1
|
Karasik A, Lorenzi HA, DePass AV, Guydosh NR. Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response. Cell Rep 2024; 43:114287. [PMID: 38823018 PMCID: PMC11251458 DOI: 10.1016/j.celrep.2024.114287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 04/05/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024] Open
Abstract
Viral infection triggers several double-stranded RNA (dsRNA) sensors that lead to changes in gene expression in the cell. One of these sensors activates an endonuclease, ribonuclease L (RNase L), that cleaves single-stranded RNA. However, how the resultant widespread RNA fragmentation affects gene expression is not fully understood. Here, we show that this fragmentation induces the ribotoxic stress response via ZAKα, potentially through stalled ribosomes and/or ribosome collisions. The p38 and JNK pathways that are activated as part of this response promote outcomes that inhibit the virus, such as programmed cell death. We also show that RNase L limits the translation of stress-responsive genes. Intriguingly, we found that the activity of the generic endonuclease, RNase A, recapitulates many of the same molecular phenotypes as activated RNase L, demonstrating how widespread RNA cleavage can evoke an antiviral program.
Collapse
Affiliation(s)
- Agnes Karasik
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hernan A Lorenzi
- TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew V DePass
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
2
|
Felipin KP, Paloschi MV, Silva MDS, Ikenohuchi YJ, Santana HM, Setúbal SDS, Rego CMA, Lopes JA, Boeno CN, Serrath SN, De Medeiros EHRT, Pimentel IF, Oliveira AER, Cupolillo E, Cantanhêde LM, Ferreira RDGM, Zuliani JP. Transcriptomics analysis highlights potential ways in human pathogenesis in Leishmania braziliensis infected with the viral endosymbiont LRV1. PLoS Negl Trop Dis 2024; 18:e0012126. [PMID: 38743668 PMCID: PMC11093365 DOI: 10.1371/journal.pntd.0012126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Abstract
The parasite Leishmania (Viannia) braziliensis is widely distributed in Brazil and is one of the main species associated with human cases of different forms of tegumentary leishmaniasis (TL) such as cutaneous leishmaniasis (CL) and mucosal leishmaniasis (ML). The mechanisms underlying the pathogenesis of TL are still not fully understood, but it is known that factors related to the host and the parasite act in a synergistic and relevant way to direct the response to the infection. In the host, macrophages have a central connection with the parasite and play a fundamental role in the defense of the organism due to their ability to destroy intracellular parasites and present antigens. In the parasite, some intrinsic factors related to the species or even the strain analyzed are fundamental for the outcome of the disease. One of them is the presence of Leishmania RNA Virus 1 (LRV1), an endosymbiont virus that parasitizes some species of Leishmania that triggers a cascade of signals leading to a more severe TL phenotype, such as ML. One of the strategies for understanding factors associated with the immune response generated after Leishmania/host interaction is through the analysis of molecular patterns after infection. Thus, the gene expression profile in human monocyte-derived macrophages obtained from healthy donors infected in vitro with L. braziliensis positive (LbLRV1+) and negative (LbLRV1-) for LRV1 was evaluated. For this, the microarray assay was used and 162 differentially expressed genes were identified in the comparison LbLRV1+ vs. LbLRV1-, 126 upregulated genes for the type I and II interferons (IFN) signaling pathway, oligoadenylate synthase OAS/RNAse L, non-genomic actions of vitamin D3 and RIG-I type receptors, and 36 down-regulated. The top 10 downregulated genes along with the top 10 upregulated genes were considered for analysis. Type I interferon (IFNI)- and OAS-related pathways results were validated by RT-qPCR and Th1/Th2/Th17 cytokines were analyzed by Cytometric Bead Array (CBA) and enzyme-linked immunosorbent assay (ELISA). The microarray results validated by RT-qPCR showed differential expression of genes related to IFNI-mediated pathways with overexpression of different genes in cells infected with LbLRV1+ compared to LbLRV1- and to the control. No significant differences were found in cytokine levels between LbLRV1+ vs. LbLRV1- and control. The data suggest the activation of gene signaling pathways associated with the presence of LRV1 has not yet been reported so far. This study demonstrates, for the first time, the activation of the OAS/RNase L signaling pathway and the non-genomic actions of vitamin D3 when comparing infections with LbLRV1+ versus LbLRV1- and the control. This finding emphasizes the role of LRV1 in directing the host's immune response after infection, underlining the importance of identifying LRV1 in patients with TL to assess disease progression.
Collapse
Affiliation(s)
- Kátia Paula Felipin
- Laboratório de Epidemiologia Genética, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
| | - Mauro Valentino Paloschi
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
| | - Milena Daniela Souza Silva
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
| | - Yoda Janaina Ikenohuchi
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
| | - Hallison Mota Santana
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
| | - Sulamita da Silva Setúbal
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
| | - Cristina Matiele Alves Rego
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
| | - Jéssica Amaral Lopes
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
| | - Charles Nunes Boeno
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
| | - Suzanne Nery Serrath
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
| | | | - Iasmin Ferreira Pimentel
- Laboratório de Epidemiologia Genética, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
| | | | - Elisa Cupolillo
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- Instituto Nacional de Epidemiologia da Amazônia Ocidental, EpiAmO, Porto Velho, Brazil
| | - Lilian Motta Cantanhêde
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- Instituto Nacional de Epidemiologia da Amazônia Ocidental, EpiAmO, Porto Velho, Brazil
| | - Ricardo de Godoi Matos Ferreira
- Laboratório de Epidemiologia Genética, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- Instituto Nacional de Epidemiologia da Amazônia Ocidental, EpiAmO, Porto Velho, Brazil
| | - Juliana Pavan Zuliani
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ Rondônia, Porto Velho, Brazil
- Departamento de Medicina, Universidade Federal de Rondônia, UNIR, Porto Velho, Brazil
| |
Collapse
|
3
|
Karasik A, Lorenzi HA, DePass AV, Guydosh NR. Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555507. [PMID: 37693516 PMCID: PMC10491309 DOI: 10.1101/2023.09.01.555507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Viral infection triggers several dsRNA sensors that lead to changes in gene expression in the cell. One of these sensors activates an endonuclease, RNase L, that cleaves single stranded RNA. However, how the resultant widespread RNA fragmentation affects gene expression is not fully understood. Here we show that this fragmentation induces the Ribotoxic Stress Response via ZAKα, potentially through ribosome collisions. The p38 and JNK pathways that are activated as part of this response promote outcomes that inhibit the virus, such as programmed cell death. We also show that RNase L limits the translation of stress-responsive genes, including antiviral IFIT mRNAs and GADD34 that encodes an antagonist of the Integrated Stress Response. Intriguingly, we found the activity of the generic endonuclease, RNase A, recapitulates many of the same molecular phenotypes as activated RNase L, demonstrating how widespread RNA cleavage can evoke an antiviral program.
Collapse
Affiliation(s)
- Agnes Karasik
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Hernan A Lorenzi
- TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Andrew V DePass
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| |
Collapse
|
5
|
Ramnani B, Manivannan P, Jaggernauth S, Malathi K. ABCE1 Regulates RNase L-Induced Autophagy during Viral Infections. Viruses 2021; 13:v13020315. [PMID: 33670646 PMCID: PMC7922175 DOI: 10.3390/v13020315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 12/15/2022] Open
Abstract
Host response to a viral infection includes the production of type I interferon (IFN) and the induction of interferon-stimulated genes that have broad antiviral effects. One of the key antiviral effectors is the IFN-inducible oligoadenylate synthetase/ribonuclease L (OAS/RNase L) pathway, which is activated by double-stranded RNA to synthesize unique oligoadenylates, 2-5A, to activate RNase L. RNase L exerts an antiviral effect by cleaving diverse RNA substrates, limiting viral replication; many viruses have evolved mechanisms to counteract the OAS/RNase L pathway. Here, we show that the ATP-binding cassette E1 (ABCE1) transporter, identified as an inhibitor of RNase L, regulates RNase L activity and RNase L-induced autophagy during viral infections. ABCE1 knockdown cells show increased RNase L activity when activated by 2-5A. Compared to parental cells, the autophagy-inducing activity of RNase L in ABCE1-depleted cells is enhanced with early onset. RNase L activation in ABCE1-depleted cells inhibits cellular proliferation and sensitizes cells to apoptosis. Increased activity of caspase-3 causes premature cleavage of autophagy protein, Beclin-1, promoting a switch from autophagy to apoptosis. ABCE1 regulates autophagy during EMCV infection, and enhanced autophagy in ABCE1 knockdown cells promotes EMCV replication. We identify ABCE1 as a host protein that inhibits the OAS/RNase L pathway by regulating RNase L activity, potentially affecting antiviral effects.
Collapse
|