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Hepatitis C Virus Translation Regulation

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Hepatitis C Virus Translation Regulation International Journal of Molecular Sciences Review Hepatitis C Virus Translation Regulation Michael Niepmann * and Gesche K. Gerresheim Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, Friedrichstrasse 24, 35392 Giessen, Germany; [email protected] * Correspondence: [email protected] Received: 6 March 2020; Accepted: 25 March 2020; Published: 27 March 2020 Abstract: Translation of the hepatitis C virus (HCV) RNA genome is regulated by the internal ribosome entry site (IRES), located in the 5’-untranslated region (50UTR) and part of the core protein coding sequence, and by the 30UTR. The 50UTR 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 30UTR and the cis-acting replication element (CRE). Canonical translation initiation factors (eIFs) are involved in HCV translation initiation, including eIF3, Met eIF2, eIF1A, eIF5, and eIF5B. Alternatively, under stress conditions and limited eIF2-Met-tRNAi 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 50- and 30-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. Keywords: HCV; Hepacivirus; internal ribosome entry site; IRES; initiation; ribosome; 40S; eIF3; ITAF; stress response 1. Introduction Hepatitis C virus (HCV) is an enveloped positive strand RNA virus that preferentially replicates in the liver [1], and it is classified in the genus Hepacivirus in the family Flaviviridae. Worldwide, about 71 million people are infected with HCV [2]. The infection is usually noticed only when coincidentally diagnosed by routine testing, for example, during hospitalization, or when the liver disease becomes acute. In the latter case, liver damage by virus replication and the resulting immune responses can lead to impaired bilirubin conjugation in the liver, and unconjugated bilirubin deposits can then be noticed as a yellowish color (called jaundice), often first in the sclera in the eyes and when more severe also in the skin. An acute infection can result in severe liver damage, in rare cases even resulting in death [3,4]. However, most HCV infections remain inapparent [5,6], and the virus infection can become chronic in about 60% to 70 % of all infections [7], often without being noticed. Chronic infection can, in the long run, result in liver cirrhosis and liver cancer (hepatocellular carcinoma, HCC) [8–10], while a metabolic reprogramming of the infected cells according to the “Warburg effect” like in cancer cells can be observed only a few days after the onset of HCV replication [11]. Moreover, inapparent replication of the virus usually results in unnoticed spread of the virus to other individuals, a fact that is a major challenge for surveillance, health care, and treatment [12]. Meanwhile, very effective treatment regimens using direct acting antivirals (DAAs) are available, although they are still very Int. J. Mol. Sci. 2020, 21, 2328; doi:10.3390/ijms21072328 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2020, 21, 2328 2 of 33 expensive [13,14]. Although the error rate of the viral replicase is high and can, in principle, easily give Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW 2 of 33 rise to resistance mutations, the conserved nature of the replicase active center and the often occurring reducedreplicase fitness is of high mutants and can, result in principle, in the rareeasily appearance give rise to resistance of resistance mutations, mutations the conserved against nature nucleoside inhibitorsof the such replicase as sofosbuvir active center [15, 16and]. Anthe often effective occurr vaccinationing reducedis fitness not yet of mutants available, result also in partially the rare due to the highappearance variability of ofresistance the viral mutations RNA genome. against nucleoside Thus, further inhibitors research such as on sofosbuvir HCV is urgently[15,16]. An required to combateffective HCV vaccination infections, is andnot yet despite available, much also progress partially due in the to the understanding high variability of of HCVthe viral replication RNA the genome. Thus, further research on HCV is urgently required to combat HCV infections, and despite molecular mechanisms of HCV replication are still far from being completely understood [12]. much progress in the understanding of HCV replication the molecular mechanisms of HCV HCVreplication molecular are still biology far from research being completely essentially understood started [12]. with the first cloning of the HCV genome (“non-A non-BHCV hepatitis”) molecular biology [17] (Figure research1). essentially Further started important with landmarksthe first cloning were of the the HCV development genome of a subgenomic(“non-A replicon non-B systemhepatitis”) [18 [17]] that (Figure first analyzed1). Further intracellularimportant landmarks virus replication, were the development and the development of a of infectioussubgenomic full-length replicon clones system that [18] were that capable first an ofalyzed going intracellular through a completevirus replication, viral replication and the cycle development of infectious full-length clones that were capable of going through a complete viral including infection and new virus production [19–21]. replication cycle including infection and new virus production [19–21]. Figure 1.Figurecis-Elements 1. cis-Elements in the in the hepatitis hepatitis C C virus virus (HCV)(HCV) RNA RNA genome genome that that are involved are involved in translation in translation regulation.regulation. The HCV The HCV plus plus strand strand RNA RNA genome. genome. The in internalternal ribosome ribosome entry entry site (IRES) site (IRES) in the HCV in the HCV 5´-untranslated region (5´UTR), the entire 3´UTR and the cis-acting replication element (CRE) in the 50-untranslated region (50UTR), the entire 30UTR and the cis-acting replication element (CRE) in the NS5B coding region are involved in translation regulation [22–24]. Those regions of the 5´UTR, 3´UTR, NS5B coding region are involved in translation regulation [22–24]. Those regions of the 50UTR, 30UTR, and CRE that bind to the ribosomal 40S subunit are underlayed in light yellow. Stem-loops (SLs) in and CRE that bind to the ribosomal 40S subunit are underlayed in light yellow. Stem-loops (SLs) in the 5´UTR are numbered by roman numerals. The region of the IRES is surrounded by a dotted line. the 50UTRThe areIRES numbered includes SLs by II–IV roman of the numerals. 5´UTR but spans The regioninto the core of the protein IRES coding is surrounded region. The bycanonical a dotted line. The IRESAUG includes start codon SLs in II–IV SL IV of of the the 55´UTR0UTR (black but spans circle)into gives the rise core to translation protein codingof the polyprotein region. The which canonical AUG startis cleaved codon to in yield SL IVstructural of the 5proteins0UTR (blackand non-structural circle) gives (NS-) rise proteins, to translation including of the the viral polyprotein replicase which is cleavedNS5B. to yieldThe 3´UTR structural contains proteins the variable and region, non-structural a poly(U/C) (NS-) tract proteins,(U/C), and includingthe so-called the 3´X viral region replicase including SLs 1, 2, and 3. The stem-loop 5BSL3.2 in the 3´-region of the NS5B coding region is the NS5B. The 30UTR contains the variable region, a poly(U/C) tract (U/C), and the so-called 30X region CRE, flanked by upstream stem-loop 5BSL3.1 and downstream 5BSL3.3. The polyprotein stop codon including SLs 1, 2, and 3. The stem-loop 5BSL3.2 in the 3 -region of the NS5B coding region is the is located in the stem-loop 5BSL3.4 (asterisk). Some other0 start codons which give rise to the CRE, flankedalternative by upstreamreading frame stem-loop (ARF) in 5BSL3.1the core+1 and readin downstreamg frame [25–28] 5BSL3.3. are shown The in polyprotein grey. Positively stop and codon is locatednegatively in the stem-loop acting long-range 5BSL3.4 RNA–RNA (asterisk). interactions Some other (LRIs) start are codons shown whichin green give or red, rise respectively, to the alternative readingwith frame the (ARF)sequence in “9170” the core shown+1 reading as green frame circle. [Sele25–cted28] arebinding shown sites in for grey. microRNA-122 Positively (miR-122) and negatively acting long-rangeare shown in RNA–RNAblue. interactions (LRIs) are shown in green or red, respectively, with the sequence “9170” shown as green circle. Selected binding sites for microRNA-122 (miR-122) are shown The HCV RNA genome is about 9600 nucleotides (nts) long and codes for one long polyprotein in blue. that is co- and post-translationally processed into the mature gene products [29–31]. The viral structural proteins include the core protein, which is contained in the virus particle, as well as the The HCV RNA genome is about 9600 nucleotides (nts) long and codes for one long polyprotein envelope glycoproteins E1 and E2. The non-structural (NS) proteins are involved in HCV RNA that is co-replication and post-translationally and particle assembly. processed The first into NS the protein mature is genep7, a productsviroporin, [ 29which–31 ].is The involved viral structuralin proteinsassembly. include NS2 the is core a protease protein, and acts which as a cofactor is contained involved in in the assembly.
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