scholarly journals A bulged stem-loop structure in the 3' untranslated region of the genome of the coronavirus mouse hepatitis virus is essential for replication.

1997 ◽  
Vol 71 (10) ◽  
pp. 7567-7578 ◽  
Author(s):  
B Hsue ◽  
P S Masters
Keyword(s):  
Untranslated Region ◽  
Hepatitis Virus ◽  
Mouse Hepatitis Virus ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure

scholarly journals Role of a Stem-Loop Structure inHelicobacter pylori cagATranscript Stability

2018 ◽  
Vol 87 (2) ◽  
Author(s):  
John T. Loh ◽  
Aung Soe Lin ◽  
Amber C. Beckett ◽  
Mark S. McClain ◽  
Timothy L. Cover
Keyword(s):  
Steady State ◽  
Untranslated Region ◽  
Loop Structure ◽  
Stem Loop ◽  
Content Type ◽  
Transcript Stability ◽  
Protein Levels ◽  
Caga Protein ◽  
Stem Loop Structure ◽  
Steady State Levels

ABSTRACTHelicobacter pyloriCagA is a secreted effector protein that contributes to gastric carcinogenesis. Previous studies showed that there is variation amongH. pyloristrains in the steady-state levels of CagA and that a strain-specific motif downstream of thecagAtranscriptional start site (the +59 motif) is associated with both high levels of CagA and premalignant gastric histology. ThecagA5′ untranslated region contains a predicted stem-loop-forming structure adjacent to the +59 motif. In the current study, we investigated the effect of the +59 motif and the adjacent stem-loop oncagAtranscript levels andcagAmRNA stability. Using site-directed mutagenesis, we found that mutations predicted to disrupt the stem-loop structure resulted in decreased steady-state levels of both thecagAtranscript and the CagA protein. Additionally, these mutations resulted in a decreasedcagAmRNA half-life. Mutagenesis of the +59 motif without altering the stem-loop structure resulted in reduced steady-statecagAtranscript and CagA protein levels but did not affectcagAtranscript stability.cagAtranscript stability was not affected by increased sodium chloride concentrations, an environmental factor known to augmentcagAtranscript levels and CagA protein levels. These results indicate that both a predicted stem-loop structure and a strain-specific +59 motif in thecagA5′ untranslated region influence the levels ofcagAexpression.

scholarly journals HuR Uses AUF1 as a Cofactor To Promote p16INK4 mRNA Decay

2010 ◽  
Vol 30 (15) ◽  
pp. 3875-3886 ◽  
Author(s):  
Na Chang ◽  
Jie Yi ◽  
Gaier Guo ◽  
Xinwen Liu ◽  
Yongfeng Shang ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Untranslated Region ◽  
Mrna Decay ◽  
Loop Structure ◽  
Wild Type ◽  
Stem Loop ◽  
Human Diploid Fibroblasts ◽  
Stem Loop Structure ◽  
Chimeric Transcripts ◽  
P16 Expression

ABSTRACT In this study, we show that HuR destabilizes p16INK4 mRNA. Although the knockdown of HuR or AUF1 increased p16 expression, concomitant AUF1 and HuR knockdown had a much weaker effect. The knockdown of Ago2, a component of the RNA-induced silencing complex (RISC), stabilized p16 mRNA. The knockdown of HuR diminished the association of the p16 3′ untranslated region (3′UTR) with AUF1 and vice versa. While the knockdown of HuR or AUF1 reduced the association of Ago2 with the p16 3′UTR, Ago2 knockdown had no influence on HuR or AUF1 binding to the p16 3′UTR. The use of EGFP-p16 chimeric reporter transcripts revealed that p16 mRNA decay depended on a stem-loop structure present in the p16 3′UTR, as HuR and AUF1 destabilized EGFP-derived chimeric transcripts bearing wild-type sequences but not transcripts with mutations in the stem-loop structure. In senescent and HuR-silenced IDH4 human diploid fibroblasts, the EGFP-p16 3′UTR transcript was more stable. Our results suggest that HuR destabilizes p16 mRNA by recruiting the RISC, an effect that depends on the secondary structure of the p16 3′UTR and requires AUF1 as a cofactor.

A small predicted stem-loop structure mediates oocyte localization of Drosophila K10 mRNA

Development ◽  
1995 ◽  
Vol 121 (11) ◽  
pp. 3809-3818 ◽  
Author(s):  
T.L. Serano ◽  
R.S. Cohen
Keyword(s):  
Late Stage ◽  
Untranslated Region ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Loop Structure ◽  
Base Pairing ◽  
Mrna Transport ◽  
Nucleotide Substitutions ◽  
Stem Loop ◽  
Stem Loop Structure

The establishment of dorsoventral polarity in the Drosophila oocyte and future embryo is dependent on the efficient transport of K10 mRNA from nurse cells into the oocyte. To investigate the cis-requirements of K10 mRNA transport, we used a transgenic fly assay to analyze the expression patterns of a series of K10 deletion variants. Such studies identify a 44 nucleotide sequence within the K10 3′ untranslated region that is required and sufficient for K10 mRNA transport and subsequent localization to the oocyte's anterior cortex. An inspection of the 44 nucleotide transport/localization sequence (TLS) reveals a strong potential for the formation of a stem-loop secondary structure. Nucleotide substitutions that interfere with the predicted base-pairing of the TLS block mRNA transport and anterior localization. Conversely, mutations that alter the base composition of the TLS while maintaining predicted base-pairing do not block mRNA transport or anterior localization. We conclude that K10 mRNA transport and anterior localization is mediated by a 44 nucleotide stem-loop structure. A similar putative stem-loop structure is found in the 3′ untranslated region of the Drosophila orb mRNA, suggesting that the same factors mediate the transport and anterior localization of both K10 and orb mRNAs. Apart from orb, the K10 TLS is not found in any other localized mRNA, raising the possibility that the transport and localization of other mRNAs, e.g., bicoid, oskar and gurken, are mediated by novel sets of cis- and trans-acting factors. Moreover, we find that the K10 TLS overrides the activity of oskar cis-regulatory elements that mediate the late stage movement of the mRNA to the posterior pole. We propose the existence of a family of cis-regulatory elements that mediate mRNA transport into the oocyte, only some of which are compatible with the elements that mediate late stage movements.

scholarly journals The 5′ Untranslated Region of Alfalfa Mosaic Virus RNA 1 Is Involved in Negative-Strand RNA Synthesis

2003 ◽  
Vol 77 (20) ◽  
pp. 11284-11289 ◽  
Author(s):  
A. Corina Vlot ◽  
John F. Bol
Keyword(s):  
Mosaic Virus ◽  
Untranslated Region ◽  
Rna Synthesis ◽  
Alfalfa Mosaic Virus ◽  
Loop Structure ◽  
Stem Loop ◽  
Genomic Rnas ◽  
Negative Strand ◽  
Stem Loop Structure ◽  
Virus Rna

ABSTRACT The three genomic RNAs of alfalfa mosaic virus each contain a unique 5′ untranslated region (5′ UTR). Replacement of the 5′ UTR of RNA 1 by that of RNA 2 or 3 yielded infectious replicons. The sequence of a putative 5′ stem-loop structure in RNA 1 was found to be required for negative-strand RNA synthesis. A similar putative 5′ stem-loop structure is present in RNA 2 but not in RNA 3.

scholarly journals The perplexities of ZC3H12A self-mRNA regulation

2016 ◽  
Vol 63 (3) ◽  
Author(s):  
Mateusz Wawro ◽  
Jakub Kochan ◽  
Aneta Kasza
Keyword(s):  
Gene Expression ◽  
Biological Activity ◽  
Transcriptional Regulation ◽  
Untranslated Region ◽  
Regulation Of Gene Expression ◽  
Loop Structure ◽  
Stem Loop ◽  
Mrna Regulation ◽  
Stem Loop Structure ◽  
Post Transcriptional Regulation

The mechanisms regulating transcripts turnover are key processes in the regulation of gene expression. The list of proteins involved in mRNAs degradation is still growing, however, the details of RNase-mRNAs interaction are not fully understood. ZC3H12A is a recently discovered inflammation-related RNase engaged in the control of proinflammatory cytokines transcripts turnover. ZC3H12A regulates also its own transcript half-live. We studied the details of this regulation. Our results confirm the importance of the 3’UTR in ZC3H12A-dependent ZC3H12A mRNA degradations. We compared mouse and human stem‑loop structures present in this region and discovered that human conserved stem-loop structure is not sufficient for ZC3H12A-dependent degradation. However, this structure is important for ZC3H12A mRNA post-transcriptional regulation. Our studies emphasize the importance of surroundings of the identified stem-loop structure for its biological activity. Removing of this region together with stem-loop structure greatly inhibits ZC3H12A regulation of the investigated 3’-untranslated region (3’UTR).

scholarly journals Influence of the 5′-proximal elements of the 5′-untranslated region of classical swine fever virus on translation and replication

2011 ◽  
Vol 92 (5) ◽  
pp. 1087-1096 ◽  
Author(s):  
Ming Xiao ◽  
Yujing Wang ◽  
Zailing Zhu ◽  
Chengli Ding ◽  
Jialin Yu ◽  
...  
Keyword(s):  
Classical Swine Fever Virus ◽  
Untranslated Region ◽  
Classical Swine Fever ◽  
Fever Virus ◽  
Loop Structure ◽  
Terminal Sequence ◽  
Entry Site ◽  
Stem Loop ◽  
Internal Ribosome Entry ◽  
Stem Loop Structure

The 5′-terminal sequence spanning nt 1–29 of the 5′-untranslated region of classical swine fever virus (CSFV) forms a 5′-proximal stem–loop structure known as domain Ia. Deletions and replacement mutations were performed to examine the role of this domain. Deletion of the 5′-proximal nucleotides and disruption of the stem–loop structure greatly increased internal ribosome entry site-mediated translation but abolished the replication of the replicons. Internal deletions resulting in a change in the size of the loop of domain Ia, and even removal of the entire domain, did not substantially change the translation activity, but reduced the replication of CSFV replicons provided the replicons contained the extreme 5′-GUAU terminal sequence. Internal replacements leading to a change in the nucleotide sequence of the loop did not alter the translation and replication activities of the CSFV RNA replicon, and did not influence the rescue of viruses and growth characteristics of new viruses. These results may be important for our understanding of the regulation of translation, replication and encapsidation in CSFV and other positive-sense RNA viruses.

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