scholarly journals Prediction of the structure of the common perimitochondrial localization signal of nuclear transcripts in yeast.

2007 ◽  
Vol 54 (1) ◽  
pp. 55-61 ◽  
Author(s):  
Radoslaw K Ejsmont ◽  
Pawel Golik ◽  
Piotr P Stepien
Keyword(s):  
Subcellular Localization ◽  
Mitochondrial Proteins ◽  
Consensus Structure ◽  
Stem Loop ◽  
Cis Acting ◽  
Stem Loop Structure ◽  
Expression Studies ◽  
Genes Encoding ◽  
Specific Localization ◽  
Localization Signal

Many nuclear genes encoding mitochondrial proteins require specific localization of their mRNAs to the vicinity of mitochondria for proper expression. Studies in Saccharomyces cerevisiae have shown that the cis-acting signal responsible for subcellular localization of mRNAs is localized in the 3' UTR of the transcript. In this paper we present an in silico approach for prediction of a common perimitochondrial localization signal of nuclear transcripts encoding mitochondrial proteins. We computed a consensus structure for this signal by comparison of 3' UTR models for about 3000 yeast transcripts with known localization. Our studies show a short stem-loop structure which appears in most mRNAs localized to the vicinity of mitochondria. The degree of similarity of a given 3' UTR to our consensus structure strongly correlates with experimentally determined perimitochondrial localization of the mRNA, therefore we believe that the structure we predicted acts as a subcellular localization signal. Since our algorithm operates on structures, it seems to be more reliable than sequence-based algorithms. The good predictive value of our model is supported by statistical analysis.

scholarly journals Identification and characterization of a sequence motif involved in nonsense-mediated mRNA decay.

1995 ◽  
Vol 15 (4) ◽  
pp. 2231-2244 ◽  
Author(s):  
S Zhang ◽  
M J Ruiz-Echevarria ◽  
Y Quan ◽  
S W Peltz
Keyword(s):  
Mrna Decay ◽  
Sequence Motif ◽  
Nonsense Mutations ◽  
Stem Loop ◽  
Cis Acting ◽  
Stem Loop Structure ◽  
Nonsense Codon ◽  
Nonsense Mediated Mrna Decay

In both prokaryotes and eukaryotes, nonsense mutations in a gene can enhance the decay rate or reduce the abundance of the mRNA transcribed from that gene, and we call this process nonsense-mediated mRNA decay. We have been investigating the cis-acting sequences involved in this decay pathway. Previous experiments have demonstrated that, in addition to a nonsense codon, specific sequences 3' of a nonsense mutation, which have been defined as downstream elements, are required for mRNA destabilization. The results presented here identify a sequence motif (TGYYGATGYYYYY, where Y stands for either T or C) that can predict regions in genes that, when positioned 3' of a nonsense codon, promote rapid decay of its mRNA. Sequences harboring two copies of the motif from five regions in the PGK1, ADE3, and HIS4 genes were able to function as downstream elements. In addition, four copies of this motif can function as an independent downstream element. The sequences flanking the motif played a more significant role in modulating its activity when fewer copies of the sequence motif were present. Our results indicate the sequences 5' of the motif can modulate its activity by maintaining a certain distance between the sequence motif and the termination codon. We also suggest that the sequences 3' of the motif modulate the activity of the downstream element by forming RNA secondary structures. Consistent with this view, a stem-loop structure positioned 3' of the sequence motif can enhance the activity of the downstream element. This sequence motif is one of the few elements that have been identified that can predict regions in genes that can be involved in mRNA turnover. The role of these sequences in mRNA decay is discussed.

scholarly journals Identification of a specific exon sequence that is a major determinant in the selection between a natural and a cryptic 5' splice site.

1991 ◽  
Vol 11 (9) ◽  
pp. 4581-4590 ◽  
Author(s):  
L Domenjoud ◽  
H Gallinaro ◽  
L Kister ◽  
S Meyer ◽  
M Jacob
Keyword(s):  
Splice Site ◽  
Adenovirus Type ◽  
Loop Structure ◽  
Stem Loop ◽  
Cis Acting ◽  
Stem Loop Structure ◽  
Natural Site ◽  
Proximal Site ◽  
Exon 1 ◽  
Long Stem

The first intron of the early region 3 from adenovirus type 2 contains a cryptic 5' splice site, Dcr1, 74 nucleotides downstream from the natural site D1. The cryptic site can be activated when the natural site is inactivated by mutagenesis. To investigate the basis for selection between a natural and a cryptic 5' splice site, we searched for cis-acting elements responsible for the exclusive selection of the natural site. We show that both the relative intrinsic strength of the sites and the sequence context affect the selection. A 120-nucleotide segment located at the 3' end of exon 1 enhances splicing at the proximal site D1; in its absence the two sites are used according to their strength. Thus, three cis-acting elements are involved in the silencing of the cryptic site: the sequence of D1, the sequence of Dcr1, and an upstream exonic sequence. We show that the exonic element folds, in solution, into a 113-nucleotide-long stem-loop structure. We propose that this potential stem-loop structure which is located 6 nucleotides upstream of the exon 1-intron junction is responsible for the preferential use of the natural 5' splice site.

scholarly journals cis-Acting Sequences Required for Coronavirus Infectious Bronchitis Virus Defective-RNA Replication and Packaging

2001 ◽  
Vol 75 (1) ◽  
pp. 125-133 ◽  
Author(s):  
Kevin Dalton ◽  
Rosa Casais ◽  
Kathy Shaw ◽  
Kathleen Stirrups ◽  
Sharon Evans ◽  
...  
Keyword(s):  
Infectious Bronchitis Virus ◽  
Rna Replication ◽  
Replicase Gene ◽  
Loop Structure ◽  
Stem Loop ◽  
Cis Acting ◽  
Infectious Bronchitis ◽  
Stem Loop Structure ◽  
Defective Rna ◽  
Region Ii

ABSTRACT The parts of the RNA genome of infectious bronchitis virus (IBV) required for replication and packaging of the RNA were investigated using deletion mutagenesis of a defective RNA (D-RNA) CD-61 (6.1 kb) containing a chloramphenicol acetyltransferase reporter gene. A D-RNA with the first 544, but not as few as 338, nucleotides (nt) of the 5′ terminus was replicated; the 5′ untranslated region (UTR) comprises 528 nt. Region I of the 3′ UTR, adjacent to the nucleocapsid protein gene, comprised 212 nt and could be removed without impairment of replication or packaging of D-RNAs. A D-RNA with the final 338 nt, including the 293 nt in the highly conserved region II of the 3′ UTR, was replicated. Thus, the 5′-terminal 544 nt and 3′-terminal 338 nt contained the necessary signals for RNA replication. Phylogenetic analysis of 19 strains of IBV and 3 strains of turkey coronavirus predicted a conserved stem-loop structure at the 5′ end of region II of the 3′ UTR. Removal of the predicted stem-loop structure abolished replication of the D-RNAs. D-RNAs in which replicase gene 1b-derived sequences had been removed or replaced with all the downstream genes were replicated well but were rescued poorly, suggesting inefficient packaging. However, no specific part of the 1b gene was required for efficient packaging.

scholarly journals The Foot-and-Mouth Disease Virus cis-Acting Replication Element (cre) Can Be Complemented in trans within Infected Cells

2003 ◽  
Vol 77 (3) ◽  
pp. 2243-2246 ◽  
Author(s):  
Laurence Tiley ◽  
Andrew M. Q. King ◽  
Graham J. Belsham
Keyword(s):  
Disease Virus ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Temperature Sensitive ◽  
Stem Loop ◽  
Cis Acting ◽  
Stem Loop Structure ◽  
Mouth Disease Virus ◽  
Foot And Mouth ◽  
Infected Cells

ABSTRACT A temperature-sensitive (ts) mutation was identified within the 5′-untranslated region of foot-and-mouth disease virus (FMDV) RNA. The mutation destabilizes a stem-loop structure recently identified as a cis-acting replication element (cre). Genetic analyses indicated that the ts defect in virus replication could be complemented. Thus, the FMDV cre can function in trans. It is suggested that the cre be renamed a 3B-uridylylation site (bus).

scholarly journals Identification of a specific exon sequence that is a major determinant in the selection between a natural and a cryptic 5' splice site

1991 ◽  
Vol 11 (9) ◽  
pp. 4581-4590
Author(s):  
L Domenjoud ◽  
H Gallinaro ◽  
L Kister ◽  
S Meyer ◽  
M Jacob
Keyword(s):  
Splice Site ◽  
Adenovirus Type ◽  
Loop Structure ◽  
Stem Loop ◽  
Cis Acting ◽  
Stem Loop Structure ◽  
Natural Site ◽  
Proximal Site ◽  
Exon 1 ◽  
Long Stem

The first intron of the early region 3 from adenovirus type 2 contains a cryptic 5' splice site, Dcr1, 74 nucleotides downstream from the natural site D1. The cryptic site can be activated when the natural site is inactivated by mutagenesis. To investigate the basis for selection between a natural and a cryptic 5' splice site, we searched for cis-acting elements responsible for the exclusive selection of the natural site. We show that both the relative intrinsic strength of the sites and the sequence context affect the selection. A 120-nucleotide segment located at the 3' end of exon 1 enhances splicing at the proximal site D1; in its absence the two sites are used according to their strength. Thus, three cis-acting elements are involved in the silencing of the cryptic site: the sequence of D1, the sequence of Dcr1, and an upstream exonic sequence. We show that the exonic element folds, in solution, into a 113-nucleotide-long stem-loop structure. We propose that this potential stem-loop structure which is located 6 nucleotides upstream of the exon 1-intron junction is responsible for the preferential use of the natural 5' splice site.

scholarly journals Analysis of secondary structure within sgm and kgmB mRNA

2010 ◽  
Vol 62 (3) ◽  
pp. 515-524 ◽  
Author(s):  
Sandra Vojnovic ◽  
Tatjana Ilic-Tomic ◽  
Ivana Moric ◽  
Branka Vasiljevic
Keyword(s):  
Secondary Structure ◽  
Regulatory Sequence ◽  
Loop Structure ◽  
In Silico Prediction ◽  
Stable Secondary Structure ◽  
Stem Loop ◽  
Cis Acting ◽  
Stem Loop Structure ◽  
Structure Probing ◽  
A Site

Sgm methyltransferase from Micromonospora zionensis and KgmB methyltransferase from Streptoalloteichus tenebrarius are resistant to aminoglycoside antibiotics as a result of their ability to specifically methylate G1405 within the bacterial 16S rRNA A-site. The (C)CGCCC motif, assumed to be a regulatory sequence responsible for the autoregulation of the sgm gene, could most likely also be responsible for the autoregulation of the kgmB gene. This sequence, found within the 5' untranslated region of both sgm and kgmB mRNAs, as indicated by in silico prediction, may be involved in the formation of a specific stem-loop structure. Sgm and KgmB are mutually down-regulated and it is likely that they share the same cis-acting elements. Structure probing experiments confirmed the existence of a stable secondary structure within the 5' UTR of the sgm mRNA, while the analysis of kgmB mRNA failed to confirm the predicted structure. .

scholarly journals A 3′ terminal stem–loop structure in Nodamura virus RNA2 forms an essential cis-acting signal for RNA replication

2010 ◽  
Vol 150 (1-2) ◽  
pp. 12-21 ◽  
Author(s):  
John J. Rosskopf ◽  
John H. Upton ◽  
Lizette Rodarte ◽  
Tammy A. Romero ◽  
Ming-Ying Leung ◽  
...  
Keyword(s):  
Rna Replication ◽  
Loop Structure ◽  
Stem Loop ◽  
Cis Acting ◽  
Stem Loop Structure ◽  
Nodamura Virus

scholarly journals trp RNA-Binding Attenuation Protein-5′ Stem-Loop RNA Interaction Is Required for Proper Transcription Attenuation Control of the Bacillus subtilis trpEDCFBAOperon

2000 ◽  
Vol 182 (7) ◽  
pp. 1819-1827 ◽  
Author(s):  
Hansen Du ◽  
Alexander V. Yakhnin ◽  
Subramanian Dharmaraj ◽  
Paul Babitzke
Keyword(s):  
Bacillus Subtilis ◽  
Rna Structure ◽  
Rna Binding ◽  
Structure Mapping ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
Expression Studies ◽  
Attenuation Mechanism ◽  
Transcription Attenuation ◽  
Rna Interaction

ABSTRACT The trp RNA-binding attenuation protein (TRAP) regulates expression of the Bacillus subtilis trpEDCFBAoperon by a novel transcription attenuation mechanism. Tryptophan-activated TRAP binds to the nascent trp leader transcript by interacting with 11 (G/U)AG repeats, 6 of which are present in an antiterminator structure. TRAP binding to these repeats prevents formation of the antiterminator, thereby promoting formation of an overlapping intrinsic terminator. A third stem-loop structure that forms at the extreme 5′ end of the trp leader transcript also plays a role in the transcription attenuation mechanism. The 5′ stem-loop increases the affinity of TRAP fortrp leader RNA. Results from RNA structure mapping experiments demonstrate that the 5′ stem-loop consists of a 3-bp lower stem, a 5-by-2 asymmetric internal loop, a 6-bp upper stem, and a hexaloop at the apex of the structure. Footprinting results indicate that TRAP interacts with the 5′ stem-loop and that this interaction differs depending on the number of downstream (G/U)AG repeats present in the transcript. Expression studies with trpE′-′lacZtranslational fusions demonstrate that TRAP-5′ stem-loop interaction is required for proper regulation of the trp operon. 3′ RNA boundary experiments indicate that the 5′ structure reduces the number of (G/U)AG repeats required for stable TRAP-trp leader RNA association. Thus, TRAP-5′ stem-loop interaction may increase the likelihood that TRAP will bind to the (G/U)AG repeats in time to block antiterminator formation.

scholarly journals An AU-rich stem–loop structure is a critical feature of the perinuclear localization signal of c-myc mRNA

2005 ◽  
Vol 392 (3) ◽  
pp. 475-483 ◽  
Author(s):  
Hervé Chabanon ◽  
Ian Mickleburgh ◽  
Brian Burtle ◽  
Christopher Pedder ◽  
John Hesketh
Keyword(s):  
Rna Structure ◽  
Bioinformatic Analysis ◽  
Loop Structure ◽  
Critical Feature ◽  
Stem Loop ◽  
Loop Region ◽  
Stem Loop Structure ◽  
Protein Complex Formation ◽  
Perinuclear Cytoplasm ◽  
Localization Signal

In eukaryotic cells, several mRNAs including those of c-myc and c-fos are localized to the perinuclear cytoplasm and associated with the cytoskeleton. The localization element of c-myc mRNA is present within its 3′UTR (3′-untranslated region) but the precise nature of this signal has remained unidentified. Chemical/enzymatic cleavage with RNases (ribonucleases) and lead have identified single-stranded and double-stranded regions in RNA transcripts of nucleotides 194–280 of the c-myc 3′UTR. Combined with computer predicted structure these results indicate that this region folds so that part of it forms a stem-loop structure. A mutation, that has been previously shown to prevent localization, leads to a different secondary RNA structure in this region as indicated by altered cleavage patterns. Competitive gel-retardation assays, using labelled transcripts corresponding to nucleotides 205–280 of c-myc 3′UTR, and fibroblast extracts revealed that the stem-loop region was sufficient for RNA–protein complex formation. In situ hybridization studies in cells transfected with reporter constructs, in which all or parts of the region corresponding to this stem-loop were linked to β-globin, indicated that this region was sufficient for localization and that deletion of the nucleotides corresponding to the proposed upper-stem or terminal loop prevented localization. Our hypothesis is that an AU-rich stem-loop structure within nt 222–267 in the c-myc 3′UTR forms the perinuclear localization signal. Bioinformatic analysis suggests that this signal shares features with 3′UTRs of other localized mRNAs and that these features may represent a conserved form of signal in mRNA localization mechanisms.

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