RACK1 mediates rewiring of intracellular networks induced by hepatitis C virus infection

Lee, Jae Seung; Tabata, Keisuke; Twu, Woan-Ing; Rahman, Sharif; Kim, Hee Sun; Yu, Jin Bae; Jee, Min Hyeok; Bartenschlager, Ralf; Jang, Sung Key

doi:10.1371/journal.ppat.1008021

Cited by 38 publications

(30 citation statements)

References 65 publications

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“…Reduction of HCV infectivity in eS25- and RACK1-depleted cells could instead result from indirect effects ( 15 , 26 ). For RACK1 this notion is supported by other reports ( 72 , 73 ), and we note that neither of these RPs emerged in genome-wide screens for resistance to HCV infection and replication ( 47 , 74 , 75 ).…”

Section: Resultssupporting

confidence: 88%

A memory of eS25 loss drives resistance phenotypes

Johnson

Lapointe

Ooi

et al. 2020

Nucleic Acids Research

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In order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Remarkably, many cell types can withstand genetic lesions of certain ribosomal protein genes, some of which are linked to diverse cellular phenotypes and human disease. Yet the direct and indirect consequences from these lesions are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the ribosomal proteins RPS25 or RACK1 in a human cell line, as both proteins are implicated in direct translational control. Prompted by the unexpected detection of an off-target ribosome alteration in the RPS25 knockout, we closely interrogated cellular phenotypes. We found that multiple RPS25 knockout clones display viral- and toxin-resistance phenotypes that cannot be rescued by functional cDNA expression, suggesting that RPS25 loss elicits a cell state transition. We characterized this state and found that it underlies pleiotropic phenotypes and has a common rewiring of gene expression. Rescuing RPS25 expression by genomic locus repair failed to correct for the phenotypic and expression hysteresis. Our findings illustrate how the elasticity of cells to a ribosome perturbation can drive specific phenotypic outcomes that are indirectly linked to translation and suggests caution in the interpretation of ribosomal protein gene mutation data.

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Section: Resultssupporting

confidence: 88%

A memory of eS25 loss drives resistance phenotypes

Johnson

Lapointe

Ooi

et al. 2020

Nucleic Acids Research

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“…Thus, the previously observed reduction of HCV infectivity in eS25-and RACK1-depleted cells (Landry et al, 2009;Majzoub et al, 2014) may not be due to defects in IRES-mediated translation and may be accompanied by indirect effects. For RACK1 this notion was supported by two recent reports (Gallo et al, 2018;Lee et al, 2019), and we note that neither of these RPs emerged in genome-wide CRISPR/Cas9 or siRNA screens for resistance to HCV infection and replication (Li et al, 2009;Marceau et al, 2016;Tai et al, 2009). In light of potential broad phenotypic consequences of RP loss, these results dampened our previous rational for mechanistic analyses of RP deletion on HCV IRES function, and catalyzed our pursuit of the cellular consequences of RP loss.…”

Section: Resultssupporting

confidence: 62%

A memory of RPS25 loss drives resistance phenotypes

Johnson

Flynn

Lapointe

et al. 2019

Preprint

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In order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Remarkably, many cell types can withstand the genetic disruption of numerous ribosomal protein genes, indicating that select ribosome variants can sustain cellular life. Genetic alterations of ribosomal protein genes have been further linked to diverse cellular phenotypes and human disease, yet the direct and indirect consequences of sustained alterations in ribosomal protein levels are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the small subunit ribosomal proteins RPS25 or RACK1 in a human haploid cell line. To our surprise, we found that multiple cellular phenotypes previously assumed to result from a direct effect on translation were instead caused by indirect effects. During characterization of ribosomes isolated from the RPS25 knockout cell line, we discovered a partial remodeling of the large subunit via the ribosomal protein paralog eL22L1. Upon further examination, we found that RPS25 knockout clones display irreversible rewiring of viral-and toxin-resistance phenotypes, suggesting that the cells had undergone a stable transition to a new cell state. This new state appears to drive pleiotropic phenotypes and is characterized by a dramatically altered transcriptome and membrane proteome. By homology-directed repair of a RPS25 knockout cell line, we demonstrate that even when RPS25 expression is rescued at the native genomic locus, cells fail to correct for the phenotypic hysteresis. Our results illustrate how the elasticity of cells to a ribosome perturbation can manifest as specific but indirect phenotypic outcomes. The eukaryotic ribosome is comprised of four strands of rRNA and ~80 ribosomal proteins (RPs)

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“…For example, NS5A. Cyclophilin A (CypA), receptor for activated protein C kinase 1 (RACK1) and ATG14L were found to participate in DMV formation for HCV replication by interacting with NS5A [ 39 , 40 , 41 , 42 ], while Surf4 and prolactin regulatory element-binding (PREB) participated by interacting with NS4B [ 43 , 44 ]. PSTPIP2 (Proline-serine-threonine phosphatase interacting protein 2) with membrane-deforming activity and PLA2G4C (cytosolic phospholipase A2 gamma) are also important for HCV RO formation via direct interactions with NS4B and NS5A [ 45 , 46 ].…”

Section: Viral Replication Organelles (Ro)mentioning

confidence: 99%

Hepatitis C Viral Replication Complex

Yang

2021

Viruses

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The life cycle of the hepatitis C virus (HCV) can be divided into several stages, including viral entry, protein translation, RNA replication, viral assembly, and release. HCV genomic RNA replication occurs in the replication organelles (RO) and is tightly linked to ER membrane alterations containing replication complexes (proteins NS3 to NS5B). The amplification of HCV genomic RNA could be regulated by the RO biogenesis, the viral RNA structure (i.e., cis-acting replication elements), and both viral and cellular proteins. Studies on HCV replication have led to the development of direct-acting antivirals (DAAs) targeting the replication complex. This review article summarizes the viral and cellular factors involved in regulating HCV genomic RNA replication and the DAAs that inhibit HCV replication.

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RACK1 mediates rewiring of intracellular networks induced by hepatitis C virus infection

Cited by 38 publications

References 65 publications

A memory of eS25 loss drives resistance phenotypes

A memory of eS25 loss drives resistance phenotypes

A memory of RPS25 loss drives resistance phenotypes

Hepatitis C Viral Replication Complex

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