regulatory mechanisms were first discovered in viral systems, the current study endeavored to: (i) identify -1 PRF signals in genomic databases,...
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PMID: 17158156
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)6 2007
Abstract
The protein antizyme is a negative regulator of intracellular polyamine levels. Ribosomes synthesizing antizyme start in one ORF and at the codon 5' adjacent to its stop codon, shift +1 to a second and partially overlapping ORF which encodes most of the protein. The ribosomal frameshifting is a sens...
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PMID: 17332016
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)16 2007
Abstract
We investigated here whether the tRNA occupying the ribosomal E site that precedes a slippery site influences -1 PRF. Using the human immunodeficiency virus type 1 (HIV-1) frameshift region, we found that mutating the E-site codon altered the -1 PRF efficiency. When the HIV-1 slippery sequence was r...
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PMID: 17704133
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)4 2007
Abstract
We show here, by expressing in E. coli several plant cDNAs with and without single nucleotide deletions close to the translation initiation codons, that pDEST17 is intrinsically susceptible to -1 ribosomal frameshifting at the sequence C-AAA-AAA. The deletion mutants produce correct-sized, active en...
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PMID: 17272299
PDF is available here.
PDF is available here.
Journal of Biochemistry (140)5 2006
Abstract
We have optimized two tissue-culture assays in 96-well format, to allow the rapid screening of a 750-member polyamine analog library for compounds which induce antizyme frameshifting and fail to substitute for the natural polyamines in growth. Five analogs (MQTPA1-5) containing xylene (1,4-dimethyl...
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PMID: 16998202
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (281)43 2006
Abstract
Helix 38 (H38) in 23 S rRNA, which is known as the "A-site finger (ASF)," is located in the intersubunit space of the ribosomal 50 S subunit and, together with protein S13 in the 30 S subunit, it forms bridge B1a. It is known that throughout the decoding process, ASF interacts directly with the A-si...
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PMID: 16950778
PDF is available here.
PDF is available here.
Bioinformatics (22)20 2006
Abstract
We describe a novel computer tool that allows automatic discrimination of genes encoding class-I bacterial release factors, RF1, RF2 and RFH. Most usefully, this program identifies and automatically annotates +1 frameshifting in RF2 encoding genes. Comparison of ARFA performance with existing annota...
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PMID: 16895933
PDF is available here.
PDF is available here.
Experimental Cell Research (312)16 2006
Abstract
We have identified a novel rodent gene encoding for a neural regeneration protein (NRP) with an activity spectrum similar to the chemokine stromal-derived factor (SDF)-1, but with much greater potency. The Nrp gene is encoded as a forward frameshift to the hypothetical alkylated DNA repair protein A...
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PMID: 16860792
PDF is available here.
PDF is available here.
Abstract
Fourier analysis of the short-range periodicities for the complete set of sequences coding for tRNA genes in genome of Bacillus subtilis proves that periodicities with periods p = 2, 3, 4, and 6 sites are the inherent properties of tRNAs. The related periodicities should be understood in a broad sta...
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PMID: 16928142
PDF is available here.
PDF is available here.
Abstract
We have investigated the history of programmed +1 frameshifting in fungi. We find that frameshifting has persisted in two structural genes in budding yeasts, ABP140 and EST3 for about 150 million years. Further, the tRNAs that stimulate the event are equally old. Species that diverged from the linea...
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PMID: 16838213
PDF is available here.
PDF is available here.
Journal of Bacteriology (188)20 2006
Abstract
These results were obtained using three data sets of transposase genes from the same IS family that were collected based on the level of amino acid similarity, the presence of an inverted repeat, and the number of sequences in the data sets. Neither recombination nor ribosomal frameshifting, which m...
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PMID: 17015656
PDF is available here.
PDF is available here.
Journal of Bacteriology (188)17 2006
Abstract
The lytic lactococcal phage Q54 was previously isolated from a failed sour cream production. Its complete genomic sequence (26,537 bp) is reported here, and the analysis indicated that it represents a new Lactococcus lactis phage species. A striking feature of phage Q54 is the low level of similarit...
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PMID: 16923877
PDF is available here.
PDF is available here.
Abstract
Life depends on the faithful translation of the genetic information into proteins. Ribosomes have developed remarkable mechanisms to ensure the accurate synthesis of proteins. In the first part of this review various types of ribosomal errors and their importance for cell-life are surveyed, while in...
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PMID: 16644089
PDF is available here.
PDF is available here.
Virus Research (119)1 2006
Abstract
Ribosomal frameshifting is a mechanism of gene expression used by several RNA viruses to express replicase enzymes. This article focuses on frameshifting in two human pathogens, the retrovirus human immunodeficiency virus type 1 (HIV-1) and the coronavirus responsible for severe acute respiratory sy...
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PMID: 16310880
PDF is available here.
PDF is available here.
Abstract
We show that this stimulator also increases the usage of non-AUG initiation codons in the bacterium Escherichia coli but not in S. cerevisiae. These data suggest that in E. coli, though not in yeast, an element of the ribosome's elongation accuracy mechanism ensures initiation accuracy....
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PMID: 16682566
PDF is available here.
PDF is available here.