1
|
Yerlici VT, Astori A, Kejiou NS, Jordan CA, Khosraviani N, Chan JNY, Hakem R, Raught B, Palazzo AF, Mekhail K. SARS-CoV-2 targets ribosomal RNA biogenesis. Cell Rep 2024; 43:113891. [PMID: 38427561 DOI: 10.1016/j.celrep.2024.113891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 10/02/2023] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hinders host gene expression, curbing defenses and licensing viral protein synthesis and virulence. During SARS-CoV-2 infection, the virulence factor non-structural protein 1 (Nsp1) targets the mRNA entry channel of mature cytoplasmic ribosomes, limiting translation. We show that Nsp1 also restrains translation by targeting nucleolar ribosome biogenesis. SARS-CoV-2 infection disrupts 18S and 28S ribosomal RNA (rRNA) processing. Expression of Nsp1 recapitulates the processing defects. Nsp1 abrogates rRNA production without altering the expression of critical processing factors or nucleolar organization. Instead, Nsp1 localizes to the nucleolus, interacting with precursor-rRNA and hindering its maturation separately from the viral protein's role in restricting mature ribosomes. Thus, SARS-CoV-2 Nsp1 limits translation by targeting ribosome biogenesis and mature ribosomes. These findings revise our understanding of how SARS-CoV-2 Nsp1 controls human protein synthesis, suggesting that efforts to counter Nsp1's effect on translation should consider the protein's impact from ribosome manufacturing to mature ribosomes.
Collapse
Affiliation(s)
- V Talya Yerlici
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Audrey Astori
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Nevraj S Kejiou
- Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Chris A Jordan
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Negin Khosraviani
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Janet N Y Chan
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Razqallah Hakem
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1M1, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Alexander F Palazzo
- Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1M1, Canada.
| |
Collapse
|
2
|
Palazzo AF, Qiu Y, Kang YM. mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts. RNA Biol 2024; 21:1-12. [PMID: 38091265 PMCID: PMC10732640 DOI: 10.1080/15476286.2023.2293339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
The division of the cellular space into nucleoplasm and cytoplasm promotes quality control mechanisms that prevent misprocessed mRNAs and junk RNAs from gaining access to the translational machinery. Here, we explore how properly processed mRNAs are distinguished from both misprocessed mRNAs and junk RNAs by the presence or absence of various 'identity features'.
Collapse
Affiliation(s)
| | - Yi Qiu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yoon Mo Kang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
3
|
Lee VW, Kam KQ, Mohamed AR, Musa H, Anandakrishnan P, Shen Q, Palazzo AF, Dale RC, Lim M, Thomas T. Defining the Clinicoradiologic Syndrome of SARS-CoV-2 Acute Necrotizing Encephalopathy: A Systematic Review and 3 New Pediatric Cases. Neurol Neuroimmunol Neuroinflamm 2024; 11:e200186. [PMID: 38086061 PMCID: PMC10758947 DOI: 10.1212/nxi.0000000000200186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/02/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND AND OBJECTIVES We characterize clinical and neuroimaging features of SARS-CoV-2-related acute necrotizing encephalopathy (ANE). METHODS Systematic review of English language publications in PubMed and reference lists between January 1, 2020, and June 30, 2023, in accordance with PRISMA guidelines. Patients with SARS-CoV-2 infection who fulfilled diagnostic criteria for sporadic and genetic ANE were included. RESULTS From 899 articles, 20 cases (17 single case reports and 3 additional cases) were curated for review (50% female; 8 were children). Associated COVID-19 illnesses were febrile upper respiratory tract infections in children while adults had pneumonia (45.6%) and myocarditis (8.2%). Children had early neurologic deterioration (median day 2 in children vs day 4 in adults), seizures (5 (62.5%) children vs 3 of 9 (33.3%) adults), and motor abnormalities (6 of 7 (85.7%) children vs 3 of 7 (42.9%) adults). Eight of 12 (66.7%) adults and 4 (50.0%) children had high-risk ANE scores. Five (62.5%) children and 12 (66.7%) adults had brain lesions bilaterally and symmetrically in the putamina, external capsules, insula cortex, or medial temporal lobes, in addition to typical thalamic lesions of ANE. Hypotension was only seen in adults (30%). Hematologic derangements were common: lymphopenia (66.7%), coagulopathy (60.0%), or elevated D-dimers (100%), C-reactive protein (91.7%), and ferritin (62.5%). A pathogenic heterozygous c/.1754 C>T variant in RANBP2 was present in 2 children: one known to have this before SARS-CoV-2 infection, and a patient tested because the SARS-CoV-2 infection was the second encephalopathic illness. Three other children with no prior encephalopathy or family history of encephalopathy were negative for this variant. Fifteen (75%) received immunotherapy (with IV methylprednisolone, immunoglobulins, tocilizumab, or plasma exchange): 6 (40.0%) with monotherapy and 9 (60.0%) had combination therapy. Deaths were in 8 of 17 with data (47.1%): a 2-month-old male infant and 7 adults (87.5%) of median age 56 years (33-70 years), 4 of whom did not receive immunotherapy. DISCUSSION Children and adults with SARS-CoV-2 ANE have similar clinical features and neuroimaging characteristics. Mortality is high, predominantly in patients not receiving immunotherapy and at the extremes of age.
Collapse
Affiliation(s)
- Vanessa W Lee
- From the Children's Neurosciences (V.W.L., M.L.), Evelina London Children's Hospital at Guy's and St Thomas' NHS Foundation Trust, King's Health Partners Academic Health Science Centre; Infectious Disease Service (K.Q.K.), Department of Paediatrics, KK Women's and Children's Hospital; SingHealth Duke-NUS Paediatrics Academic Clinical Program (ACP) (K.Q.K., T.T.), KK Women's and Children's Hospital, Singapore; Paediatric Neurology Unit (A.R.M., H.M., P.A.), Hospital Tunku Azizah, Kuala Lumpur; Department of Paediatrics (H.M.), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang; Department of Immunology (Q.S.), School of Basic Medical Sciences, Fujian Medical University; Department of Obstetrics (Q.S.), Fujian Maternity and Child Health Hospital, Fuzhou, China; Department of Biochemistry (A.F.P.), University of Toronto, Ontario, Canada; Kids Neuroscience Centre (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney; Clinical School (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia; Department Women and Children's Health (M.L.), School of Life Course Sciences (SoLCS), King's College London, United Kingdom; and Neurology Service (T.T.), Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Kai Qian Kam
- From the Children's Neurosciences (V.W.L., M.L.), Evelina London Children's Hospital at Guy's and St Thomas' NHS Foundation Trust, King's Health Partners Academic Health Science Centre; Infectious Disease Service (K.Q.K.), Department of Paediatrics, KK Women's and Children's Hospital; SingHealth Duke-NUS Paediatrics Academic Clinical Program (ACP) (K.Q.K., T.T.), KK Women's and Children's Hospital, Singapore; Paediatric Neurology Unit (A.R.M., H.M., P.A.), Hospital Tunku Azizah, Kuala Lumpur; Department of Paediatrics (H.M.), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang; Department of Immunology (Q.S.), School of Basic Medical Sciences, Fujian Medical University; Department of Obstetrics (Q.S.), Fujian Maternity and Child Health Hospital, Fuzhou, China; Department of Biochemistry (A.F.P.), University of Toronto, Ontario, Canada; Kids Neuroscience Centre (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney; Clinical School (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia; Department Women and Children's Health (M.L.), School of Life Course Sciences (SoLCS), King's College London, United Kingdom; and Neurology Service (T.T.), Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Ahmad R Mohamed
- From the Children's Neurosciences (V.W.L., M.L.), Evelina London Children's Hospital at Guy's and St Thomas' NHS Foundation Trust, King's Health Partners Academic Health Science Centre; Infectious Disease Service (K.Q.K.), Department of Paediatrics, KK Women's and Children's Hospital; SingHealth Duke-NUS Paediatrics Academic Clinical Program (ACP) (K.Q.K., T.T.), KK Women's and Children's Hospital, Singapore; Paediatric Neurology Unit (A.R.M., H.M., P.A.), Hospital Tunku Azizah, Kuala Lumpur; Department of Paediatrics (H.M.), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang; Department of Immunology (Q.S.), School of Basic Medical Sciences, Fujian Medical University; Department of Obstetrics (Q.S.), Fujian Maternity and Child Health Hospital, Fuzhou, China; Department of Biochemistry (A.F.P.), University of Toronto, Ontario, Canada; Kids Neuroscience Centre (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney; Clinical School (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia; Department Women and Children's Health (M.L.), School of Life Course Sciences (SoLCS), King's College London, United Kingdom; and Neurology Service (T.T.), Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Husna Musa
- From the Children's Neurosciences (V.W.L., M.L.), Evelina London Children's Hospital at Guy's and St Thomas' NHS Foundation Trust, King's Health Partners Academic Health Science Centre; Infectious Disease Service (K.Q.K.), Department of Paediatrics, KK Women's and Children's Hospital; SingHealth Duke-NUS Paediatrics Academic Clinical Program (ACP) (K.Q.K., T.T.), KK Women's and Children's Hospital, Singapore; Paediatric Neurology Unit (A.R.M., H.M., P.A.), Hospital Tunku Azizah, Kuala Lumpur; Department of Paediatrics (H.M.), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang; Department of Immunology (Q.S.), School of Basic Medical Sciences, Fujian Medical University; Department of Obstetrics (Q.S.), Fujian Maternity and Child Health Hospital, Fuzhou, China; Department of Biochemistry (A.F.P.), University of Toronto, Ontario, Canada; Kids Neuroscience Centre (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney; Clinical School (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia; Department Women and Children's Health (M.L.), School of Life Course Sciences (SoLCS), King's College London, United Kingdom; and Neurology Service (T.T.), Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Poorani Anandakrishnan
- From the Children's Neurosciences (V.W.L., M.L.), Evelina London Children's Hospital at Guy's and St Thomas' NHS Foundation Trust, King's Health Partners Academic Health Science Centre; Infectious Disease Service (K.Q.K.), Department of Paediatrics, KK Women's and Children's Hospital; SingHealth Duke-NUS Paediatrics Academic Clinical Program (ACP) (K.Q.K., T.T.), KK Women's and Children's Hospital, Singapore; Paediatric Neurology Unit (A.R.M., H.M., P.A.), Hospital Tunku Azizah, Kuala Lumpur; Department of Paediatrics (H.M.), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang; Department of Immunology (Q.S.), School of Basic Medical Sciences, Fujian Medical University; Department of Obstetrics (Q.S.), Fujian Maternity and Child Health Hospital, Fuzhou, China; Department of Biochemistry (A.F.P.), University of Toronto, Ontario, Canada; Kids Neuroscience Centre (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney; Clinical School (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia; Department Women and Children's Health (M.L.), School of Life Course Sciences (SoLCS), King's College London, United Kingdom; and Neurology Service (T.T.), Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Qingtang Shen
- From the Children's Neurosciences (V.W.L., M.L.), Evelina London Children's Hospital at Guy's and St Thomas' NHS Foundation Trust, King's Health Partners Academic Health Science Centre; Infectious Disease Service (K.Q.K.), Department of Paediatrics, KK Women's and Children's Hospital; SingHealth Duke-NUS Paediatrics Academic Clinical Program (ACP) (K.Q.K., T.T.), KK Women's and Children's Hospital, Singapore; Paediatric Neurology Unit (A.R.M., H.M., P.A.), Hospital Tunku Azizah, Kuala Lumpur; Department of Paediatrics (H.M.), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang; Department of Immunology (Q.S.), School of Basic Medical Sciences, Fujian Medical University; Department of Obstetrics (Q.S.), Fujian Maternity and Child Health Hospital, Fuzhou, China; Department of Biochemistry (A.F.P.), University of Toronto, Ontario, Canada; Kids Neuroscience Centre (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney; Clinical School (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia; Department Women and Children's Health (M.L.), School of Life Course Sciences (SoLCS), King's College London, United Kingdom; and Neurology Service (T.T.), Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Alexander F Palazzo
- From the Children's Neurosciences (V.W.L., M.L.), Evelina London Children's Hospital at Guy's and St Thomas' NHS Foundation Trust, King's Health Partners Academic Health Science Centre; Infectious Disease Service (K.Q.K.), Department of Paediatrics, KK Women's and Children's Hospital; SingHealth Duke-NUS Paediatrics Academic Clinical Program (ACP) (K.Q.K., T.T.), KK Women's and Children's Hospital, Singapore; Paediatric Neurology Unit (A.R.M., H.M., P.A.), Hospital Tunku Azizah, Kuala Lumpur; Department of Paediatrics (H.M.), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang; Department of Immunology (Q.S.), School of Basic Medical Sciences, Fujian Medical University; Department of Obstetrics (Q.S.), Fujian Maternity and Child Health Hospital, Fuzhou, China; Department of Biochemistry (A.F.P.), University of Toronto, Ontario, Canada; Kids Neuroscience Centre (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney; Clinical School (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia; Department Women and Children's Health (M.L.), School of Life Course Sciences (SoLCS), King's College London, United Kingdom; and Neurology Service (T.T.), Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Russell C Dale
- From the Children's Neurosciences (V.W.L., M.L.), Evelina London Children's Hospital at Guy's and St Thomas' NHS Foundation Trust, King's Health Partners Academic Health Science Centre; Infectious Disease Service (K.Q.K.), Department of Paediatrics, KK Women's and Children's Hospital; SingHealth Duke-NUS Paediatrics Academic Clinical Program (ACP) (K.Q.K., T.T.), KK Women's and Children's Hospital, Singapore; Paediatric Neurology Unit (A.R.M., H.M., P.A.), Hospital Tunku Azizah, Kuala Lumpur; Department of Paediatrics (H.M.), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang; Department of Immunology (Q.S.), School of Basic Medical Sciences, Fujian Medical University; Department of Obstetrics (Q.S.), Fujian Maternity and Child Health Hospital, Fuzhou, China; Department of Biochemistry (A.F.P.), University of Toronto, Ontario, Canada; Kids Neuroscience Centre (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney; Clinical School (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia; Department Women and Children's Health (M.L.), School of Life Course Sciences (SoLCS), King's College London, United Kingdom; and Neurology Service (T.T.), Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Ming Lim
- From the Children's Neurosciences (V.W.L., M.L.), Evelina London Children's Hospital at Guy's and St Thomas' NHS Foundation Trust, King's Health Partners Academic Health Science Centre; Infectious Disease Service (K.Q.K.), Department of Paediatrics, KK Women's and Children's Hospital; SingHealth Duke-NUS Paediatrics Academic Clinical Program (ACP) (K.Q.K., T.T.), KK Women's and Children's Hospital, Singapore; Paediatric Neurology Unit (A.R.M., H.M., P.A.), Hospital Tunku Azizah, Kuala Lumpur; Department of Paediatrics (H.M.), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang; Department of Immunology (Q.S.), School of Basic Medical Sciences, Fujian Medical University; Department of Obstetrics (Q.S.), Fujian Maternity and Child Health Hospital, Fuzhou, China; Department of Biochemistry (A.F.P.), University of Toronto, Ontario, Canada; Kids Neuroscience Centre (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney; Clinical School (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia; Department Women and Children's Health (M.L.), School of Life Course Sciences (SoLCS), King's College London, United Kingdom; and Neurology Service (T.T.), Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Terrence Thomas
- From the Children's Neurosciences (V.W.L., M.L.), Evelina London Children's Hospital at Guy's and St Thomas' NHS Foundation Trust, King's Health Partners Academic Health Science Centre; Infectious Disease Service (K.Q.K.), Department of Paediatrics, KK Women's and Children's Hospital; SingHealth Duke-NUS Paediatrics Academic Clinical Program (ACP) (K.Q.K., T.T.), KK Women's and Children's Hospital, Singapore; Paediatric Neurology Unit (A.R.M., H.M., P.A.), Hospital Tunku Azizah, Kuala Lumpur; Department of Paediatrics (H.M.), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang; Department of Immunology (Q.S.), School of Basic Medical Sciences, Fujian Medical University; Department of Obstetrics (Q.S.), Fujian Maternity and Child Health Hospital, Fuzhou, China; Department of Biochemistry (A.F.P.), University of Toronto, Ontario, Canada; Kids Neuroscience Centre (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney; Clinical School (R.C.D.), The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia; Department Women and Children's Health (M.L.), School of Life Course Sciences (SoLCS), King's College London, United Kingdom; and Neurology Service (T.T.), Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| |
Collapse
|
4
|
Li J, Su L, Jiang J, Wang YE, Ling Y, Qiu Y, Yu H, Huang Y, Wu J, Jiang S, Zhang T, Palazzo AF, Shen Q. RanBP2/Nup358 Mediates Sumoylation of STAT1 and Antagonizes Interferon-α-Mediated Antiviral Innate Immunity. Int J Mol Sci 2023; 25:299. [PMID: 38203469 PMCID: PMC10778711 DOI: 10.3390/ijms25010299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Type I interferon (IFN-I)-induced signaling plays a critical role in host antiviral innate immune responses. Despite this, the mechanisms that regulate this signaling pathway have yet to be fully elucidated. The nucleoporin Ran Binding Protein 2 (RanBP2) (also known as Nucleoporin 358 KDa, Nup358) has been implicated in a number of cellular processes, including host innate immune signaling pathways, and is known to influence viral infection. In this study, we documented that RanBP2 mediates the sumoylation of signal transducers and activators of transcription 1 (STAT1) and inhibits IFN-α-induced signaling. Specifically, we found that RanBP2-mediated sumoylation inhibits the interaction of STAT1 and Janus kinase 1 (JAK1), as well as the phosphorylation and nuclear accumulation of STAT1 after IFN-α stimulation, thereby antagonizing the IFN-α-mediated antiviral innate immune signaling pathway and promoting viral infection. Our findings not only provide insights into a novel function of RanBP2 in antiviral innate immunity but may also contribute to the development of new antiviral therapeutic strategies.
Collapse
Affiliation(s)
- Jiawei Li
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (J.L.); (L.S.); (J.J.); (Y.L.); (H.Y.); (Y.H.); (J.W.); (S.J.); (T.Z.)
| | - Lili Su
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (J.L.); (L.S.); (J.J.); (Y.L.); (H.Y.); (Y.H.); (J.W.); (S.J.); (T.Z.)
| | - Jing Jiang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (J.L.); (L.S.); (J.J.); (Y.L.); (H.Y.); (Y.H.); (J.W.); (S.J.); (T.Z.)
| | - Yifan E. Wang
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; (Y.E.W.); (Y.Q.)
| | - Yingying Ling
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (J.L.); (L.S.); (J.J.); (Y.L.); (H.Y.); (Y.H.); (J.W.); (S.J.); (T.Z.)
| | - Yi Qiu
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; (Y.E.W.); (Y.Q.)
| | - Huahui Yu
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (J.L.); (L.S.); (J.J.); (Y.L.); (H.Y.); (Y.H.); (J.W.); (S.J.); (T.Z.)
| | - Yucong Huang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (J.L.); (L.S.); (J.J.); (Y.L.); (H.Y.); (Y.H.); (J.W.); (S.J.); (T.Z.)
| | - Jiangmin Wu
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (J.L.); (L.S.); (J.J.); (Y.L.); (H.Y.); (Y.H.); (J.W.); (S.J.); (T.Z.)
| | - Shan Jiang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (J.L.); (L.S.); (J.J.); (Y.L.); (H.Y.); (Y.H.); (J.W.); (S.J.); (T.Z.)
| | - Tao Zhang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (J.L.); (L.S.); (J.J.); (Y.L.); (H.Y.); (Y.H.); (J.W.); (S.J.); (T.Z.)
| | - Alexander F. Palazzo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; (Y.E.W.); (Y.Q.)
| | - Qingtang Shen
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (J.L.); (L.S.); (J.J.); (Y.L.); (H.Y.); (Y.H.); (J.W.); (S.J.); (T.Z.)
| |
Collapse
|
5
|
Gouy B, Decorsière A, Desgraupes S, Duan W, Ouyang H, Wang YE, Yeh EA, Palazzo AF, Moraes TJ, Nisole S, Arhel NJ. Rapid and inexpensive bedside diagnosis of RAN binding protein 2-associated acute necrotizing encephalopathy. Front Neurol 2023; 14:1282059. [PMID: 38046586 PMCID: PMC10690583 DOI: 10.3389/fneur.2023.1282059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/01/2023] [Indexed: 12/05/2023] Open
Abstract
Acute necrotizing encephalopathy 1 (ANE1) is a very rare disorder associated with a dominant heterozygous mutation in the RANBP2 (RAN binding protein 2) gene. ANE1 is frequently triggered by a febrile infection and characterized by serious and irreversible neurological damage. Although only a few hundred cases have been reported, mutations in RANBP2 are only partially penetrant and can occur de novo, suggesting that their frequency may be higher in some populations. Genetic diagnosis is a lengthy process, potentially delaying definitive diagnosis. We therefore developed a rapid bedside qPCR-based tool for early diagnosis and screening of ANE1 mutations. Primers were designed to specifically assess RANBP2 and not RGPD (RANBP2 and GCC2 protein domains) and discriminate between wild-type or mutant RANBP2. Nasal epithelial cells were obtained from two individuals with known RANBP2 mutations and two healthy control individuals. RANBP2-specific reverse transcription followed by allele-specific primer qPCR amplification confirmed the specific detection of heterozygously expressed mutant RANBP2 in the ANE1 samples. This study demonstrates that allele-specific qPCR can be used as a rapid and inexpensive diagnostic tool for ANE1 using preexisting equipment at local hospitals. It can also be used to screen non-hospitalized family members and at risk-population to better establish the frequency of non-ANE-associated RANBP2 mutations, as well as possible tissue-dependent expression patterns. Systematic review registration The protocol was registered in the international prospective register of systematic reviews (PROSPERO- CRD42023443257).
Collapse
Affiliation(s)
- Benoît Gouy
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, Montpellier, France
- Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Adrien Decorsière
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, Montpellier, France
| | - Sophie Desgraupes
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, Montpellier, France
| | - Wenming Duan
- Program in Translational Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Hong Ouyang
- Program in Translational Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Yifan E. Wang
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - E. Ann Yeh
- Department of Pediatrics, Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Division of Neuroscience and Mental Health, The Hospital for Sick Children Research Institute, University of Toronto, Toronto, ON, Canada
| | | | - Theo J. Moraes
- Program in Translational Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Pediatrics, Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sébastien Nisole
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, Montpellier, France
| | - Nathalie J. Arhel
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, Montpellier, France
| |
Collapse
|
6
|
Bley CJ, Nie S, Mobbs GW, Petrovic S, Gres AT, Liu X, Mukherjee S, Harvey S, Huber FM, Lin DH, Brown B, Tang AW, Rundlet EJ, Correia AR, Chen S, Regmi SG, Stevens TA, Jette CA, Dasso M, Patke A, Palazzo AF, Kossiakoff AA, Hoelz A. Architecture of the cytoplasmic face of the nuclear pore. Science 2022; 376:eabm9129. [PMID: 35679405 DOI: 10.1126/science.abm9129] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION The subcellular compartmentalization of eukaryotic cells requires selective transport of folded proteins and protein-nucleic acid complexes. Embedded in nuclear envelope pores, which are generated by the circumscribed fusion of the inner and outer nuclear membranes, nuclear pore complexes (NPCs) are the sole bidirectional gateways for nucleocytoplasmic transport. The ~110-MDa human NPC is an ~1000-protein assembly that comprises multiple copies of ~34 different proteins, collectively termed nucleoporins. The symmetric core of the NPC is composed of an inner ring encircling the central transport channel and outer rings formed by Y‑shaped coat nucleoporin complexes (CNCs) anchored atop both sides of the nuclear envelope. The outer rings are decorated with compartment‑specific asymmetric nuclear basket and cytoplasmic filament nucleoporins, which establish transport directionality and provide docking sites for transport factors and the small guanosine triphosphatase Ran. The cytoplasmic filament nucleoporins also play an essential role in the irreversible remodeling of messenger ribonucleoprotein particles (mRNPs) as they exit the central transport channel. Unsurprisingly, the NPC's cytoplasmic face represents a hotspot for disease‑associated mutations and is commonly targeted by viral virulence factors. RATIONALE Previous studies established a near-atomic composite structure of the human NPC's symmetric core by combining (i) biochemical reconstitution to elucidate the interaction network between symmetric nucleoporins, (ii) crystal and single-particle cryo-electron microscopy structure determination of nucleoporins and nucleoporin complexes to reveal their three-dimensional shape and the molecular details of their interactions, (iii) quantitative docking in cryo-electron tomography (cryo-ET) maps of the intact human NPC to uncover nucleoporin stoichiometry and positioning, and (iv) cell‑based assays to validate the physiological relevance of the biochemical and structural findings. In this work, we extended our approach to the cytoplasmic filament nucleoporins to reveal the near-atomic architecture of the cytoplasmic face of the human NPC. RESULTS Using biochemical reconstitution, we elucidated the protein-protein and protein-RNA interaction networks of the human and Chaetomium thermophilum cytoplasmic filament nucleoporins, establishing an evolutionarily conserved heterohexameric cytoplasmic filament nucleoporin complex (CFNC) held together by a central heterotrimeric coiled‑coil hub that tethers two separate mRNP‑remodeling complexes. Further biochemical analysis and determination of a series of crystal structures revealed that the metazoan‑specific cytoplasmic filament nucleoporin NUP358 is composed of 16 distinct domains, including an N‑terminal S‑shaped α‑helical solenoid followed by a coiled‑coil oligomerization element, numerous Ran‑interacting domains, an E3 ligase domain, and a C‑terminal prolyl‑isomerase domain. Physiologically validated quantitative docking into cryo-ET maps of the intact human NPC revealed that pentameric NUP358 bundles, conjoined by the oligomerization element, are anchored through their N‑terminal domains to the central stalk regions of the CNC, projecting flexibly attached domains as far as ~600 Å into the cytoplasm. Using cell‑based assays, we demonstrated that NUP358 is dispensable for the architectural integrity of the assembled interphase NPC and RNA export but is required for efficient translation. After NUP358 assignment, the remaining 4-shaped cryo‑ET density matched the dimensions of the CFNC coiled‑coil hub, in close proximity to an outer-ring NUP93. Whereas the N-terminal NUP93 assembly sensor motif anchors the properly assembled related coiled‑coil channel nucleoporin heterotrimer to the inner ring, biochemical reconstitution confirmed that the NUP93 assembly sensor is reused in anchoring the CFNC to the cytoplasmic face of the human NPC. By contrast, two C. thermophilum CFNCs are anchored by a divergent mechanism that involves assembly sensors located in unstructured portions of two CNC nucleoporins. Whereas unassigned cryo‑ET density occupies the NUP358 and CFNC binding sites on the nuclear face, docking of the nuclear basket component ELYS established that the equivalent position on the cytoplasmic face is unoccupied, suggesting that mechanisms other than steric competition promote asymmetric distribution of nucleoporins. CONCLUSION We have substantially advanced the biochemical and structural characterization of the asymmetric nucleoporins' architecture and attachment at the cytoplasmic and nuclear faces of the NPC. Our near‑atomic composite structure of the human NPC's cytoplasmic face provides a biochemical and structural framework for elucidating the molecular basis of mRNP remodeling, viral virulence factor interference with NPC function, and the underlying mechanisms of nucleoporin diseases at the cytoplasmic face of the NPC. [Figure: see text].
Collapse
Affiliation(s)
- Christopher J Bley
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Si Nie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - George W Mobbs
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Stefan Petrovic
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Anna T Gres
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Xiaoyu Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sho Harvey
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ferdinand M Huber
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Bonnie Brown
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Aaron W Tang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Emily J Rundlet
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ana R Correia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Shane Chen
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Saroj G Regmi
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Taylor A Stevens
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Claudia A Jette
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alina Patke
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| |
Collapse
|
7
|
Lee ES, Smith HW, Wolf EJ, Guvenek A, Wang YE, Emili A, Tian B, Palazzo AF. ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motifs within nuclear speckles. RNA 2022; 28:878-894. [PMID: 35351812 PMCID: PMC9074902 DOI: 10.1261/rna.079104.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/12/2022] [Indexed: 05/22/2023]
Abstract
Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5' splice site (5'SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Using high-throughput sequencing of cellular fractions, we now demonstrate that IPA transcripts require the zinc finger protein ZFC3H1 for their nuclear retention and degradation. Using reporter mRNAs, we demonstrate that ZFC3H1 promotes the nuclear retention of mRNAs with intact 5'SS motifs by sequestering them into nuclear speckles. Furthermore, we find that U1-70K, a component of the spliceosomal U1 snRNP, is also required for the nuclear retention of these reporter mRNAs and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of reporter mRNAs with 5'SS motifs. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs by sequestering them into nuclear speckles.
Collapse
Affiliation(s)
- Eliza S Lee
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Harrison W Smith
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Eric J Wolf
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Aysegul Guvenek
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Yifan E Wang
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Andrew Emili
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Bin Tian
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | | |
Collapse
|
8
|
Abstract
Dominant missense mutations in RanBP2/Nup358 cause Acute Necrotizing Encephalopathy (ANE), a pediatric disease where seemingly healthy individuals develop a cytokine storm that is restricted to the central nervous system in response to viral infection. Untreated, this condition leads to seizures, coma, long-term neurological damage and a high rate of mortality. The exact mechanism by which RanBP2 mutations contribute to the development of ANE remains elusive. In November 2021, a number of clinicians and basic scientists presented their work on this disease and on the interactions between RanBP2/Nup358, viral infections, the innate immune response and other cellular processes.
Collapse
Affiliation(s)
| | - Jomon Joseph
- National Centre for Cell Science, S.P. Pune University Campus, Pune, India
| | - Ming Lim
- Children's Neurosciences, Evelina London Children's Hospital, and the Department of Women and Children's Health, King's College London, London, UK
| | - Kiran T Thakur
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, and the New York Presbyterian Hospital, New York
| |
Collapse
|
9
|
Jiang J, Wang YE, Palazzo AF, Shen Q. Roles of Nucleoporin RanBP2/Nup358 in Acute Necrotizing Encephalopathy Type 1 (ANE1) and Viral Infection. Int J Mol Sci 2022; 23:ijms23073548. [PMID: 35408907 PMCID: PMC8998323 DOI: 10.3390/ijms23073548] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/23/2022] Open
Abstract
Ran Binding Protein 2 (RanBP2 or Nucleoporin358) is one of the main components of the cytoplasmic filaments of the nuclear pore complex. Mutations in the RANBP2 gene are associated with acute necrotizing encephalopathy type 1 (ANE1), a rare condition where patients experience a sharp rise in cytokine production in response to viral infection and undergo hyperinflammation, seizures, coma, and a high rate of mortality. Despite this, it remains unclear howRanBP2 and its ANE1-associated mutations contribute to pathology. Mounting evidence has shown that RanBP2 interacts with distinct viruses to regulate viral infection. In addition, RanBP2 may regulate innate immune response pathways. This review summarizes recent advances in our understanding of how mutations in RANBP2 contribute to ANE1 and discusses how RanBP2 interacts with distinct viruses and affects viral infection. Recent findings indicate that RanBP2 might be an important therapeutic target, not only in the suppression of ANE1-driven cytokine storms, but also to combat hyperinflammation in response to viral infections.
Collapse
Affiliation(s)
- Jing Jiang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China;
| | - Yifan E. Wang
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada;
| | - Alexander F. Palazzo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada;
- Correspondence: (A.F.P.); (Q.S.)
| | - Qingtang Shen
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China;
- Correspondence: (A.F.P.); (Q.S.)
| |
Collapse
|
10
|
Abstract
With the discovery of the double helical structure of DNA, a shift occurred in how biologists investigated questions surrounding cellular processes, such as protein synthesis. Instead of viewing biological activity through the lens of chemical reactions, this new field used biological information to gain a new profound view of how biological systems work. Molecular biologists asked new types of questions that would have been inconceivable to the older generation of researchers, such as how cellular machineries convert inherited biological information into functional molecules like proteins. This new focus on biological information also gave molecular biologists a way to link their findings to concepts developed by genetics and the modern synthesis. However, by the late 1960s this all changed. Elevated rates of mutation, unsustainable genetic loads, and high levels of variation in populations, challenged Darwinian evolution, a central tenant of the modern synthesis, where adaptation was the main driver of evolutionary change. Building on these findings, Motoo Kimura advanced the neutral theory of molecular evolution, which advocates that selection in multicellular eukaryotes is weak and that most genomic changes are neutral and due to random drift. This was further elaborated by Jack King and Thomas Jukes, in their paper “Non-Darwinian Evolution”, where they pointed out that the observed changes seen in proteins and the types of polymorphisms observed in populations only become understandable when we take into account biochemistry and Kimura’s new theory. Fifty years later, most molecular biologists remain unaware of these fundamental advances. Their adaptionist viewpoint fails to explain data collected from new powerful technologies which can detect exceedingly rare biochemical events. For example, high throughput sequencing routinely detects RNA transcripts being produced from almost the entire genome yet are present less than one copy per thousand cells and appear to lack any function. Molecular biologists must now reincorporate ideas from classical biochemistry and absorb modern concepts from molecular evolution, to craft a new lens through which they can evaluate the functionality of transcriptional units, and make sense of our messy, intricate, and complicated genome.
Collapse
|
11
|
Go CD, Knight JDR, Rajasekharan A, Rathod B, Hesketh GG, Abe KT, Youn JY, Samavarchi-Tehrani P, Zhang H, Zhu LY, Popiel E, Lambert JP, Coyaud É, Cheung SWT, Rajendran D, Wong CJ, Antonicka H, Pelletier L, Palazzo AF, Shoubridge EA, Raught B, Gingras AC. Author Correction: A proximity-dependent biotinylation map of a human cell. Nature 2022; 602:E16. [PMID: 35017685 DOI: 10.1038/s41586-021-04308-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christopher D Go
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - James D R Knight
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Archita Rajasekharan
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Bhavisha Rathod
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Geoffrey G Hesketh
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Kento T Abe
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ji-Young Youn
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Payman Samavarchi-Tehrani
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Hui Zhang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Lucie Y Zhu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Evelyn Popiel
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Medicine, Cancer Research Centre, Big Data Research Centre, Université Laval, Quebec City, Quebec, Canada.,CHU de Québec-Université Laval Research Center (CHUL), Quebec City, Quebec, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,PRISM INSERM U1192, Université de Lille, Villeneuve d'Ascq, France
| | - Sally W T Cheung
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Dushyandi Rajendran
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Hana Antonicka
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Eric A Shoubridge
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
12
|
Shen Q, Wang YE, Palazzo AF. Crosstalk between nucleocytoplasmic trafficking and the innate immune response to viral infection. J Biol Chem 2021; 297:100856. [PMID: 34097873 PMCID: PMC8254040 DOI: 10.1016/j.jbc.2021.100856] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
The nuclear pore complex is the sole gateway connecting the nucleoplasm and cytoplasm. In humans, the nuclear pore complex is one of the largest multiprotein assemblies in the cell, with a molecular mass of ∼110 MDa and consisting of 8 to 64 copies of about 34 different nuclear pore proteins, termed nucleoporins, for a total of 1000 subunits per pore. Trafficking events across the nuclear pore are mediated by nuclear transport receptors and are highly regulated. The nuclear pore complex is also used by several RNA viruses and almost all DNA viruses to access the host cell nucleoplasm for replication. Viruses hijack the nuclear pore complex, and nuclear transport receptors, to access the nucleoplasm where they replicate. In addition, the nuclear pore complex is used by the cell innate immune system, a network of signal transduction pathways that coordinates the first response to foreign invaders, including viruses and other pathogens. Several branches of this response depend on dynamic signaling events that involve the nuclear translocation of downstream signal transducers. Mounting evidence has shown that these signaling cascades, especially those steps that involve nucleocytoplasmic trafficking events, are targeted by viruses so that they can evade the innate immune system. This review summarizes how nuclear pore proteins and nuclear transport receptors contribute to the innate immune response and highlights how viruses manipulate this cellular machinery to favor infection. A comprehensive understanding of nuclear pore proteins in antiviral innate immunity will likely contribute to the development of new antiviral therapeutic strategies.
Collapse
Affiliation(s)
- Qingtang Shen
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
| | - Yifan E Wang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
13
|
Lee ES, Wolf EJ, Ihn SSJ, Smith HW, Emili A, Palazzo AF. TPR is required for the efficient nuclear export of mRNAs and lncRNAs from short and intron-poor genes. Nucleic Acids Res 2021; 48:11645-11663. [PMID: 33091126 PMCID: PMC7672458 DOI: 10.1093/nar/gkaa919] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/21/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022] Open
Abstract
While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here, we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export in human cells. By sequencing mRNA from the nucleus and cytosol of control and TPR-depleted cells, we provide evidence that TPR is required for the efficient nuclear export of mRNAs and lncRNAs that are generated from short transcripts that tend to have few introns, and we validate this with reporter constructs. Moreover, in TPR-depleted cells reporter mRNAs generated from short transcripts accumulate in nuclear speckles and are bound to Nxf1. These observations suggest that TPR acts downstream of Nxf1 recruitment and may allow mRNAs to leave nuclear speckles and properly dock with the nuclear pore. In summary, our study provides one of the first examples of a factor that is specifically required for the nuclear export of intronless and intron-poor mRNAs and lncRNAs.
Collapse
Affiliation(s)
- Eliza S Lee
- University of Toronto, Department of Biochemistry, Canada
| | - Eric J Wolf
- University of Toronto, Department of Molecular Genetics, Canada
| | - Sean S J Ihn
- University of Toronto, Department of Biochemistry, Canada
| | | | - Andrew Emili
- University of Toronto, Department of Molecular Genetics, Canada.,Boston University School of Medicine, Department of Biochemistry, Boston, MA, USA
| | | |
Collapse
|
14
|
Shen Q, Wang YE, Truong M, Mahadevan K, Wu JJ, Zhang H, Li J, Smith HW, Smibert CA, Palazzo AF. RanBP2/Nup358 enhances miRNA activity by sumoylating Argonautes. PLoS Genet 2021; 17:e1009378. [PMID: 33600493 PMCID: PMC7924746 DOI: 10.1371/journal.pgen.1009378] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 03/02/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023] Open
Abstract
Mutations in RanBP2 (also known as Nup358), one of the main components of the cytoplasmic filaments of the nuclear pore complex, contribute to the overproduction of acute necrotizing encephalopathy (ANE1)-associated cytokines. Here we report that RanBP2 represses the translation of the interleukin 6 (IL6) mRNA, which encodes a cytokine that is aberrantly up-regulated in ANE1. Our data indicates that soon after its production, the IL6 messenger ribonucleoprotein (mRNP) recruits Argonautes bound to let-7 microRNA. After this mRNP is exported to the cytosol, RanBP2 sumoylates mRNP-associated Argonautes, thereby stabilizing them and enforcing mRNA silencing. Collectively, these results support a model whereby RanBP2 promotes an mRNP remodelling event that is critical for the miRNA-mediated suppression of clinically relevant mRNAs, such as IL6.
Collapse
Affiliation(s)
- Qingtang Shen
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yifan E. Wang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Mathew Truong
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kohila Mahadevan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jingze J. Wu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Hui Zhang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jiawei Li
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Harrison W. Smith
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Craig A. Smibert
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | | |
Collapse
|
15
|
Palazzo AF, Kang YM. GC-content biases in protein-coding genes act as an "mRNA identity" feature for nuclear export. Bioessays 2020; 43:e2000197. [PMID: 33165929 DOI: 10.1002/bies.202000197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 01/11/2023]
Abstract
It has long been observed that human protein-coding genes have a particular distribution of GC-content: the 5' end of these genes has high GC-content while the 3' end has low GC-content. In 2012, it was proposed that this pattern of GC-content could act as an mRNA identity feature that would lead to it being better recognized by the cellular machinery to promote its nuclear export. In contrast, junk RNA, which largely lacks this feature, would be retained in the nucleus and targeted for decay. Now two recent papers have provided evidence that GC-content does promote the nuclear export of many mRNAs in human cells.
Collapse
Affiliation(s)
- Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Yoon Mo Kang
- Department of Biochemistry, University of Toronto, Toronto, ON, M5G 1M1, Canada
| |
Collapse
|
16
|
Palazzo AF, Koonin EV. Functional Long Non-coding RNAs Evolve from Junk Transcripts. Cell 2020; 183:1151-1161. [PMID: 33068526 DOI: 10.1016/j.cell.2020.09.047] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/20/2020] [Accepted: 09/17/2020] [Indexed: 12/30/2022]
Abstract
Transcriptome studies reveal pervasive transcription of complex genomes, such as those of mammals. Despite popular arguments for functionality of most, if not all, of these transcripts, genome-wide analysis of selective constraints indicates that most of the produced RNA are junk. However, junk is not garbage. On the contrary, junk transcripts provide the raw material for the evolution of diverse long non-coding (lnc) RNAs by non-adaptive mechanisms, such as constructive neutral evolution. The generation of many novel functional entities, such as lncRNAs, that fuels organismal complexity does not seem to be driven by strong positive selection. Rather, the weak selection regime that dominates the evolution of most multicellular eukaryotes provides ample material for functional innovation with relatively little adaptation involved.
Collapse
Affiliation(s)
- Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| |
Collapse
|
17
|
Affiliation(s)
- Stefan Linquist
- Department of Philosophy, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - W. Ford Doolittle
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | |
Collapse
|
18
|
Abstract
In eukaryotes, most mRNAs that encode secretory or membrane-bound proteins are translated by ribosomes associated with the surface of the endoplasmic reticulum (ER). Other such mRNAs are tethered to the ER by mRNA receptors. However, there has been much debate as to whether all mRNAs, regardless of their encoded polypeptide, are anchored to the ER at some low level. Here we describe a protocol to visualize ER-associated mRNAs in tissue culture cells by single-molecule fluorescence in situ hybridization (smFISH). Using this protocol, we have established that a subset of all mRNAs, regardless of whether they encode secretory or cytosolic proteins, are ER associated in a ribosome-dependent manner.
Collapse
Affiliation(s)
- Jingze J Wu
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | | |
Collapse
|
19
|
Voigt F, Zhang H, Cui XA, Triebold D, Liu AX, Eglinger J, Lee ES, Chao JA, Palazzo AF. Single-Molecule Quantification of Translation-Dependent Association of mRNAs with the Endoplasmic Reticulum. Cell Rep 2019; 21:3740-3753. [PMID: 29281824 DOI: 10.1016/j.celrep.2017.12.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 09/29/2017] [Accepted: 12/04/2017] [Indexed: 10/25/2022] Open
Abstract
It is well established that mRNAs encoding secretory or membrane-bound proteins are translated on the surface of the endoplasmic reticulum (ER). The extent to which mRNAs that encode cytosolic proteins associate with the ER, however, remains controversial. To address this question, we quantified the number of cytosolic protein-encoding mRNAs that co-localize with the ER using single-molecule RNA imaging in fixed and living cells. We found that a small but significant number of mRNAs that encode cytosolic proteins associate with the ER and show that this interaction is translation dependent. Furthermore, we demonstrate that cytosolic protein-encoding transcripts can remain on the ER with dwell times consistent with multiple rounds of translation and have higher ribosome occupancies than transcripts translated in the cytosol. These results advance our understanding of the diversity and dynamics of localized translation on the ER.
Collapse
Affiliation(s)
- Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Hui Zhang
- Department of Biochemistry, University of Toronto, 1 King's College Circle, MSB Room 5336, Toronto, ON M5S 1A8, Canada
| | - Xianying A Cui
- Department of Biochemistry, University of Toronto, 1 King's College Circle, MSB Room 5336, Toronto, ON M5S 1A8, Canada
| | - Désirée Triebold
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Ai Xin Liu
- Department of Biochemistry, University of Toronto, 1 King's College Circle, MSB Room 5336, Toronto, ON M5S 1A8, Canada
| | - Jan Eglinger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Eliza S Lee
- Department of Biochemistry, University of Toronto, 1 King's College Circle, MSB Room 5336, Toronto, ON M5S 1A8, Canada
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
| | - Alexander F Palazzo
- Department of Biochemistry, University of Toronto, 1 King's College Circle, MSB Room 5336, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
20
|
Chan JTH, Liu Y, Khan S, St-Germain JR, Zou C, Leung LYT, Yang J, Shi M, Grunebaum E, Campisi P, Propst EJ, Holler T, Bar-Or A, Wither JE, Cairo CW, Moran MF, Palazzo AF, Cooper MD, Ehrhardt GRA. A tyrosine sulfation-dependent HLA-I modification identifies memory B cells and plasma cells. Sci Adv 2018; 4:eaar7653. [PMID: 30417091 PMCID: PMC6221509 DOI: 10.1126/sciadv.aar7653] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
Memory B cells and plasma cells are antigen-experienced cells tasked with the maintenance of humoral protection. Despite these prominent functions, definitive cell surface markers have not been identified for these cells. We report here the isolation and characterization of the monoclonal variable lymphocyte receptor B (VLRB) N8 antibody from the evolutionarily distant sea lamprey that specifically recognizes memory B cells and plasma cells in humans. Unexpectedly, we determined that VLRB N8 recognizes the human leukocyte antigen-I (HLA-I) antigen in a tyrosine sulfation-dependent manner. Furthermore, we observed increased binding of VLRB N8 to memory B cells in individuals with autoimmune disorders multiple sclerosis and systemic lupus erythematosus. Our study indicates that lamprey VLR antibodies uniquely recognize a memory B cell- and plasma cell-specific posttranslational modification of HLA-I, the expression of which is up-regulated during B cell activation.
Collapse
Affiliation(s)
- Justin T. H. Chan
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Yanling Liu
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Srijit Khan
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | | | - Chunxia Zou
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | | | - Judi Yang
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Mengyao Shi
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Eyal Grunebaum
- Division of Immunology and Allergy, Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Paolo Campisi
- Department of Otolaryngology-Head and Neck Surgery, Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Evan J. Propst
- Department of Otolaryngology-Head and Neck Surgery, Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Theresa Holler
- Department of Otolaryngology-Head and Neck Surgery, Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Amit Bar-Or
- Department of Neurology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Joan E. Wither
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Christopher W. Cairo
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Michael F. Moran
- Department of Molecular Genetics, Hospital for Sick Children, Toronto, ON, Canada
| | | | - Max D. Cooper
- Department of Pathology and Laboratory Medicine and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | | |
Collapse
|
21
|
Abstract
Eukaryotes are divided into two major compartments: the nucleus where RNA is synthesized and processed, and the cytoplasm, where mRNA is translated into proteins. Although many different RNAs are made, only a subset is allowed access to the cytoplasm, primarily RNAs involved in protein synthesis (mRNA, tRNA, and rRNA). In contrast, nuclear retained transcripts are mostly long non-coding RNAs (lncRNAs) whose role in cell physiology has been a source of much investigation in the past few years. In addition, it is likely that many non-functional RNAs, which arise by spurious transcription and misprocessing of functional RNAs, are also retained in the nucleus and degraded. In this review, the main sequence features that dictate whether any particular mRNA or lncRNA is a substrate for retention in the nucleus, or export to the cytoplasm, are discussed. Although nuclear export is promoted by RNA-splicing due to the fact that the spliceosome can help recruit export factors to the mature RNA, nuclear export does not require splicing. Indeed, most stable unspliced transcripts are well exported and associate with these same export factors in a splicing-independent manner. In contrast, nuclear retention is promoted by specialized cis-elements found in certain RNAs. This new understanding of the determinants of nuclear retention and cytoplasmic export provides a deeper understanding of how information flow is regulated in eukaryotic cells. Ultimately these processes promote the evolution of complexity in eukaryotes by shaping the genomic content through constructive neutral evolution.
Collapse
|
22
|
Lee ES, Palazzo AF. Assessing mRNA nuclear export in mammalian cells by microinjection. Methods 2017; 126:76-85. [DOI: 10.1016/j.ymeth.2017.05.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/23/2017] [Accepted: 05/29/2017] [Indexed: 11/17/2022] Open
|
23
|
Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ, Roth FP. A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification. RNA 2017; 23:270-283. [PMID: 27994090 PMCID: PMC5311483 DOI: 10.1261/rna.059105.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/14/2016] [Indexed: 06/01/2023]
Abstract
Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: Genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with >80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 5' proximal-intron-minus-like-coding regions ("5IM" transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5' cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the exon junction complex (EJC) at noncanonical 5' proximal positions. Finally, N1-methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising ∼20% of human transcripts. This class is defined by depletion of 5' proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N1-methyladenosines in the early coding region, and enrichment for noncanonical binding by the EJC.
Collapse
Affiliation(s)
- Can Cenik
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Hon Nian Chua
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto M5S 3E1, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto M5G 1X5, Ontario, Canada
- DataRobot, Inc., Boston, Massachusetts 02109, USA
| | - Guramrit Singh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Abdalla Akef
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Melissa J Moore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Frederick P Roth
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto M5S 3E1, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto M5G 1X5, Ontario, Canada
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston 02215, Massachusetts, USA
- The Canadian Institute for Advanced Research, Toronto M5G 1Z8, Ontario, Canada
| |
Collapse
|
24
|
Kejiou NS, Palazzo AF. mRNA localization as a rheostat to regulate subcellular gene expression. WIREs RNA 2017; 8. [DOI: 10.1002/wrna.1416] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Nevraj S. Kejiou
- Department of Biochemistry; University of Toronto; Toronto Canada
| | | |
Collapse
|
25
|
Affiliation(s)
| | - Mathew Truong
- Department of Biochemistry; University of Toronto; Toronto ON Canada
| |
Collapse
|
26
|
Akef A, Lee ES, Palazzo AF. Splicing promotes the nuclear export of β-globin mRNA by overcoming nuclear retention elements. RNA 2015; 21:1908-20. [PMID: 26362019 PMCID: PMC4604431 DOI: 10.1261/rna.051987.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/20/2015] [Indexed: 05/14/2023]
Abstract
Most current models of mRNA nuclear export in vertebrate cells assume that an mRNA must have specialized signals in order to be exported from the nucleus. Under such a scenario, mRNAs that lack these specialized signals would be shunted into a default pathway where they are retained in the nucleus and eventually degraded. These ideas were based on the selective use of model mRNA reporters. For example, it has been shown that splicing promotes the nuclear export of certain model mRNAs, such as human β-globin, and that in the absence of splicing, the cDNA-derived mRNA is retained in the nucleus and degraded. Here we provide evidence that β-globin mRNA contains an element that actively retains it in the nucleus and degrades it. Interestingly, this nuclear retention activity can be overcome by increasing the length of the mRNA or by splicing. Our results suggest that contrary to many current models, the default pathway for most intronless RNAs is to be exported from the nucleus, unless the RNA contains elements that actively promote its nuclear retention.
Collapse
Affiliation(s)
- Abdalla Akef
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Eliza S Lee
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
27
|
Cui XA, Zhang H, Ilan L, Liu AX, Kharchuk I, Palazzo AF. mRNA encoding Sec61β, a tail-anchored protein, is localized on the endoplasmic reticulum. J Cell Sci 2015; 128:3398-410. [PMID: 26272916 PMCID: PMC4582399 DOI: 10.1242/jcs.168583] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 08/04/2015] [Indexed: 12/30/2022] Open
Abstract
Although one pathway for the post-translational targeting of tail-anchored proteins to the endoplasmic reticulum (ER) has been well defined, it is unclear whether additional pathways exist. Here, we provide evidence that a subset of mRNAs encoding tail-anchored proteins, including Sec61β and nesprin-2, is partially localized to the surface of the ER in mammalian cells. In particular, Sec61b mRNA can be targeted to, and later maintained on, the ER using both translation-dependent and -independent mechanisms. Our data suggests that this process is independent of p180 (also known as RRBP1), a known mRNA receptor on the ER, and the transmembrane domain recognition complex (TRC) pathway components, TRC40 (also known as ASNA1) and BAT3 (also known as BAG6). In addition, our data indicates that Sec61b mRNA might access translocon-bound ribosomes. Our results show that certain tail-anchored proteins are likely to be synthesized directly on the ER, and this facilitates their membrane insertion. Thus, it is clear that mammalian cells utilize multiple mechanisms to ensure efficient targeting of tail-anchored proteins to the surface of the ER. Highlighted Article: The mRNA encoding certain tail-anchored proteins is directly localized to the surface of the endoplasmic reticulum, facilitating the insertion of newly synthesized proteins into the membrane.
Collapse
Affiliation(s)
- Xianying A Cui
- University of Toronto, Department of Biochemistry, 1 King's College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| | - Hui Zhang
- University of Toronto, Department of Biochemistry, 1 King's College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| | - Lena Ilan
- University of Toronto, Department of Biochemistry, 1 King's College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| | - Ai Xin Liu
- University of Toronto, Department of Biochemistry, 1 King's College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| | - Iryna Kharchuk
- University of Toronto, Department of Biochemistry, 1 King's College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| | - Alexander F Palazzo
- University of Toronto, Department of Biochemistry, 1 King's College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| |
Collapse
|
28
|
Abstract
In eukaryotes, mRNAs are synthesized in the nucleus and then exported to the cytoplasm where they are translated into proteins. We have mapped an element, which when present in the 3’terminal exon or in an unspliced mRNA, inhibits mRNA nuclear export. This element has the same sequence as the consensus 5’splice site motif that is used to define the start of introns. Previously it was shown that when this motif is retained in the mRNA, it causes defects in 3’cleavage and polyadenylation and promotes mRNA decay. Our new data indicates that this motif also inhibits nuclear export and promotes the targeting of transcripts to nuclear speckles, foci within the nucleus which have been linked to splicing. The motif, however, does not disrupt splicing or the recruitment of UAP56 or TAP/Nxf1 to the RNA, which are normally required for nuclear export. Genome wide analysis of human mRNAs, lncRNA and eRNAs indicates that this motif is depleted from naturally intronless mRNAs and eRNAs, but less so in lncRNAs. This motif is also depleted from the beginning and ends of the 3’terminal exons of spliced mRNAs, but less so for lncRNAs. Our data suggests that the presence of the 5’splice site motif in mature RNAs promotes their nuclear retention and may help to distinguish mRNAs from misprocessed transcripts and transcriptional noise.
Collapse
Affiliation(s)
- Eliza S. Lee
- Department of Biochemistry, University of Toronto, 1 King’s College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| | - Abdalla Akef
- Department of Biochemistry, University of Toronto, 1 King’s College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| | - Kohila Mahadevan
- Department of Biochemistry, University of Toronto, 1 King’s College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| | - Alexander F. Palazzo
- Department of Biochemistry, University of Toronto, 1 King’s College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
- * E-mail:
| |
Collapse
|
29
|
Abstract
The genomes of large multicellular eukaryotes are mostly comprised of non-protein coding DNA. Although there has been much agreement that a small fraction of these genomes has important biological functions, there has been much debate as to whether the rest contributes to development and/or homeostasis. Much of the speculation has centered on the genomic regions that are transcribed into RNA at some low level. Unfortunately these RNAs have been arbitrarily assigned various names, such as “intergenic RNA,” “long non-coding RNAs” etc., which have led to some confusion in the field. Many researchers believe that these transcripts represent a vast, unchartered world of functional non-coding RNAs (ncRNAs), simply because they exist. However, there are reasons to question this Panglossian view because it ignores our current understanding of how evolution shapes eukaryotic genomes and how the gene expression machinery works in eukaryotic cells. Although there are undoubtedly many more functional ncRNAs yet to be discovered and characterized, it is also likely that many of these transcripts are simply junk. Here, we discuss how to determine whether any given ncRNA has a function. Importantly, we advocate that in the absence of any such data, the appropriate null hypothesis is that the RNA in question is junk.
Collapse
Affiliation(s)
| | - Eliza S Lee
- Department of Biochemistry, University of Toronto Toronto, ON, Canada
| |
Collapse
|
30
|
Affiliation(s)
- Alexander F. Palazzo
- University of Toronto, Department of Biochemistry, Toronto, Ontario, Canada
- * E-mail: (AP); (TG)
| | - T. Ryan Gregory
- University of Guelph, Department of Integrative Biology, Guelph, Ontario, Canada
- * E-mail: (AP); (TG)
| |
Collapse
|
31
|
Cui XA, Palazzo AF. Localization of mRNAs to the endoplasmic reticulum. Wiley Interdiscip Rev RNA 2014; 5:481-92. [PMID: 24644132 DOI: 10.1002/wrna.1225] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 12/17/2022]
Abstract
Almost all cells use mRNA localization to establish spatial control of protein synthesis. One of the best-studied examples is the targeting and anchoring of mRNAs encoding secreted, organellar, and membrane-bound proteins to the surface of the endoplasmic reticulum (ER). In this review, we provide a historical perspective on the research that elucidated the canonical protein-mediated targeting of nascent-chain ribosome mRNA complexes to the surface of the ER. We then discuss subsequent studies which provided concrete evidence that a subpopulation of mRNAs utilize a translation-independent mechanism to localize to the surface of this organelle. This alternative mechanism operates alongside the signal recognition particle (SRP) mediated co-translational targeting pathway to promote proper mRNA localization to the ER. Recent work has uncovered trans-acting factors, such as the mRNA receptor p180, and cis-acting elements, such as transmembrane domain coding regions, that are responsible for this alternative mRNA localization process. Furthermore, some unanticipated observations have raised the possibility that this alternative pathway may be conserved from bacteria to mammalian cells.
Collapse
Affiliation(s)
- Xianying A Cui
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | | |
Collapse
|
32
|
Cui XA, Zhang Y, Hong SJ, Palazzo AF. Identification of a region within the placental alkaline phosphatase mRNA that mediates p180-dependent targeting to the endoplasmic reticulum. J Biol Chem 2013; 288:29633-41. [PMID: 24019514 DOI: 10.1074/jbc.m113.482505] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In both eukaryotic and prokaryotic cells, it has been recently established that mRNAs encoding secreted and membrane proteins can be localized to the surface of membranes via both translation-dependent and RNA element-mediated mechanisms. Previously, we showed that the placental alkaline phosphatase (ALPP) mRNA can be localized to the ER membrane independently of translation, and this localization is mediated by p180, an mRNA receptor present in the ER. In this article, we aimed to identify the cis-acting RNA element in ALPP. Using chimera constructs containing fragments of the ALPP mRNA, we demonstrate that the ER-localizing RNA element is present within the 3' end of the open reading frame and codes for a transmembrane domain. In addition, we show that this region requires p180 for efficient ER anchoring. Taken together, we provide the first insight into the nature of cis-acting ER-localizing RNA elements responsible for localizing mRNAs on the ER in mammalian cells.
Collapse
Affiliation(s)
- Xianying A Cui
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | | | | |
Collapse
|
33
|
Abstract
In vertebrates, the majority of mRNAs that encode secreted, membrane-bound or mitochondrial proteins contain RNA elements that activate an alternative mRNA nuclear export (ALREX) pathway. Here we demonstrate that mRNAs containing ALREX-promoting elements are trafficked through nuclear speckles. Although ALREX-promoting elements enhance nuclear speckle localization, additional features within the mRNA largely drive this process. Depletion of two TREX-associated RNA helicases, UAP56 and its paralog URH49, or inhibition of the TREX-associated nuclear transport factor, TAP, not only inhibits ALREX, but also appears to trap these mRNAs in nuclear speckles. mRNAs that contain ALREX-promoting elements associate with UAP56 in vivo. Finally, we demonstrate that mRNAs lacking a poly(A)-tail are not efficiently exported by the ALREX pathway and show enhanced association with nuclear speckles. Our data suggest that within the speckle, ALREX-promoting elements, in conjunction with the poly(A)-tail, likely stimulate UAP56/URH49 and TAP dependent steps that lead to the eventual egress of the export-competent mRNP from these structures.
Collapse
Affiliation(s)
- Abdalla Akef
- Department of Biochemistry; University of Toronto; Toronto, ON Canada; Division of Integrated Life Science; Graduate School of Biostudies; Kyoto University; Kyoto, Japan
| | | | | | | |
Collapse
|
34
|
Palazzo AF, Mahadevan K, Tarnawsky SP. ALREX-elements and introns: two identity elements that promote mRNA nuclear export. Wiley Interdiscip Rev RNA 2013; 4:523-33. [PMID: 23913896 DOI: 10.1002/wrna.1176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 04/24/2013] [Accepted: 04/26/2013] [Indexed: 11/09/2022]
Abstract
The mechanisms that dictate whether a particular mRNA is exported from the nucleus are still poorly defined. However, it has become increasingly clear that these mechanisms act to promote the expression of protein-coding mRNAs over the high levels of spurious transcription that is endemic to most eukaryotic genomes. For example, mRNA processing events that are associated with protein-coding transcripts, such as splicing, act as mRNA identity elements that promote nuclear export of these transcripts. Six years ago, we made the serendipitous discovery that regions within the open reading frame of an mRNA that encode short secretory or mitochondrial-targeting peptides can also act as an mRNA identity element which promotes an alternative mRNA nuclear export (ALREX) pathway. These regions are enriched in protein coding genes and have particular features that can be used to identify this class of protein-coding mRNA. In this article we review our current knowledge of how mRNA export evolved in response to particular events that occurred at the base of the eukaryotic tree. We will then focus on our current understanding of ALREX and compare its features to splicing-dependent export, the main mRNA export pathway in metazoans.
Collapse
|
35
|
Mahadevan K, Zhang H, Akef A, Cui XA, Gueroussov S, Cenik C, Roth FP, Palazzo AF. RanBP2/Nup358 potentiates the translation of a subset of mRNAs encoding secretory proteins. PLoS Biol 2013; 11:e1001545. [PMID: 23630457 PMCID: PMC3635865 DOI: 10.1371/journal.pbio.1001545] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/07/2013] [Indexed: 12/14/2022] Open
Abstract
After nuclear export, mRNAs encoding secretory proteins interact with RanBP2/Nup358 on the cytoplasmic face of the nuclear pore, a step that is required for the efficient translation of these mRNAs. In higher eukaryotes, most mRNAs that encode secreted or membrane-bound proteins contain elements that promote an alternative mRNA nuclear export (ALREX) pathway. Here we report that ALREX-promoting elements also potentiate translation in the presence of upstream nuclear factors. These RNA elements interact directly with, and likely co-evolved with, the zinc finger repeats of RanBP2/Nup358, which is present on the cytoplasmic face of the nuclear pore. Finally we show that RanBP2/Nup358 is not only required for the stimulation of translation by ALREX-promoting elements, but is also required for the efficient global synthesis of proteins targeted to the endoplasmic reticulum (ER) and likely the mitochondria. Thus upon the completion of export, mRNAs containing ALREX-elements likely interact with RanBP2/Nup358, and this step is required for the efficient translation of these mRNAs in the cytoplasm. ALREX-elements thus act as nucleotide platforms to coordinate various steps of post-transcriptional regulation for the majority of mRNAs that encode secreted proteins. About one-fifth of the protein-coding genes in the human genome code for secreted and/or membrane-bound proteins. In the nucleus these genes are transcribed into messenger RNAs (mRNAs), which are then exported to the cytoplasm. These mRNAs are then transported to the surface of the endoplasmic reticulum where they are translated into proteins destined for the secretory pathway. Most of these mRNAs contain signal sequence coding regions (SSCRs), which code for short hydrophobic polypeptides that target the newly synthesized proteins for translocation across the endoplasmic reticulum membrane. Previously, we found that many SSCRs also act as RNA elements that promote the efficient nuclear export of mRNAs. Here we present evidence that upon the completion of nuclear export, SSCR-containing mRNAs interact with RanBP2/Nup358, a large protein found on the cytoplasmic face of the nuclear pore. This interaction is mediated by direct binding between the SSCR and zinc finger repeats found within RanBP2/Nup358, and is ultimately required for the efficient translation of SSCR-containing mRNAs into secretory and/or membrane-bound proteins. Our work demonstrates that SSCRs act as nucleotide platforms that recruit various factors to the mRNA throughout its life to regulate distinct events, such as nuclear export and translation.
Collapse
Affiliation(s)
- Kohila Mahadevan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Hui Zhang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Abdalla Akef
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Xianying A. Cui
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Serge Gueroussov
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Can Cenik
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Frederick P. Roth
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Toronto, Ontario, Canada
| | - Alexander F. Palazzo
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
36
|
Abstract
In eukaryotes, most of the messenger RNAs (mRNAs) that encode secreted and membrane proteins are localized to the surface of the endoplasmic reticulum (ER). However, the visualization of these mRNAs can be challenging. This is especially true when only a fraction of the mRNA is ER-associated and their distribution to this organelle is obstructed by non-targeted (i.e. "free") transcripts. In order to monitor ER-associated mRNAs, we have developed a method in which cells are treated with a short exposure to a digitonin extraction solution that selectively permeabilizes the plasma membrane, and thus removes the cytoplasmic contents, while simultaneously maintaining the integrity of the ER. When this method is coupled with fluorescent in situ hybridization (FISH), one can clearly visualize ER-bound mRNAs by fluorescent microscopy. Using this protocol the degree of ER-association for either bulk poly(A) transcripts or specific mRNAs can be assessed and even quantified. In the process, one can use this assay to investigate the nature of mRNA-ER interactions.
Collapse
|
37
|
Cui XA, Zhang H, Palazzo AF. p180 promotes the ribosome-independent localization of a subset of mRNA to the endoplasmic reticulum. PLoS Biol 2012; 10:e1001336. [PMID: 22679391 PMCID: PMC3362647 DOI: 10.1371/journal.pbio.1001336] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 04/12/2012] [Indexed: 12/21/2022] Open
Abstract
The localization of many secretory mRNAs to the endoplasmic reticulum does not require ribosomes or translation, but is instead promoted by p180, an abundant, membrane-bound protein that likely binds directly to mRNA. In metazoans, the majority of mRNAs coding for secreted and membrane-bound proteins are translated on the surface of the endoplasmic reticulum (ER). Although the targeting of these transcripts to the surface of the ER can be mediated by the translation of a signal sequence and their maintenance is mediated by interactions between the ribosome and the translocon, it is becoming increasingly clear that additional ER-localization pathways exist. Here we demonstrate that many of these mRNAs can be targeted to, and remain associated with, the ER independently of ribosomes and translation. Using a mass spectrometry analysis of proteins that associate with ER-bound polysomes, we identified putative mRNA receptors that may mediate this alternative mechanism, including p180, an abundant, positively charged membrane-bound protein. We demonstrate that p180 over-expression can enhance the association of generic mRNAs with the ER. We then show that p180 contains a lysine-rich region that can directly interact with RNA in vitro. Finally, we demonstrate that p180 is required for the efficient ER-anchoring of bulk poly(A) and of certain transcripts, such as placental alkaline phosphatase and calreticulin, to the ER. In summary, we provide, to our knowledge, the first mechanistic details for an alternative pathway to target and maintain mRNA at the ER. It is likely that this alternative pathway not only enhances the fidelity of protein sorting, but also localizes mRNAs to various subdomains of the ER and thus contributes to cellular organization. Messenger RNAs (mRNAs) that encode secreted or membrane-bound proteins must be delivered to, and then maintained on, the surface of the endoplasmic reticulum (ER). These mRNAs encode a short polypeptide that targets the mRNA/ribosome/nascent protein complexes to the ER surface during translation; however, recent studies support the existence of additional ER-localization signals that might be present within the mRNA molecules themselves. Here, we demonstrate that a fraction of these mRNAs, whose encoded proteins are destined for secretion, contain information that targets and anchors them to the ER independently of their encoded polypeptide or their association to ribosomes. We identify proteins on the ER that may serve as receptors for these mRNAs. We then show that one of these candidate membrane-bound receptors, p180, is required for the maintenance of certain mRNAs on the surface of the ER even after their translation into protein is disrupted. We also demonstrate that p180 contains a region that binds directly to RNA and likely mediates the anchoring of mRNA to the ER. Our study thus provides the first mechanistic details of an alternative pathway used to ensure that secretory mRNAs, and their encoded proteins, reach their proper destination in the ER.
Collapse
Affiliation(s)
| | | | - Alexander F. Palazzo
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
38
|
Tarnawsky SP, Palazzo AF. Positional requirements for the stimulation of mRNA nuclear export by ALREX-promoting elements. Mol BioSyst 2012; 8:2527-30. [DOI: 10.1039/c2mb25016k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
39
|
Shibata Y, Shemesh T, Prinz WA, Palazzo AF, Kozlov MM, Rapoport TA. Mechanisms determining the morphology of the peripheral ER. Cell 2010; 143:774-88. [PMID: 21111237 PMCID: PMC3008339 DOI: 10.1016/j.cell.2010.11.007] [Citation(s) in RCA: 372] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 09/03/2010] [Accepted: 10/26/2010] [Indexed: 01/08/2023]
Abstract
The endoplasmic reticulum (ER) consists of the nuclear envelope and a peripheral network of tubules and membrane sheets. The tubules are shaped by the curvature-stabilizing proteins reticulons and DP1/Yop1p, but how the sheets are formed is unclear. Here, we identify several sheet-enriched membrane proteins in the mammalian ER, including proteins that translocate and modify newly synthesized polypeptides, as well as coiled-coil membrane proteins that are highly upregulated in cells with proliferated ER sheets, all of which are localized by membrane-bound polysomes. These results indicate that sheets and tubules correspond to rough and smooth ER, respectively. One of the coiled-coil proteins, Climp63, serves as a "luminal ER spacer" and forms sheets when overexpressed. More universally, however, sheet formation appears to involve the reticulons and DP1/Yop1p, which localize to sheet edges and whose abundance determines the ratio of sheets to tubules. These proteins may generate sheets by stabilizing the high curvature of edges.
Collapse
Affiliation(s)
- Yoko Shibata
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | |
Collapse
|
40
|
Abstract
In eukaryotes, messenger RNA (mRNA) is transcribed in the nucleus and must be exported into the cytoplasm to access the translation machinery. Although the nuclear export of mRNA has been studied extensively in Xenopus oocytes1 and genetically tractable organisms such as yeast2 and the Drosophila derived S2 cell line3, few studies had been conducted in mammalian cells. Furthermore the kinetics of mRNA export in mammalian somatic cells could only be inferred indirectly4,5. In order to measure the nuclear export kinetics of mRNA in mammalian tissue culture cells, we have developed an assay that employs the power of microinjection coupled with fluorescent in situ hybridization (FISH). These assays have been used to demonstrate that in mammalian cells, the majority of mRNAs are exported in a splicing dependent manner6,7, or in manner that requires specific RNA sequences such as the signal sequence coding region (SSCR) 6. In this assay, cells are microinjected with either in vitro synthesized mRNA or plasmid DNA containing the gene of interest. The microinjected cells are incubated for various time points then fixed and the sub-cellular localization of RNA is assessed using FISH. In contrast to transfection, where transcription occurs several hours after the addition of nucleic acids, microinjection of DNA or mRNA allows for rapid expression and allows for the generation of precise kinetic data.
Collapse
|
41
|
Palazzo AF, Springer M, Shibata Y, Lee CS, Dias AP, Rapoport TA. The signal sequence coding region promotes nuclear export of mRNA. PLoS Biol 2008; 5:e322. [PMID: 18052610 PMCID: PMC2100149 DOI: 10.1371/journal.pbio.0050322] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 10/19/2007] [Indexed: 11/19/2022] Open
Abstract
In eukaryotic cells, most mRNAs are exported from the nucleus by the transcription export (TREX) complex, which is loaded onto mRNAs after their splicing and capping. We have studied in mammalian cells the nuclear export of mRNAs that code for secretory proteins, which are targeted to the endoplasmic reticulum membrane by hydrophobic signal sequences. The mRNAs were injected into the nucleus or synthesized from injected or transfected DNA, and their export was followed by fluorescent in situ hybridization. We made the surprising observation that the signal sequence coding region (SSCR) can serve as a nuclear export signal of an mRNA that lacks an intron or functional cap. Even the export of an intron-containing natural mRNA was enhanced by its SSCR. Like conventional export, the SSCR-dependent pathway required the factor TAP, but depletion of the TREX components had only moderate effects. The SSCR export signal appears to be characterized in vertebrates by a low content of adenines, as demonstrated by genome-wide sequence analysis and by the inhibitory effect of silent adenine mutations in SSCRs. The discovery of an SSCR-mediated pathway explains the previously noted amino acid bias in signal sequences and suggests a link between nuclear export and membrane targeting of mRNAs. In eukaryotic cells, precursors of messenger RNAs (mRNAs) are synthesized and processed in the nucleus. During processing, noncoding introns are spliced out, and a cap and poly-adenosine sequence are added to the beginning and end of the transcript, respectively. The resulting mature mRNA is exported from the nucleus to the cytoplasm by crossing the nuclear pore. Both the introns and the cap help to recruit factors that are necessary for nuclear export of an mRNA. Here we provide evidence for a novel mRNA export pathway that is specific for transcripts coding for secretory proteins. These proteins contain signal sequences that target them for translocation across the endoplasmic reticulum membrane. We made the surprising observation that the signal sequence coding region (SSCR) can serve as a nuclear export signal of an mRNA that lacks an intron or functional cap. Even the export of an intron-containing natural mRNA was enhanced by its SSCR. The SSCR export signal appears to be characterized in vertebrates by a low content of adenines. Our discovery of an SSCR-mediated pathway explains the previously noted amino acid bias in signal sequences, and suggests a link between nuclear export and membrane targeting of mRNAs. Signal sequences, which target newly synthesized secretory proteins to the endoplasmic reticulum, are encoded by adenine-depleted nucleotide sequences that promote the nuclear export of the mRNAs.
Collapse
Affiliation(s)
- Alexander F Palazzo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yoko Shibata
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chung-Sheng Lee
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Anusha P Dias
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tom A Rapoport
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
42
|
Abstract
Microtubule (MT) stabilization is regulated by the small guanosine triphosphate (GTP)-binding protein Rho and its effector, mammalian homolog of Diaphanous (mDia), in migrating cells, but factors responsible for localized stabilization at the leading edge are unknown. We report that integrin-mediated activation of focal adhesion kinase (FAK) at the leading edge is required for MT stabilization by the Rho-mDia signaling pathway in mouse fibroblasts. MT stabilization also involved FAK-regulated localization of a lipid raft marker, ganglioside GM1, to the leading edge. The integrin-FAK signaling pathway may facilitate Rho-mDia signaling through GM1, or through a specialized membrane domain containing GM1, to stabilize MTs in the leading edge of migrating cells.
Collapse
Affiliation(s)
- Alexander F Palazzo
- Department of Anatomy and Cell Biology, Columbia University, New York, NY 10032, USA
| | | | | | | | | |
Collapse
|
43
|
Xiao D, Pinto JT, Soh JW, Deguchi A, Gundersen GG, Palazzo AF, Yoon JT, Shirin H, Weinstein IB. Induction of apoptosis by the garlic-derived compound S-allylmercaptocysteine (SAMC) is associated with microtubule depolymerization and c-Jun NH(2)-terminal kinase 1 activation. Cancer Res 2003; 63:6825-37. [PMID: 14583480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Epidemiological and experimental carcinogenesis studies provide evidence that components of garlic (Allium sativum) have anticancer activity. We recently reported that the garlic derivative S-allylmercaptocysteine (SAMC) inhibits growth, arrests cells in G(2)-M, and induces apoptosis in human colon cancer cells (Shirin et al., Cancer Res., 61: 725-731, 2001). Because a fraction of the SAMC-treated cells are specifically arrested in mitosis, we examined the mechanism of this effect in the present study. Immunofluorescent microscopy revealed that the treatment of SW480 cells or NIH3T3 fibroblasts with 150 micro M SAMC (the IC(50) concentration) caused rapid microtubule (MT) depolymerization, MT cytoskeleton disruption, centrosome fragmentation and Golgi dispersion in interphase cells. It also induced the formation of monopolar and multipolar spindles in mitotic cells. In vitro turbidity assays indicated that SAMC acted directly on tubulin to cause MT depolymerization, apparently because it interacts with -SH groups on tubulin. To investigate the signaling pathways involved in SAMC-induced apoptosis, we assayed c-Jun NH(2)-terminal kinase (JNK) activity and found that treatment with SAMC caused a rapid and sustained induction of JNK activity. The selective JNK inhibitor SP600125 inhibited the early phase (24 h) but not the late phase (48 h and later) of apoptosis induced by SAMC. Expression of a dominant-negative mutant of JNK1 in SW480 cells inhibited apoptosis induced by SAMC at 24 h but had no protective effect at 48 h. JNK1(-/-) mouse embryonic fibroblasts were resistant to SAMC-induced apoptosis at 24 h but not at 48 h. On the other hand, the inhibition or abrogation of JNK1 activity did not inhibit the G(2)-M arrest induced by SAMC. SAMC also activated caspase-3. The general caspase inhibitor z-VAD-fmk inhibited both early and late phases of apoptosis induced by SAMC. We conclude that the garlic-derived compound SAMC exerts antiproliferative effects by binding directly to tubulin and disrupting the MT assembly, thus arresting cells in mitosis and triggering JNK1 and caspase-3 signaling pathways that lead to apoptosis.
Collapse
Affiliation(s)
- Danhua Xiao
- Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
Focal adhesions are dynamic structures in which traction forces are exerted against the substratum during cell migration and are sites for the organization of signaling complexes. Palazzo and Gundersen discuss how focal adhesions may also be the site of cross-talk between the actin-based and microtubule-based cytoskeletons. Microtubules appear to deliver factors that can regulate the formation and dissolution of focal adhesions, whereas focal adhesions contribute to microtubule localization and stability.
Collapse
Affiliation(s)
- Alexander F Palazzo
- Department of Anatomy and Cell Biology, Columbia University, New York, NY 10032, USA
| | | |
Collapse
|
45
|
Yoon JT, Palazzo AF, Xiao D, Delohery TM, Warburton PE, Bruce JN, Thompson WJ, Sperl G, Whitehead C, Fetter J, Pamukcu R, Gundersen GG, Weinstein IB. CP248, a derivative of exisulind, causes growth inhibition, mitotic arrest, and abnormalities in microtubule polymerization in glioma cells. Mol Cancer Ther 2002; 1:393-404. [PMID: 12477052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
Exisulind (sulindac sulfone) and two potent derivatives, CP248 and CP461, have been shown previously to cause growth inhibition and apoptosis in several types of human carcinoma cell lines. These and related compounds have not been previously studied with respect to glioma cell lines. In the present study, we found that these three compounds caused marked growth inhibition in four rat glioma and eight human glioma cell lines, with IC50 values of 150, 1, and 0.075 microm, respectively. When studied at these concentrations exisulind and CP461 had no significant effect on the cell cycle profile of glioma cells, but CP248 caused marked arrest in mitosis. Detailed studies of CP248 in the 9L rat gliosarcoma cell line indicated that treatment with 0.075 microM CP248 caused abnormalities in the spindle apparatus and activation of the spindle assembly check point. In interphase glioma cells, CP248 stabilized microtubules (MTs) at low concentrations (0.075 microM) and depolymerized MTs at higher concentrations (0.2-0.4 microM). In NIH 3T3 fibroblasts, 0.1 microM CP248 caused extensive MT depolymerization. CP248 also caused MT depolymerization when added to assembled MTs in vitro, which indicated that it can directly affect MTs, perhaps because it shares certain structural similarities with Colcemid. In glioma cells, the effects of CP248 on MTs were independent of the previously reported effects of this compound on activation of protein kinase G. Therefore, CP248 is a novel MT-active agent that may be useful in the treatment of glioblastoma, and possibly other types of cancer, because of its dual effects on protein kinase G and MTs.
Collapse
Affiliation(s)
- Jung-Taek Yoon
- Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Palazzo AF, Joseph HL, Chen YJ, Dujardin DL, Alberts AS, Pfister KK, Vallee RB, Gundersen GG. Cdc42, dynein, and dynactin regulate MTOC reorientation independent of Rho-regulated microtubule stabilization. Curr Biol 2001; 11:1536-41. [PMID: 11591323 DOI: 10.1016/s0960-9822(01)00475-4] [Citation(s) in RCA: 274] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In migrating adherent cells such as fibroblasts and endothelial cells, the microtubule-organizing center (MTOC) reorients toward the leading edge [1-3]. MTOC reorientation repositions the Golgi toward the front of the cell [1] and contributes to directional migration [4]. The mechanism of MTOC reorientation and its relation to the formation of stabilized microtubules (MTs) in the leading edge, which occurs concomitantly with MTOC reorientation [3], is unknown. We show that serum and the serum lipid, lysophosphatidic acid (LPA), increased Cdc42 GTP levels and triggered MTOC reorientation in serum-starved wounded monolayers of 3T3 fibroblasts. Cdc42, but not Rho or Rac, was both sufficient and necessary for LPA-stimulated MTOC reorientation. MTOC reorientation was independent of Cdc42-induced changes in actin and was not blocked by cytochalasin D. Inhibition of dynein or dynactin blocked LPA- and Cdc42-stimulated MTOC reorientation. LPA also stimulates a Rho/mDia pathway that selectively stabilizes MTs in the leading edge [5, 6]; however, activators and inhibitors of MTOC reorientation and MT stabilization showed that each response was regulated independently. These results establish an LPA/Cdc42 signaling pathway that regulates MTOC reorientation in a dynein-dependent manner. MTOC reorientation and MT stabilization both act to polarize the MT array in migrating cells, yet these processes act independently and are regulated by separate Rho family GTPase-signaling pathways.
Collapse
Affiliation(s)
- A F Palazzo
- Department of Anatomy and Cell Biology, Columbia University, New York, NY 10032, USA
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Abstract
Rho-GTPase stabilizes microtubules that are oriented towards the leading edge in serum-starved 3T3 fibroblasts through an unknown mechanism. We used a Rho-effector domain screen to identify mDia as a downstream Rho effector involved in microtubule stabilization. Constitutively active mDia or activation of endogenous mDia with the mDia-autoinhibitory domain stimulated the formation of stable microtubules that were capped and oriented towards the wound edge. mDia co-localized with stable microtubules when overexpressed and associated with microtubules in vitro. Rho kinase was not necessary for the formation of stable microtubules. Our results show that mDia is sufficient to generate and orient stable microtubules, and indicate that Dia-related formins are part of a conserved pathway that regulates the dynamics of microtubule ends.
Collapse
Affiliation(s)
- A F Palazzo
- Department of Anatomy & Cell Biology, Columbia University, New York 10032, USA
| | | | | | | |
Collapse
|