Ribosomal scanning on the highly structured insulin-like growth factor II-leader 1

Velden, Alike W van der; Nierop, Kirsten van; Voorma, Harry O.; Thomas, Adri A. M.

doi:10.1016/s1357-2725(01)00116-9

Cited by 16 publications

(13 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Finally, we evaluated the effect of the insertion of a stable hairpin structure upstream of the F luc ORF, a change that should reduce translation efficiency because such structures have to be unfolded before scanning ribosomes can proceed (15,28). At nt 300 of the 529-nt D5D 5Ј UTR, we inserted a stable hairpin (⌬G ϭ Ϫ60 kcal/mol) that was previously shown to inhibit chloramphenicol acetyltransferase expression by 92 to 98%, depending on the position of this hairpin in the insulin-like growth factor II leader 1 (40). In our hands, the presence of this hairpin in pDualLuc-scan5 reduced F luc expression by 80%, suggesting that indeed this hairpin interfered with ribosome scanning (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Subsequently, the replicase AUG was mutated into UAG (pDualLuc-scan3). Finally, the 5Ј UTR of D1-301 (see above) was inserted (pDualLuc-scan4) and a stable hairpin was introduced into this region at nt 306 to block scanning ribosomes, generating pDualLuc-scan5 (40). RK-13 cells were transfected with 1 g of plasmid and were lysed at 20 h p.t.…”

Section: Vol 79 2005mentioning

confidence: 99%

See 1 more Smart Citation

Discontinuous Subgenomic RNA Synthesis in Arteriviruses Is Guided by an RNA Hairpin Structure Located in the Genomic Leader Region

Born

Posthuma

Gultyaev

et al. 2005

J Virol

View full text Add to dashboard Cite

Nidoviruses produce an extensive 3-coterminal nested set of subgenomic (sg) mRNAs, which are used to express structural proteins and sometimes accessory proteins. In arteriviruses and coronaviruses, these mRNAs contain a common 5 leader sequence, derived from the genomic 5 end. The joining of the leader sequence to different segments derived from the 3-proximal part of the genome (mRNA bodies) presumably involves a unique mechanism of discontinuous minus-strand RNA synthesis in which base pairing between sense and antisense transcription-regulating sequences (TRSs) plays an essential role. The leader TRS is present in the loop of a hairpin structure that functions in sg mRNA synthesis. In this study, the minimal sequences in the 5-proximal region of the Equine arteritis virus genome that are required for sg RNA synthesis were delimited through mutagenesis. A full-length cDNA clone was engineered in which this domain was duplicated, allowing us to make mutations and monitor their effects on sg RNA synthesis without seriously affecting genome replication and translation. The leader TRS present in the duplicated sequence was used and yielded novel sg mRNAs with significantly extended leaders. Our combined findings suggest that the leader TRS hairpin (LTH) and its immediate flanking sequences are essential for efficient sg RNA synthesis and form an independent functional entity that could be moved 300 nucleotides downstream of its original position in the genome. We hypothesize that a conformational switch in the LTH region regulates the role of the 5-proximal region of the arterivirus genome in subgenomic RNA synthesis.Many eukaryotic plus-strand RNA (ϩRNA) viruses generate subgenomic (sg) mRNAs as a strategy to regulate the expression of one or several viral proteins (21). In addition to internal initiation of translation, sg mRNA synthesis provides a mechanism to express genes positioned downstream of the 5Ј-proximal gene in polycistronic genomes of ϩRNA viruses of eukaryotes. Different mechanisms are employed by ϩRNA viruses to achieve the transcription of sg mRNAs (47). The generation of an extensive 3Ј-coterminal nested set of sg mRNAs to express structural and/or accessory proteins is a common property of viruses belonging to the order Nidovirales (Coronaviridae, Arteriviridae, and Roniviridae) (6, 34). In the case of arteriviruses and coronaviruses, all transcripts contain a common 5Ј sequence element, the so-called "leader," which is colinear with the 5Ј-proximal part of the genome and is fused to different regions derived from the 3Ј-proximal third of the genome, which are termed "mRNA bodies" (Fig. 1A). For two other nidovirus subgroups, roniviruses and toroviruses (with the exception of sg mRNA2 of the latter), sg mRNAs without a common 5Ј leader sequence have been described (3,32,45).For sg RNAs of coronaviruses and arteriviruses, and also the largest sg RNA of toroviruses (45), the fusion of the sg RNA body to the common leader sequence has been postulated to involve the discontinuous extension of minu...

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Vol 79 2005mentioning

confidence: 99%

Discontinuous Subgenomic RNA Synthesis in Arteriviruses Is Guided by an RNA Hairpin Structure Located in the Genomic Leader Region

Born

Posthuma

Gultyaev

et al. 2005

J Virol

View full text Add to dashboard Cite

show abstract

“…To the best of our knowledge, nobody has ever aimed to quantitatively compare the efficiency of translation of mRNAs with short-versus long-structured 5ЈUTRs with mammalian cells. However, careful analysis of literature shows that the case of L1 mRNA is not unprecedented, though the authors of the corresponding reports either did not focus on these findings or did not treat it as a general feature (5,12,47,55).…”

Section: Discussionmentioning

confidence: 99%

Efficient Translation Initiation Directed by the 900-Nucleotide-Long and GC-Rich 5′ Untranslated Region of the Human Retrotransposon LINE-1 mRNA Is Strictly Cap Dependent Rather than Internal Ribosome Entry Site Mediated

Dmitriev

Andreev

Terenin

et al. 2007

Molecular and Cellular Biology

108

109

View full text Add to dashboard Cite

Retrotransposon L1 is a mobile genetic element of the LINE family that is extremely widespread in the mammalian genome. It encodes a dicistronic mRNA, which is exceptionally rare among eukaryotic cellular mRNAs. The extremely long and GC-rich L1 5 untranslated region (5UTR) directs synthesis of numerous copies of RNA-binding protein ORF1p per mRNA. One could suggest that the 5UTR of L1 mRNA contained a powerful internal ribosome entry site (IRES) element. Using transfection of cultured cells with the polyadenylated monocistronic (L1 5UTR-Fluc) or bicistronic (Rluc-L1 5UTR-Fluc) RNA constructs, capped or uncapped, it has been firmly established that the 5UTR of L1 does not contain an IRES. Uncapping reduces the initiation activity of the L1 5UTR to that of background. Moreover, the translation is inhibited by upstream AUG codons in the 5UTR. Nevertheless, this cap-dependent initiation activity of the L1 5UTR was unexpectedly high and resembles that of the beta-actin 5UTR (84 nucleotides long). Strikingly, the deletion of up to 80% of the nucleotide sequence of the L1 5UTR, with most of its stem loops, does not significantly change its translation initiation efficiency. These data can modify current ideas on mechanisms used by 40S ribosomal subunits to cope with complex 5UTRs and call into question the conception that every long GC-rich 5UTR working with a high efficiency has to contain an IRES. Our data also demonstrate that the ORF2 translation initiation is not directed by internal initiation, either. It is very inefficient and presumably based on a reinitiation event.

show abstract

“…Interestingly, a number of cellular mRNAs containing IRES elements in their 5Ј-UTRs also contain small upstream open reading frames (uORFs) located within the IRES sequence (60,65,(72)(73)(74)(75)(76). In most cases, the significance of these uORFs for translation is not clear.…”

Section: Minireview: Mystery Of Cellular Iress 23426mentioning

confidence: 99%

“…tRNA-like elements (68), initially found within the structures of viral IRES elements (69), could facilitate docking of the cellular IRESs to the E or P sites on the 40 S ribosome. Recent cryo-electron micrograph visualization of two viral (hepatitis C virus and cricket paralysis virus intergenic region CrPV) internal ribosome entry sites bound to the 40 S ribosome seems to support this suggestion (70,71).Interestingly, a number of cellular mRNAs containing IRES elements in their 5Ј-UTRs also contain small upstream open reading frames (uORFs) located within the IRES sequence (60,65,(72)(73)(74)(75)(76). In most cases, the significance of these uORFs for translation is not clear.…”

mentioning

confidence: 99%

Internal Ribosome Entry Sites in Cellular mRNAs: Mystery of Their Existence

Komar¹,

Hatzoglou

2005

Journal of Biological Chemistry

254

256

View full text Add to dashboard Cite

Although studies on viral gene expression were essential for the discovery of internal ribosome entry sites (IRESs), it is becoming increasingly clear that IRES activities are present in a significant number of cellular mRNAs. Remarkably, many of these IRES elements initiate translation of mRNAs encoding proteins that protect cells from stress (when the translation of the vast majority of cellular mRNAs is significantly impaired). The purpose of this review is to summarize the progress on the discovery and function of cellular IRESs. Recent findings on the structures of these IRESs and specifically regulation of their activity during nutritional stress, differentiation, and mitosis will be discussed.Initiation of protein synthesis in eukaryotes is a complex process requiring numerous accessory proteins called initiation factors (also termed canonical initiation factors) (1). Assembly of the 80 S ribosome at a start codon within the majority of eukaryotic mRNAs involves binding of the mRNA 5Ј-m 7 G cap structure to a group of proteins referred to as the cap-binding complex or eIF4F (which consists of three proteins: eIF4E, 1 eIF4G, and eIF4A) (1-3). This is followed by recruitment of the 40 S ribosomal subunit and associated initiation factors (43 S initiation complex comprising a 40 S subunit, eIF2⅐GTP⅐Met-tRNA i , and eIF3) and movement of the 43 S initiation complex along the 5Ј-untranslated region (5Ј-UTR) in search of the initiation codon (1-3) (Fig. 1, left panel). This mechanism of translation initiation is known as "ribosome scanning" (1-3). Initiation factor eIF4G functions as a scaffolding protein. It binds eIF4E (a capbinding protein) and eIF4A (an ATP-dependent RNA helicase, which is thought to unwind the secondary structure in the mRNA 5Ј-UTR) and bridges the mRNA and the ribosome via its interaction with the 40 S bound initiation factor eIF3 (1-3). eIF3 is a multiprotein complex directly associated with the small ribosomal subunit and was shown to impede the association of the 40 S and 60 S ribosomal subunits in the absence of eIF2⅐GTP⅐Met-tRNA i ternary complex (1-3). eIF2 binds GTP and Met-tRNA i and transfers Met-tRNA i to the 40 S ribosomal subunit (1-4). It should be noted that the availability of eIF4E for binding to eIF4G is regulated in eukaryotic cells by the phosphorylation of a small family of eIF4E-binding proteins (the 4E-BPs). Furthermore, proteins that bind the poly(A) tails of the mRNA (PABPs) were shown to facilitate initiation and recycling of ribosomes through interaction with eIF4G (1-3). However, it has become clear that some viral and eukaryotic cellular mRNAs can be translated via internal initiation, a process that involves direct binding of the ribosome to specific mRNA regions termed internal ribosome entry sites (IRESs). This translation initiation mechanism is generally independent of recognition of the 5Ј-mRNA end and involves direct recruitment of the 40 S ribosomes to the vicinity of the initiation codon (5-10) (Fig. 1, right panel). Although the debate continues over ...

show abstract

Ribosomal scanning on the highly structured insulin-like growth factor II-leader 1

Cited by 16 publications

References 34 publications

Discontinuous Subgenomic RNA Synthesis in Arteriviruses Is Guided by an RNA Hairpin Structure Located in the Genomic Leader Region

Discontinuous Subgenomic RNA Synthesis in Arteriviruses Is Guided by an RNA Hairpin Structure Located in the Genomic Leader Region

Efficient Translation Initiation Directed by the 900-Nucleotide-Long and GC-Rich 5′ Untranslated Region of the Human Retrotransposon LINE-1 mRNA Is Strictly Cap Dependent Rather than Internal Ribosome Entry Site Mediated

Internal Ribosome Entry Sites in Cellular mRNAs: Mystery of Their Existence

Contact Info

Product

Resources

About