Study of RNA-A Initiation Translation of The Infectious Pancreatic Necrosis Virus

Rivas‐Aravena, Andrea; Muñoz, Patricio Moya; Jorquera, Patricia A.; Diaz, Alvaro; Reinoso, Claudia A.; González-Catrilelbún, Sebastián; Sandino, Ana María

doi:10.1016/j.virusres.2017.07.014

Cited by 6 publications

(11 citation statements)

References 65 publications

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“…Mutations in this 5′-UTR were known to affect IPNV infectivity [18], and Boot et al [19] suggested that, since birnaviruses lack a 5′-cap and-because of the short length of the 5′-UTR-also lack an internal ribosome entry site (IRES) to use the cellencoded initiation factors, the VPg linked at the 5′-end would be involved in initiation of translation. However, it has also been reported that 5′-UTR lengths shorter than the normal 300 nt are not necessarily an impediment to constitute an IRES structure, and Rivas-Aravena et al [20] have demonstrated that the 5′-UTR forms a functional structure, efficiently acting as an IRES, which commands translation.…”

Section: Its Structure and General Characteristicsmentioning

confidence: 99%

“…At the other end of the strands, the 3´-UTR is known to be involved in second strand RNA synthesis. The infectious bursal disease virus (IBDV; a member of the related genus Avibirnavirus frequently used as reference for IPNV structure and replication) is known to have a couple of cytosines at this end allowing the VPg to act as a protein-primer thanks to its linked guanines; but to function, the 3′-UTR must maintain a specific stem-loop structure [20]. In the case of the mRNA, since its 3′-end lacks a poly(A) tail to simulate the cellular mRNA and thus to defend against exonuclear activity, and enhance its translation, its function is probably substituted by the 3′-UTR stem loop structure [19]…”

Section: Its Structure and General Characteristicsmentioning

confidence: 99%

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The Infectious Pancreatic Necrosis Virus (IPNV) and its Virulence Determinants: What is Known and What Should be Known

Dopazo

2020

Pathogens

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Infectious pancreatic necrosis (IPN) is a disease of great concern in aquaculture, mainly among salmonid farmers, since losses in salmonid fish—mostly very young rainbow trout (Salmo gairdnery) fry and Atlantic salmon (Salmo salar) post-smolt—frequently reach 80–90% of stocks. The virus causing the typical signs of the IPN disease in salmonids, named infectious pancreatic necrosis virus (IPNV), has also been isolated from other fish species either suffering related diseases (then named IPNV-like virus) or asymptomatic; the general term aquabirnavirus is used to encompass all these viruses. Aquabirnaviruses are non-enveloped, icosahedral bisegmented dsRNA viruses, whose genome codifies five viral proteins, three of which are structural, and one of them is an RNA-dependent RNA polymerase. Due to the great importance of the disease, there have been great efforts to find a way to predict the level of virulence of IPNV isolates. The viral genome and proteins have been the main focus of research. However, to date such a reliable magic marker has not been discovered. This review describes the processes followed for decades in the attempts to discover the viral determinants of virulence, and to help the reader understand how viral components can be involved in virulence modulation in vitro and in vivo. There is also a brief description of the disease, of host defenses, and of the molecular structure and function of the virus and its viral components.

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Section: Its Structure and General Characteristicsmentioning

confidence: 99%

Section: Its Structure and General Characteristicsmentioning

confidence: 99%

The Infectious Pancreatic Necrosis Virus (IPNV) and its Virulence Determinants: What is Known and What Should be Known

Dopazo

2020

Pathogens

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“…Nineteen studies measured at multiple time points after transfection. From time series experiments, it was shown that for plasmid DNA, the optimal time point to detect differences lies between 36 and 48 h post-transfection [ 205 ]. For the EMCV and HRV IRES, maximum activity in a Fluc/Rluc configuration could already be achieved at 12 h post-transfection [ 115 ].…”

Section: Resultsmentioning

confidence: 99%

“…These include an empty control (or inversed 5′ UTR), a proximal stable hairpin, and monocistronic variants with and without cap. In our literature search, we found only four articles that adhered to these recommendations [ 43 , 160 , 165 , 205 ]. In addition, it is known that eukaryotic IRESs or CITEs have strongly reduced activity in mRNA transfection experiments, which has been used to question their existence or to argue for the existence of a nuclear experience of the mRNA [ 14 , 242 ].…”

Section: Discussionmentioning

confidence: 99%

Current Practice in Bicistronic IRES Reporter Use: A Systematic Review

Akker

Zacchini

Housmans

et al. 2021

IJMS

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Bicistronic reporter assays have been instrumental for transgene expression, understanding of internal ribosomal entry site (IRES) translation, and identification of novel cap-independent translational elements (CITE). We observed a large methodological variability in the use of bicistronic reporter assays and data presentation or normalization procedures. Therefore, we systematically searched the literature for bicistronic IRES reporter studies and analyzed methodological details, data visualization, and normalization procedures. Two hundred fifty-seven publications were identified using our search strategy (published 1994–2020). Experimental studies on eukaryotic adherent cell systems and the cell-free translation assay were included for further analysis. We evaluated the following methodological details for 176 full text articles: the bicistronic reporter design, the cell line or type, transfection methods, and time point of analyses post-transfection. For the cell-free translation assay, we focused on methods of in vitro transcription, type of translation lysate, and incubation times and assay temperature. Data can be presented in multiple ways: raw data from individual cistrons, a ratio of the two, or fold changes thereof. In addition, many different control experiments have been suggested when studying IRES-mediated translation. In addition, many different normalization and control experiments have been suggested when studying IRES-mediated translation. Therefore, we also categorized and summarized their use. Our unbiased analyses provide a representative overview of bicistronic IRES reporter use. We identified parameters that were reported inconsistently or incompletely, which could hamper data reproduction and interpretation. On the basis of our analyses, we encourage adhering to a number of practices that should improve transparency of bicistronic reporter data presentation and improve methodological descriptions to facilitate data replication.

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“…During transcription, two complete mRNA strands are synthesized from each genomic segment by a strand displacement mechanism. These mRNAs lack a m 7 GTP cap structure and are probably translated by an internal ribosome entry site (IRES)‐driven mechanism (Dobos, ; Rivas‐Aravena et al, ). Genomic replication is semiconservative, and it is carried out within a ribonucleoprotein complex that contains a RNA (−) strand that serves as a template for the synthesis of 3′ truncated forms of the positive strand (Birghan, Mundt, & Gorbalenya, ; Cortez‐San Martín, Villanueva, Jashés, & Sandino, ; Villanueva et al, ).…”

Section: Introductionmentioning

confidence: 99%

Salmon cells SHK‐1 internalize infectious pancreatic necrosis virus by macropinocytosis

Levicán-Asenjo

Soto-Rifo

Aguayo

et al. 2019

Journal of Fish Diseases

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We have previously shown that infectious pancreatic necrosis virus (IPNV) enters the embryo cell line CHSE-214 by macropinocytosis. In this study, we have extended our investigation into SHK-1 cells, a macrophage-like cell line derived from the head kidney of Atlantic salmon, the most economically important host of IPNV. We show that IPNV infection stimulated fluid uptake in SHK-1 cells above the constitutive macropinocytosis level. In addition, upon infection of SHK-1 cells, IPNV produced several changes in actin dynamics, such as protrusions and ruffles, which are important features of macropinocytosis. We also observed that the Na+/H+ pump inhibitor EIPA blocked IPNV infection. On the other hand, IPNV entry was independent of clathrin, a possibility that could not be ruled out in CHSE 214 cells. In order to determine the possible role of accessory factors on the macropinocytic process, we tested several inhibitors that affect components of transduction pathways. While pharmacological intervention of PKI3, PAK-1 and Rac1 did not affect IPNV infection, inhibition of Ras and Rho GTPases as well as Cdc42 resulted in a partial decrease in IPNV infection.Further studies will be required to determine the signalling pathway involved in the macropinocytosis-mediated entry of IPNV into its target cells.

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Study of RNA-A Initiation Translation of The Infectious Pancreatic Necrosis Virus

Cited by 6 publications

References 65 publications

The Infectious Pancreatic Necrosis Virus (IPNV) and its Virulence Determinants: What is Known and What Should be Known

The Infectious Pancreatic Necrosis Virus (IPNV) and its Virulence Determinants: What is Known and What Should be Known

Current Practice in Bicistronic IRES Reporter Use: A Systematic Review

Salmon cells SHK‐1 internalize infectious pancreatic necrosis virus by macropinocytosis

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