Secondary structure conservation of the stem-loop IV sub-domain of internal ribosomal entry sites in human rhinovirus clinical isolates

ABSTRACT Analysis of the sequence immediate upstream of ohrrevealed an open reading frame, designated ohrR, with the potential to encode a 17-kDa peptide with moderate amino acid sequence homology to the MarR family of negative regulators of gene expression. ohrR was transcribed as bicistronic mRNA with ohr, while ohr mRNA was found to be 95% monocistronic and 5% bicistronic with ohrR. Expression of both genes was induced by tert-butyl hydroperoxide (tBOOH) treatment. High-level expression ofohrR negatively regulated ohr expression. This repression could be overcome by tBOOH treatment. In vivo promoter analysis showed that the ohrR promoter (P1) has organic peroxide-inducible, strong activity, while the ohrpromoter (P2) has constitutive, weak activity. Only P1 is autoregulated by OhrR. ohr primer extension results revealed three major primer extension products corresponding to the 5′ ends ofohr mRNA, and their levels were strongly induced by tBOOH treatment. Sequence analysis of regions upstream of these sites showed no typical Xanthomonas promoter. Instead, the regions can form a stem-loop secondary structure with the 5′ ends ofohr mRNA located in the loop section. The secondary structure resembles the structure recognized and processed by RNase III enzyme. These findings suggest that the P1 promoter is responsible for tBOOH-induced expression of the ohrR-ohr operon. The bicistronic mRNA is then processed by RNase III-like enzymes to give high levels of ohr mRNA, while ohrR mRNA is rapidly degraded.

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Genomic determinants of the efficiency of internal ribosomal entry sites of viral and cellular origin

Nucleic Acids Research ◽

10.1093/nar/gkn812 ◽

2008 ◽

Vol 36 (21) ◽

pp. 6918-6925 ◽

Cited By ~ 12

Author(s):

Kayole Kazadi ◽

Corinne Loeuillet ◽

Samuel Deutsch ◽

Angela Ciuffi ◽

Miguel Muñoz ◽

...

Keyword(s):

Internal Ribosomal Entry Sites ◽

Cellular Origin ◽

Ribosomal Entry

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Internal Ribosomal Entry Sites

10.1007/springerreference_35663 ◽

2011 ◽

Keyword(s):

Internal Ribosomal Entry Sites ◽

Ribosomal Entry

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The non-primate hepacivirus 5′ untranslated region possesses internal ribosomal entry site activity

Journal of General Virology ◽

10.1099/vir.0.055764-0 ◽

2013 ◽

Vol 94 (12) ◽

pp. 2657-2663 ◽

Cited By ~ 9

Author(s):

Hazel Stewart ◽

Cheryl Walter ◽

Dale Jones ◽

Sinead Lyons ◽

Peter Simmonds ◽

...

Keyword(s):

Untranslated Region ◽

Internal Ribosomal Entry Site ◽

Rna Replication ◽

Entry Site ◽

Subgenomic Replicon ◽

Stem Loop ◽

Long Range Interactions ◽

Ribosomal Entry ◽

Internal Translation ◽

And Function

The 5′ untranslated region (5′UTR) of the recently described non-primate hepacivirus (NPHV) contains a region with sequence homology to the internal ribosomal entry site (IRES) of hepatitis C virus (HCV) and GB virus B (GBV-B). Here, we demonstrated internal translation initiation by the NPHV 5′UTR in a bicistronic vector. An RNA stem–loop upstream of the NPHV IRES was structurally distinct from corresponding regions in HCV and GBV-B, and was not required for IRES function. Insertion of the NPHV stem–loop into the corresponding region of the HCV 5′UTR within the HCV subgenomic replicon significantly impaired RNA replication, indicating that long-range interactions between the 5′UTR and cis-acting downstream elements within the NPHV genome are not interchangeable with those of HCV. Despite similarities in IRES structure and function between hepaciviruses, replication elements in the NPHV 5′UTR appear functionally distinct from those of HCV.

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Dual Stem Loops within the Poliovirus Internal Ribosomal Entry Site Control Neurovirulence

Journal of Virology ◽

10.1128/jvi.73.2.958-964.1999 ◽

1999 ◽

Vol 73 (2) ◽

pp. 958-964 ◽

Cited By ~ 100

Author(s):

Matthias Gromeier ◽

Birgit Bossert ◽

Mineo Arita ◽

Akio Nomoto ◽

Eckard Wimmer

Keyword(s):

Internal Ribosomal Entry Site ◽

Internal Constraints ◽

Virus Propagation ◽

Entry Site ◽

Stem Loop ◽

Nontranslated Region ◽

Growth Properties ◽

Ribosomal Entry ◽

Site Control

ABSTRACT In the human central nervous system, susceptibility to poliovirus (PV) infection is largely confined to a specific subpopulation of neuronal cells. PV tropism is likely to be determined by cell-external components such as the PV receptor CD155, as well as cell-internal constraints such as the availability of a suitable microenvironment for virus propagation. We reported previously that the exchange of the cognate internal ribosomal entry site (IRES) within the 5′ nontranslated region of PV with its counterpart from human rhinovirus type 2 (HRV2) can eliminate the neuropathogenic phenotype in a transgenic mouse model for poliomyelitis without diminishing the growth properties in HeLa cells. We now show that attenuation of neurovirulence of PV/HRV2 chimeras is not confined to CD155 transgenic mice but is evident also after intraspinal inoculation intoCynomolgus monkeys. We have dissected the PV and HRV2 IRES elements to determine those structures responsible for neurovirulence (or attenuation) of these chimeric viruses. We report that two adjacent stem loop structures within the IRES cooperatively determine neuropathogenicity.

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Proteins Involved in the Function of Picornavirus Internal Ribosomal Entry Sites

Molecular Biology of Picornavirus ◽

10.1128/9781555817916.ch15 ◽

2014 ◽

pp. 171-183 ◽

Cited By ~ 3

Author(s):

Richard J. Jackson

Keyword(s):

Internal Ribosomal Entry Sites ◽

Ribosomal Entry

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A new entropy model for RNA: part II. Persistence-related entropic contributions to RNA secondary structure free energy calculations

Journal of Nucleic Acids Investigation ◽

10.4081/jnai.2013.2651 ◽

2013 ◽

Vol 4 (1) ◽

pp. 2 ◽

Cited By ~ 2

Author(s):

Wayne Dawson ◽

Kenji Yamamoto ◽

Kentaro Shimizu ◽

Gota Kawai

Keyword(s):

Free Energy ◽

Secondary Structure ◽

Degrees Of Freedom ◽

Free Energy Calculations ◽

Local Entropy ◽

Entropy Model ◽

Stem Loop ◽

Entropy Correction ◽

The Cross ◽

Folded Rna

In previous work, we have shown that the entropy of a folded RNA molecule can be divided into local and global contributions using the cross-linking entropy (CLE) model, where, in the case of RNA, the cross- links are the base-pair stacking interactions. The local contribution to the CLE is revealed in the Kuhn length (a measure of the stiffness of the RNA). The Kuhn length acts as a scaling parameter. When the size of the system is rescaled, the relationship between local and global free energy must be renormalized to reflect this rescaling. In this renormalization process, the Kuhn length increases, the local entropy also increases due to freezing out of the local conformational degrees of freedom. At the same time, as the number of degrees of freedom decrease, there is a significant reduction in the global entropy. Here we present a method, based on the concepts of renormalization theory, to quantitatively estimate the size of the contribution from the local entropy as a function of the Kuhn length. The local entropy correction is used to predict the current empirically derived constant in the Jacobson-Stockmayer equation. The variation in the Kuhn length is shown to be largely influenced by the length of the double-stranded RNA stems formed in the secondary structure of folded RNA. This result is used to test the resulting entropy under a variable Kuhn length in stem-loop structures. Comparisons between a variable Kuhn length and a static Kuhn length on a short stem-loop of RNA are also examined. The model is quite general and is also directly applicable to protein structure and folding problems.

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mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis inArabidopsis thaliana

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2003733117 ◽

2020 ◽

Vol 117 (35) ◽

pp. 21785-21795 ◽

Cited By ~ 2

Author(s):

Susheel Sagar Bhat ◽

Dawid Bielewicz ◽

Tomasz Gulanicz ◽

Zsuzsanna Bodi ◽

Xiang Yu ◽

...

Keyword(s):

Secondary Structure ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Rna Structure ◽

Methylation Status ◽

Mirna Biogenesis ◽

Stem Loop ◽

Structure Probing ◽

Plant Transcriptome ◽

Loop Regions

InArabidopsis thaliana, the METTL3 homolog, mRNA adenosine methylase (MTA) introducesN6-methyladenosine (m6A) into various coding and noncoding RNAs of the plant transcriptome. Here, we show that an MTA-deficient mutant (mta) has decreased levels of microRNAs (miRNAs) but accumulates primary miRNA transcripts (pri-miRNAs). Moreover, pri-miRNAs are methylated by MTA, and RNA structure probing analysis reveals a decrease in secondary structure within stem–loop regions of these transcripts inmtamutant plants. We demonstrate interaction between MTA and both RNA Polymerase II and TOUGH (TGH), a plant protein needed for early steps of miRNA biogenesis. Both MTA and TGH are necessary for efficient colocalization of the Microprocessor components Dicer-like 1 (DCL1) and Hyponastic Leaves 1 (HYL1) with RNA Polymerase II. We propose that secondary structure of miRNA precursors induced by their MTA-dependent m6A methylation status, together with direct interactions between MTA and TGH, influence the recruitment of Microprocessor to plant pri-miRNAs. Therefore, the lack of MTA inmtamutant plants disturbs pri-miRNA processing and leads to the decrease in miRNA accumulation. Furthermore, our findings reveal that reduced miR393b levels likely contributes to the impaired auxin response phenotypes ofmtamutant plants.

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Structural Characterization of the Rous Sarcoma Virus RNA Stability Element

Journal of Virology ◽

10.1128/jvi.02113-08 ◽

2008 ◽

Vol 83 (5) ◽

pp. 2119-2129 ◽

Cited By ~ 23

Author(s):

Jason E. Weil ◽

Michalis Hadjithomas ◽

Karen L. Beemon

Keyword(s):

Secondary Structure ◽

Rous Sarcoma Virus ◽

Translation Termination ◽

Rna Stability ◽

Premature Termination Codon ◽

Termination Codon ◽

Stem Loop ◽

Future Design ◽

Rous Sarcoma ◽

Sarcoma Virus

ABSTRACT In eukaryotic cells, an mRNA bearing a premature termination codon (PTC) or an abnormally long 3′ untranslated region (UTR) is often degraded by the nonsense-mediated mRNA decay (NMD) pathway. Despite the presence of a 5- to 7-kb 3′ UTR, unspliced retroviral RNA escapes this degradation. We previously identified the Rous sarcoma virus (RSV) stability element (RSE), an RNA element downstream of the gag natural translation termination codon that prevents degradation of the unspliced viral RNA. Insertion of this element downstream of a PTC in the RSV gag gene also inhibits NMD. Using partial RNase digestion and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry, we determined the secondary structure of this element. Incorporating RNase and SHAPE data into structural prediction programs definitively shows that the RSE contains an AU-rich stretch of about 30 single-stranded nucleotides near the 5′ end and two substantial stem-loop structures. The overall secondary structure of the RSE appears to be conserved among 20 different avian retroviruses. The structural aspects of this element will serve as a tool in the future design of cis mutants in addressing the mechanism of stabilization.

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