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Sun ZC, Jiang Z, Xu X, Li M, Zeng Q, Zhu Y, Wang S, Li Y, Tian XL, Hu C. Fish Paralog Proteins RNASEK-a and -b Enhance Type I Interferon Secretion and Promote Apoptosis. Front Immunol 2021; 12:762162. [PMID: 34880860 PMCID: PMC8645942 DOI: 10.3389/fimmu.2021.762162] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022] Open
Abstract
Type I interferon and apoptosis elicit multifaceted effects on host defense and various diseases, such as viral infections and cancers. However, the gene/protein network regulating type I interferon and apoptosis has not been elucidated completely. In this study, we selected grass carp (Ctenopharyngodon idella) as an experimental model to investigate the modulation of RNASEK on the secretion of type I interferon and apoptosis. We first cloned two paralogs RNASEK-a and -b in grass carp, defined three exons in each gene, and found the length of both coding regions is 306 bp with 73.27% of protein homology. The protein sequences of the two paralogs are highly conserved across species. Two proteins were mainly localized in early and late endosomes and endoplasmic reticulum. Further, quantitative real-time PCR demonstrated that dsRNA poly I:C and grass carp reovirus upregulated RNASEK-a and -b in grass carp cells and tissues. Overexpression of RNASEK-a and -b individually induced type I interferon expression and the phosphorylation of IRF3/IRF7 shown by Western blot and immunofluorescent staining, increased Bax/Bcl-2 mRNA ratio, DNA fragmentations, TUNEL-positive cells, and the proportion of Annexin V-positive signals in flow cytometry, and activated eIF2α, opposite to that observed when RNASEK-a and -b were knocked down in multiple cell types. Taken together, we claim for the first time that fish paralog proteins RNASEK-a and -b enhance type I interferon secretion and promote apoptosis, which may be involved in the phosphorylation of IRF3/IRF7 and eIF2α, respectively. Our study reveals a previously unrecognized role of RNASEK as a new positive regulator of type I interferon and apoptosis.
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Affiliation(s)
- Zhi-Chao Sun
- College of Life Science, Nanchang University, Nanchang, China.,Human Aging Research Institute, Nanchang University, Nanchang, China.,Jiangxi Key Laboratory of Human Aging, Nanchang University, Nanchang, China
| | - Zeyin Jiang
- College of Life Science, Nanchang University, Nanchang, China
| | - Xiaowen Xu
- College of Life Science, Nanchang University, Nanchang, China
| | - Meifeng Li
- College of Life Science, Nanchang University, Nanchang, China
| | - Qing Zeng
- College of Life Science, Nanchang University, Nanchang, China
| | - Ying Zhu
- College of Life Science, Nanchang University, Nanchang, China.,Human Aging Research Institute, Nanchang University, Nanchang, China.,Jiangxi Key Laboratory of Human Aging, Nanchang University, Nanchang, China.,Blood Transfusion Department, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Shanghong Wang
- College of Life Science, Nanchang University, Nanchang, China
| | - Yuanyuan Li
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiao-Li Tian
- College of Life Science, Nanchang University, Nanchang, China.,Human Aging Research Institute, Nanchang University, Nanchang, China.,Jiangxi Key Laboratory of Human Aging, Nanchang University, Nanchang, China
| | - Chengyu Hu
- College of Life Science, Nanchang University, Nanchang, China
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Shigematsu M, Kawamura T, Morichika K, Izumi N, Kiuchi T, Honda S, Pliatsika V, Matsubara R, Rigoutsos I, Katsuma S, Tomari Y, Kirino Y. RNase κ promotes robust piRNA production by generating 2',3'-cyclic phosphate-containing precursors. Nat Commun 2021; 12:4498. [PMID: 34301931 PMCID: PMC8302750 DOI: 10.1038/s41467-021-24681-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/01/2021] [Indexed: 11/13/2022] Open
Abstract
In animal germlines, PIWI proteins and the associated PIWI-interacting RNAs (piRNAs) protect genome integrity by silencing transposons. Here we report the extensive sequence and quantitative correlations between 2',3'-cyclic phosphate-containing RNAs (cP-RNAs), identified using cP-RNA-seq, and piRNAs in the Bombyx germ cell line and mouse testes. The cP-RNAs containing 5'-phosphate (P-cP-RNAs) identified by P-cP-RNA-seq harbor highly consistent 5'-end positions as the piRNAs and are loaded onto PIWI protein, suggesting their direct utilization as piRNA precursors. We identified Bombyx RNase Kappa (BmRNase κ) as a mitochondria-associated endoribonuclease which produces cP-RNAs during piRNA biogenesis. BmRNase κ-depletion elevated transposon levels and disrupted a piRNA-mediated sex determination in Bombyx embryos, indicating the crucial roles of BmRNase κ in piRNA biogenesis and embryonic development. Our results reveal a BmRNase κ-engaged piRNA biogenesis pathway, in which the generation of cP-RNAs promotes robust piRNA production.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Takuya Kawamura
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Keisuke Morichika
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Natsuko Izumi
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Shozo Honda
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Venetia Pliatsika
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ryuma Matsubara
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Yukihide Tomari
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.
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Adamopoulos PG, Kontos CK, Scorilas A, Sideris DC. Identification of novel alternative transcripts of the human Ribonuclease κ (RNASEK) gene using 3′ RACE and high-throughput sequencing approaches. Genomics 2020; 112:943-951. [DOI: 10.1016/j.ygeno.2019.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/13/2019] [Accepted: 06/10/2019] [Indexed: 01/25/2023]
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4
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Kladi-Skandali A, Mavridis K, Scorilas A, Sideris DC. Expressional profiling and clinical relevance of RNase κ in prostate cancer: a novel indicator of favorable progression-free survival. J Cancer Res Clin Oncol 2018; 144:2049-2057. [PMID: 30054827 DOI: 10.1007/s00432-018-2719-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/19/2018] [Indexed: 01/26/2023]
Abstract
PURPOSE Considering the unmet need for novel molecular tumor markers capable of improving prostate cancer (CaP) patients' management along with the fruitful results regarding the future use of ribonucleases (RNases) as molecular diagnostic and prognostic markers in CaP, we aimed to study the expressional profile of RNase κ in CaP and BPH and to investigate its clinical significance in CaP. METHODS Total RNA was extracted from 212 prostatic tissue samples (101 BPH and 111 CaP) and, following cDNA synthesis, quantitative real-time PCR (qPCR) was performed for the expressional quantification of RNase κ. Extensive statistical analysis, including bootstrap resampling, was performed to investigate the differential expression of RNase κ in patients with BPH and CaP and its associations with patients' clinicopathological and survival data. RESULTS RNase κ was significantly downregulated (P = 0.002) in CaP patients compared to BPH ones. RNase κ overexpression was associated with decreased risk of CaP development and can discriminate between CaP and BPH independently of serum PSA levels (crude odds ratio = 0.93, P = 0.001). RNase κ upregulation was also associated with less advanced (P = 0.018) and less aggressive (P = 0.001) tumors as well as with longer progression-free survival (PFS) (P = 0.003). Finally univariate bootstrap Cox regression confirmed that RNase κ was associated with favorable prognosis (HR = 0.85, P = 0.002). CONCLUSIONS RNase κ is a biomarker of favorable prognosis in CaP, which is significantly associated with less advanced and aggressive disease, as well as with enhanced PFS.
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Affiliation(s)
- Athina Kladi-Skandali
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Panepistimiopolis, Athens, Greece
| | - Konstantinos Mavridis
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Panepistimiopolis, Athens, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, 70013, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Panepistimiopolis, Athens, Greece
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Panepistimiopolis, Athens, Greece.
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5
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Hackett BA, Yasunaga A, Panda D, Tartell MA, Hopkins KC, Hensley SE, Cherry S. RNASEK is required for internalization of diverse acid-dependent viruses. Proc Natl Acad Sci U S A 2015; 112:7797-802. [PMID: 26056282 PMCID: PMC4485095 DOI: 10.1073/pnas.1424098112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses must gain entry into cells to establish infection. In general, viruses enter either at the plasma membrane or from intracellular endosomal compartments. Viruses that use endosomal pathways are dependent on the cellular factors that control this process; however, these genes have proven to be essential for endogenous cargo uptake, and thus are of limited value for therapeutic intervention. The identification of genes that are selectively required for viral uptake would make appealing drug targets, as their inhibition would block an early step in the life cycle of diverse viruses. At this time, we lack pan-antiviral therapeutics, in part because of our lack of knowledge of such cellular factors. RNAi screening has begun to reveal previously unknown genes that play roles in viral infection. We identified dRNASEK in two genome-wide RNAi screens performed in Drosophila cells against West Nile and Rift Valley Fever viruses. Here we found that ribonuclease kappa (RNASEK) is essential for the infection of human cells by divergent and unrelated positive- and negative-strand-enveloped viruses from the Flaviviridae, Togaviridae, Bunyaviridae, and Orthomyxoviridae families that all enter cells from endosomal compartments. In contrast, RNASEK was dispensable for viruses, including parainfluenza virus 5 and Coxsackie B virus, that enter at the plasma membrane. RNASEK is dispensable for attachment but is required for uptake of these acid-dependent viruses. Furthermore, this requirement appears specific, as general endocytic uptake of transferrin is unaffected in RNASEK-depleted cells. Therefore, RNASEK is a potential host cell Achilles' heel for viral infection.
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Affiliation(s)
- Brent A Hackett
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Ari Yasunaga
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Debasis Panda
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Michael A Tartell
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Kaycie C Hopkins
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | | | - Sara Cherry
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104;
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A subtle alternative splicing event gives rise to a widely expressed human RNase k isoform. PLoS One 2014; 9:e96557. [PMID: 24797913 PMCID: PMC4010519 DOI: 10.1371/journal.pone.0096557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 04/09/2014] [Indexed: 12/30/2022] Open
Abstract
Subtle alternative splicing leads to the formation of RNA variants lacking or including a small number of nucleotides. To date, the impact of subtle alternative splicing phenomena on protein biosynthesis has been studied in frame-preserving incidents. On the contrary, mRNA isoforms derived from frame-shifting events were poorly studied and generally characterized as non-coding. This work provides evidence for a frame-shifting subtle alternative splicing event which results in the production of a novel protein isoform. We applied a combined molecular approach for the cloning and expression analysis of a human RNase κ transcript (RNase κ-02) which lacks four consecutive bases compared to the previously isolated RNase κ isoform. RNase κ-02 mRNA is expressed in all human cell lines tested end encodes the synthesis of a 134-amino-acid protein by utilizing an alternative initiation codon. The expression of RNase κ-02 in the cytoplasm of human cells was verified by Western blot and immunofluorescence analysis using a specific polyclonal antibody developed on the basis of the amino-acid sequence difference between the two protein isoforms. The results presented here show that subtle changes during mRNA splicing can lead to the expression of significantly altered protein isoforms.
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McCormick M, Chen K, Ramaswamy P, Kenyon C. New genes that extend Caenorhabditis elegans' lifespan in response to reproductive signals. Aging Cell 2012; 11:192-202. [PMID: 22081913 DOI: 10.1111/j.1474-9726.2011.00768.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In Caenorhabditis elegans and Drosophila, removing germline stem cells increases lifespan. In C. elegans, this lifespan extension requires DAF-16, a FOXO transcription factor, and DAF-12, a nuclear hormone receptor. To better understand the regulatory relationships between DAF-16 and DAF-12, we used microarray analysis to identify downstream genes. We found that these two transcription factors influence the expression of distinct but overlapping sets of genes in response to loss of the germline. In addition, we identified several new genes that are required for loss of the germline to increase lifespan. One, phi-62, encodes a conserved, predicted RNA-binding protein. PHI-62 influences DAF-16-dependent transcription, possibly by collaborating with TCER-1, a putative transcription elongation factor, and FTT-2, a 14-3-3 protein known to bind DAF-16. Three other genes encode proteins involved in lipid metabolism; one is a triacylglycerol lipase, and another is an acyl-CoA reductase. These genes do not noticeably affect bulk fat storage levels; therefore, we propose a model in which they may influence production of a lifespan-extending signal or metabolite.
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Affiliation(s)
- Mark McCormick
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
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Kiritsi MN, Fragoulis EG, Sideris DC. Essential cysteine residues for human RNase κ catalytic activity. FEBS J 2012; 279:1318-26. [DOI: 10.1111/j.1742-4658.2012.08526.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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A hybrid-specific, polymerase chain reaction-based amplification approach for chromosomal walking. Anal Biochem 2009; 388:342-4. [DOI: 10.1016/j.ab.2009.02.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 02/25/2009] [Accepted: 02/25/2009] [Indexed: 11/21/2022]
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