Cooperative enhancement of translation by two adjacent microRNA-122/Argonaute 2 complexes binding to the 5′ untranslated region of hepatitis C virus RNA

Nieder-Röhrmann, Anika; Dünnes, Nadia; Gerresheim, Gesche K.; Shalamova, Lyudmila; Herchenröther, Andreas; Niepmann, Michael

doi:10.1099/jgv.0.000697

Cited by 16 publications

(16 citation statements)

References 52 publications

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“…Individual analysis of Sites 1 and 2 alone revealed that Site 1 has a higher overall binding affinity than Site 2; however, miR-122 binding to Site 2 was more exothermic and entropically favoured suggesting that in this isolated system, Site 2 binding to miR-122 brings the system to a lower energy ordered state (Table 1). This is in agreement with previous results with a J6/JFH-1 (genotype 2a) isolate (52); but is in contrast to studies with Con 1b (genotype 1b), where miR-122 binding to Site 2 had a stronger binding affinity than Site 1 (22). Although both ITC experiments were done similarly, it is possible that our results vary due to differences in the sequences between these two genotypes as well as the specific lengths used for binding experiments of the individual sites, since the tail of miR-122 bound to Site 2 would be predicted to have extended binding into the Site 1 seed region in the absence of Site 1-bound miR-122 (22).…”

Section: Discussionsupporting

confidence: 93%

miR-122 and Ago interactions with the HCV genome alter the structure of the viral 5′ terminus

Chahal

Gebert

Gan

et al. 2019

Nucleic Acids Research

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Hepatitis C virus (HCV) is a positive-sense RNA virus that interacts with the liver-specific microRNA, miR-122. miR-122 binds to two sites in the 5′ untranslated region (UTR) and this interaction promotes HCV RNA accumulation, although the precise role of miR-122 in the HCV life cycle remains unclear. Using biophysical analyses and Selective 2′ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) we investigated miR-122 interactions with the 5′ UTR. Our data suggests that miR-122 binding results in alteration of nucleotides 1–117 to suppress an alternative secondary structure and promote functional internal ribosomal entry site (IRES) formation. Furthermore, we demonstrate that two hAgo2:miR-122 complexes are able to bind to the HCV 5′ terminus simultaneously and SHAPE analyses revealed further alterations to the structure of the 5′ UTR to accommodate these complexes. Finally, we present a computational model of the hAgo2:miR-122:HCV RNA complex at the 5′ terminus of the viral genome as well as hAgo2:miR-122 interactions with the IRES–40S complex that suggest hAgo2 is likely to form additional interactions with SLII which may further stabilize the HCV IRES. Taken together, our results support a model whereby hAgo2:miR-122 complexes alter the structure of the viral 5′ terminus and promote formation of the HCV IRES.

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Section: Discussionsupporting

confidence: 93%

miR-122 and Ago interactions with the HCV genome alter the structure of the viral 5′ terminus

Chahal

Gebert

Gan

et al. 2019

Nucleic Acids Research

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“…However, at that time it was not clear which specific step in the HCV replication cycle may be affected: RNA translation, RNA synthesis, RNA genome stability and/or other steps. Later, it was shown that one such effector function of miR-122 is the stimulation of HCV translation ( Henke et al, 2008 ), confirmed by several other studies ( Bung et al, 2010 ; Jangra et al, 2010b ; Roberts et al, 2011 , 2014 ; Wilson et al, 2011 ; Fehr et al, 2012 ; Goergen and Niepmann, 2012 ; Zhang et al, 2012 ; Bradrick et al, 2013 ; Conrad et al, 2013 ; Huys et al, 2013 ; Nieder-Röhrmann et al, 2017 ). While the mechanisms of translation stimulation by the miR-122/Ago2 complexes binding to the 5′ UTR are not yet clear, changes in RNA template stability were shown not to be the primary cause for the effect of miR-122 on HCV translation ( Henke et al, 2008 ; Bradrick et al, 2013 ; Huys et al, 2013 ; Roberts et al, 2014 ; Nieder-Röhrmann et al, 2017 ).…”

Section: The Liver-specific Microrna-122mentioning

confidence: 57%

“…The seed target nucleotides and the so-called supplementary binding region are separated by the SL I in target site 1, and by some intervening nucleotides conserved not to pair to miR-122 in target site 2. Due to the conserved proximity of both target sites in the HCV 5′ UTR, the two miR-122/Ago2 complexes bind cooperatively to these sites ( Thibault et al, 2015 ; Nieder-Röhrmann et al, 2017 ). This cooperative binding may be the reason for the observation that mutations in any of these two sites generally affect the downstream effector functions of these complexes – no matter which of the different effector functions is analyzed.…”

Section: The Liver-specific Microrna-122mentioning

confidence: 99%

Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication

et al. 2018

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Hepatitis C virus (HCV) preferentially replicates in the human liver and frequently causes chronic infection, often leading to cirrhosis and liver cancer. HCV is an enveloped virus classified in the genus Hepacivirus in the family Flaviviridae and has a single-stranded RNA genome of positive orientation. The HCV RNA genome is translated and replicated in the cytoplasm. Translation is controlled by the Internal Ribosome Entry Site (IRES) in the 5′ untranslated region (5′ UTR), while also downstream elements like the cis-replication element (CRE) in the coding region and the 3′ UTR are involved in translation regulation. The cis-elements controlling replication of the viral RNA genome are located mainly in the 5′- and 3′-UTRs at the genome ends but also in the protein coding region, and in part these signals overlap with the signals controlling RNA translation. Many long-range RNA–RNA interactions (LRIs) are predicted between different regions of the HCV RNA genome, and several such LRIs are actually involved in HCV translation and replication regulation. A number of RNA cis-elements recruit cellular RNA-binding proteins that are involved in the regulation of HCV translation and replication. In addition, the liver-specific microRNA-122 (miR-122) binds to two target sites at the 5′ end of the viral RNA genome as well as to at least three additional target sites in the coding region and the 3′ UTR. It is involved in the regulation of HCV RNA stability, translation and replication, thereby largely contributing to the hepatotropism of HCV. However, we are still far from completely understanding all interactions that regulate HCV RNA genome translation, stability, replication and encapsidation. In particular, many conclusions on the function of cis-elements in HCV replication have been obtained using full-length HCV genomes or near-full-length replicon systems. These include both genome ends, making it difficult to decide if a cis-element in question acts on HCV replication when physically present in the plus strand genome or in the minus strand antigenome. Therefore, it may be required to use reduced systems that selectively focus on the analysis of HCV minus strand initiation and/or plus strand initiation.

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“…There are five to six target sequences conserved in the HCV genome, two in the 5 UTR [62], one in the 3 UTR, and two to three in the NS5B coding region (depending on genotype) [63]. Cooperative binding of two miR-122 molecules to the two adjacent target sites in the HCV 5 UTR contributes to RNA stability by protecting against cellular nucleases [64,65] and has a positive effect on the efficiency of HCV translation [66][67][68][69][70][71][72]. Although some studies investigated the possible roles of the conserved potential miR-122 binding sites in the NS5B coding region and in the 3 UTR, it is not yet clear if physical binding of miR-122 to these sites results in effector functions [73][74][75][76], leaving some doubts why these sequences are conserved among HCV isolates.…”

Section: Introductionmentioning

confidence: 99%

Hepatitis C Virus Translation Regulation

Niepmann

Gerresheim

2020

IJMS

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Translation of the hepatitis C virus (HCV) RNA genome is regulated by the internal ribosome entry site (IRES), located in the 5’-untranslated region (5′UTR) and part of the core protein coding sequence, and by the 3′UTR. The 5′UTR has some highly conserved structural regions, while others can assume different conformations. The IRES can bind to the ribosomal 40S subunit with high affinity without any other factors. Nevertheless, IRES activity is modulated by additional cis sequences in the viral genome, including the 3′UTR and the cis-acting replication element (CRE). Canonical translation initiation factors (eIFs) are involved in HCV translation initiation, including eIF3, eIF2, eIF1A, eIF5, and eIF5B. Alternatively, under stress conditions and limited eIF2-Met-tRNAiMet availability, alternative initiation factors such as eIF2D, eIF2A, and eIF5B can substitute for eIF2 to allow HCV translation even when cellular mRNA translation is downregulated. In addition, several IRES trans-acting factors (ITAFs) modulate IRES activity by building large networks of RNA-protein and protein–protein interactions, also connecting 5′- and 3′-ends of the viral RNA. Moreover, some ITAFs can act as RNA chaperones that help to position the viral AUG start codon in the ribosomal 40S subunit entry channel. Finally, the liver-specific microRNA-122 (miR-122) stimulates HCV IRES-dependent translation, most likely by stabilizing a certain structure of the IRES that is required for initiation.

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Cooperative enhancement of translation by two adjacent microRNA-122/Argonaute 2 complexes binding to the 5′ untranslated region of hepatitis C virus RNA

Cited by 16 publications

References 52 publications

miR-122 and Ago interactions with the HCV genome alter the structure of the viral 5′ terminus

miR-122 and Ago interactions with the HCV genome alter the structure of the viral 5′ terminus

Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication

Hepatitis C Virus Translation Regulation

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