1
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Garg A, Shang R, Cvetanovic T, Lai EC, Joshua-Tor L. The structural landscape of Microprocessor-mediated processing of pri-let-7 miRNAs. Mol Cell 2024:S1097-2765(24)00741-X. [PMID: 39368465 DOI: 10.1016/j.molcel.2024.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 07/25/2024] [Accepted: 09/06/2024] [Indexed: 10/07/2024]
Abstract
MicroRNA (miRNA) biogenesis is initiated upon cleavage of a primary miRNA (pri-miRNA) hairpin by the Microprocessor (MP), composed of the Drosha RNase III enzyme and its partner DGCR8. Multiple pri-miRNA sequence motifs affect MP recognition, fidelity, and efficiency. Here, we performed cryoelectron microscopy (cryo-EM) and biochemical studies of several let-7 family pri-miRNAs in complex with human MP. We show that MP has the structural plasticity to accommodate a range of pri-miRNAs. These structures revealed key features of the 5' UG sequence motif, more comprehensively represented as the "flipped U with paired N" (fUN) motif. Our analysis explains how cleavage of class-II pri-let-7 members harboring a bulged nucleotide generates a non-canonical precursor with a 1-nt 3' overhang. Finally, the MP-SRSF3-pri-let-7f1 structure reveals how SRSF3 contributes to MP fidelity by interacting with the CNNC motif and Drosha's Piwi/Argonaute/Zwille (PAZ)-like domain. Overall, this study sheds light on the mechanisms for flexible recognition, accurate cleavage, and regulated processing of different pri-miRNAs by MP.
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Affiliation(s)
- Ankur Garg
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Todor Cvetanovic
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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2
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Li JN, Wang MY, Ruan JW, Lyu YJ, Weng YH, Brindangnanam P, Coumar MS, Chen PS. A transcription-independent role for HIF-1α in modulating microprocessor assembly. Nucleic Acids Res 2024:gkae792. [PMID: 39319577 DOI: 10.1093/nar/gkae792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 08/22/2024] [Accepted: 08/31/2024] [Indexed: 09/26/2024] Open
Abstract
Microprocessor is an essential nuclear complex responsible for the initial RNase-mediated cleavage of primary miRNA, which is a tightly controlled maturation process that requires the proper assembly of Drosha and DGCR8. Unlike previously identified mechanisms directly targeting the enzymatic subunit Drosha, current knowledge about the biological ways of controlling miRNA nuclear maturation through DGCR8 is less addressed. In this study, we unveiled that the microprocessor assembly is governed by a master gene regulator HIF-1α irrespective of its canonical transcriptional activity. First, a widespread protein binding of HIF-1α with DGCR8 instead of Drosha was observed in response to biological stimulations. Similar protein interactions between their corresponding orthologues in model organisms were also observed. After dissecting the essential protein domains, we noticed that HIF-1α suppresses microprocessor assembly via binding to DGCR8. Furthermore, our results showed that HIF-1α hijacks monomeric DGCR8 thus reducing its dimer formation prior to microprocessor assembly, and consequently, the suppressed microprocessor formation and nuclear processing of primary miRNA were demonstrated. In conclusion, here we unveiled the mechanism of how microprocessor assembly is regulated by HIF-1α, which not only demonstrates a non-transcriptional function of nuclear HIF-1α but also provides new molecular insights into the regulation of microprocessor assembly through DGCR8.
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Affiliation(s)
- Jie-Ning Li
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Breast Medical Center, National Cheng Kung University Hospital, Tainan, Taiwan
- Research Center for Medical Laboratory Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ming-Yang Wang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
- Department of Surgical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Jhen-Wei Ruan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Research Center for Medical Laboratory Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Jhen Lyu
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Hsiu Weng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Research Center for Medical Laboratory Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Pownraj Brindangnanam
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India
| | - Pai-Sheng Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Breast Medical Center, National Cheng Kung University Hospital, Tainan, Taiwan
- Research Center for Medical Laboratory Biotechnology, National Cheng Kung University, Tainan, Taiwan
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3
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Garg A, Shang R, Cvetanovic T, Lai EC, Joshua-Tor L. The structural landscape of Microprocessor mediated pri- let-7 miRNA processing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593372. [PMID: 38766155 PMCID: PMC11100773 DOI: 10.1101/2024.05.09.593372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
miRNA biogenesis is initiated upon cleavage of a primary miRNA (pri-miRNA) hairpin by the Microprocessor (MP), composed of the Drosha RNase III enzyme and its partner DGCR8. Multiple pri-miRNA sequence motifs affect MP recognition, fidelity, and efficiency. Here, we performed cryo-EM and biochemical studies of several let-7 family pri-miRNAs in complex with human MP. We show that MP has the structural plasticity to accommodate a range of pri-miRNAs. These structures revealed key features of the 5' UG sequence motif, more comprehensively represented as the "fUN" motif. Our analysis explains how cleavage of class-II pri-let-7 members harboring a bulged nucleotide generates a noncanonical precursor with a 1-nt 3' overhang. Finally, the MP-SRSF3-pri-let-7f1 structure reveals how SRSF3 contributes to MP fidelity by interacting with the CNNC-motif and Drosha's PAZ-like domain. Overall, this study sheds light on the mechanisms for flexible recognition, accurate cleavage, and regulated processing of different pri-miRNAs by MP.
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Affiliation(s)
- Ankur Garg
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Todor Cvetanovic
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Lead Contact
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4
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Leitão AL, Enguita FJ. A Structural View of miRNA Biogenesis and Function. Noncoding RNA 2022; 8:ncrna8010010. [PMID: 35202084 PMCID: PMC8874510 DOI: 10.3390/ncrna8010010] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/16/2022] Open
Abstract
Micro-RNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of gene expression. Since their discovery in 1993, they have been the subject of deep study due to their involvement in many important biological processes. Compared with other ncRNAs, miRNAs are generated from devoted transcriptional units which are processed by a specific set of endonucleases. The contribution of structural biology methods for understanding miRNA biogenesis and function has been essential for the dissection of their roles in cell biology and human disease. In this review, we summarize the application of structural biology for the characterization of the molecular players involved in miRNA biogenesis (processors and effectors), starting from the X-ray crystallography methods to the more recent cryo-electron microscopy protocols.
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Affiliation(s)
- Ana Lúcia Leitão
- MEtRICs, Department of Sciences and Technology of Biomass, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal;
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Correspondence:
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5
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Cupido-Sánchez MG, Herrera-González NE, Mendoza CCB, Hernández MLM, Ramón-Gallegos E. In silico analysis of the association of hsa-miR-16 expression and cell survival in MDA-MB-231 breast cancer cells subjected to photodynamic therapy. Photodiagnosis Photodyn Ther 2020; 33:102106. [PMID: 33217568 DOI: 10.1016/j.pdpdt.2020.102106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 10/28/2020] [Accepted: 11/09/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND Breast cancer is the most common malignancy effecting women, and the triple-negative breast cancer (TNBC) subtype is particularly aggressive. This study aimed to evaluate the differential expression pattern of microRNAs (miRNAs) between untreated MDA-MB-231 cells (TNBC cell model) and those that survived photodynamic therapy (PDT) to gain insights into cell survival mechanisms. METHODS Two PDT cycles were applied to MDA-MB-231 cells, using δ-aminolevulinic acid (ALA) followed by laser light at 635 nm. RNA was obtained from cells surviving PDT and untreated cells. The miRNAs expression profile was analyzed to detect the differences between the two groups. The potential target network of hsa-miR-16 was examined in silico with the integrative database Ingenuity® Pathway Analysis software. RESULTS After the first and second PDT cycles, 17.8% and 49.6% of the MDA-MB-231 cells were viable. Microarray profiling of miRNAs showed decreased hsa-miR-16 expression (p < 0.05) in MDA-MB-231 cells surviving PDT when compared to the control cells. The predicted downstream targets of hsa-miR-16 were: 1) tumor suppressor protein 53; 2) molecules related to the cell cycle, such as cyclin D1, D3, and E1, and checkpoint kinase 1; 3) cell proliferation molecules, including fibroblast growth factor 1, 2 and 7 and fibroblast growth factor receptor 1; and 4) apoptosis-related molecules, consisting of BCL-2, B-cell leukemia/lymphoma 2, caspase 3, and cytochrome c. CONCLUSIONS The differential expression of hsa-miR-16 between untreated MDA-MB-231 cells and those surviving PDT has not been previously reported. There was a lower expression of hsa-miR-16 in treated cells, which probably altered its downstream target network. In silico analysis predicted, a network related to the cell cycle, proliferation and apoptosis. These results are congruent with previous descriptions of hsa-miR-16 as a tumor suppressor and suggest that the treated population has increased their capacity to survive.
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Affiliation(s)
- María Guadalupe Cupido-Sánchez
- Molecular Oncology Lab, Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomás, 11340, Ciudad de México, Mexico.
| | - Norma Estela Herrera-González
- Molecular Oncology Lab, Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomás, 11340, Ciudad de México, Mexico.
| | - Columba Citlalli Barrera Mendoza
- Environmental Cytopathology Lab, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Wilfrido Massieu, Esq. Cda. Manuel Stampa Zacatenco, Gustavo A. Madero, 07736, Ciudad de México, Mexico.
| | - María Luisa Morales Hernández
- Environmental Cytopathology Lab, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Wilfrido Massieu, Esq. Cda. Manuel Stampa Zacatenco, Gustavo A. Madero, 07736, Ciudad de México, Mexico.
| | - Eva Ramón-Gallegos
- Environmental Cytopathology Lab, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Wilfrido Massieu, Esq. Cda. Manuel Stampa Zacatenco, Gustavo A. Madero, 07736, Ciudad de México, Mexico.
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6
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Nguyen HM, Nguyen TD, Nguyen TL, Nguyen TA. Orientation of Human Microprocessor on Primary MicroRNAs. Biochemistry 2018; 58:189-198. [DOI: 10.1021/acs.biochem.8b00944] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Huong Minh Nguyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Trung Duc Nguyen
- Division of Life Science, Hong Kong University of Science & Technology, Hong Kong, China
| | - Thuy Linh Nguyen
- Division of Life Science, Hong Kong University of Science & Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, Hong Kong University of Science & Technology, Hong Kong, China
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7
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Beuerle M, Kussmann J, Ochsenfeld C. Screening methods for linear-scaling short-range hybrid calculations on CPU and GPU architectures. J Chem Phys 2017; 146:144108. [DOI: 10.1063/1.4978476] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Matthias Beuerle
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 München, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5-13, D-81377 München, Germany
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 München, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5-13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 München, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5-13, D-81377 München, Germany
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8
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Hines JP, Smith AT, Jacob JP, Lukat-Rodgers GS, Barr I, Rodgers KR, Guo F, Burstyn JN. CO and NO bind to Fe(II) DiGeorge critical region 8 heme but do not restore primary microRNA processing activity. J Biol Inorg Chem 2016; 21:1021-1035. [PMID: 27766492 DOI: 10.1007/s00775-016-1398-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/10/2016] [Indexed: 01/29/2023]
Abstract
The RNA-binding heme protein DiGeorge critical region 8 (DGCR8) and its ribonuclease partner Drosha cleave primary transcripts of microRNA (pri-miRNA) as part of the canonical microRNA (miRNA) processing pathway. Previous studies show that bis-cysteine thiolate-coordinated Fe(III) DGCR8 supports pri-miRNA processing activity, while Fe(II) DGCR8 does not. In this study, we further characterized Fe(II) DGCR8 and tested whether CO or NO might bind and restore pri-miRNA processing activity to the reduced protein. Fe(II) DGCR8 RNA-binding heme domain (Rhed) undergoes a pH-dependent transition from 6-coordinate to 5-coordinate, due to protonation and loss of a lysine ligand; the ligand bound throughout the pH change is a histidine. Fe(II) Rhed binds CO and NO from 6- and 5-coordinate states, forming common CO and NO adducts at all pHs. Fe(II)-CO Rhed is 6-coordinate, low-spin, and pH insensitive with the histidine ligand retained, suggesting that the protonatable lysine ligand has been replaced by CO. Fe(II)-NO Rhed is 5-coordinate and pH insensitive. Fe(II)-NO also forms slowly upon reaction of Fe(III) Rhed with excess NO via a stepwise process. Heme reduction by NO is rate-limiting, and the rate would be negligible at physiological NO concentrations. Importantly, in vitro pri-miRNA processing assays show that both CO- and NO-bound DGCR8 species are inactive. Fe(II), Fe(II)-CO, and Fe(II)-NO Rhed do not bear either of the cysteine ligands found in the Fe(III) state. These data support a model in which the bis-cysteine thiolate ligand environment of Fe(III) DGCR8 is necessary for establishing proper pri-miRNA binding and enabling processing activity.
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Affiliation(s)
- Judy P Hines
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706-1322, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250-0001, USA
| | - Jose P Jacob
- Department of Biological Chemistry, David Geffen School of Medicine, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, 90095-3075, USA
| | - Gudrun S Lukat-Rodgers
- Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Ian Barr
- Department of Biological Chemistry, David Geffen School of Medicine, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, 90095-3075, USA
| | - Kenton R Rodgers
- Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Feng Guo
- Department of Biological Chemistry, David Geffen School of Medicine, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, 90095-3075, USA
| | - Judith N Burstyn
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706-1322, USA.
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9
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Girvan HM, Bradley JM, Cheesman MR, Kincaid JR, Liu Y, Czarnecki K, Fisher K, Leys D, Rigby SEJ, Munro AW. Analysis of Heme Iron Coordination in DGCR8: The Heme-Binding Component of the Microprocessor Complex. Biochemistry 2016; 55:5073-83. [DOI: 10.1021/acs.biochem.6b00204] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hazel M. Girvan
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Justin M. Bradley
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Myles R. Cheesman
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - James R. Kincaid
- Department
of Chemistry, Marquette University, 535 North 14th Street, Milwaukee, Wisconsin 53233, United States
| | - Yilin Liu
- Department
of Chemistry, Marquette University, 535 North 14th Street, Milwaukee, Wisconsin 53233, United States
| | - Kazimierz Czarnecki
- Department
of Chemistry, Marquette University, 535 North 14th Street, Milwaukee, Wisconsin 53233, United States
| | - Karl Fisher
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - David Leys
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Stephen E. J. Rigby
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Andrew W. Munro
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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10
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Jakob L, Treiber T, Treiber N, Gust A, Kramm K, Hansen K, Stotz M, Wankerl L, Herzog F, Hannus S, Grohmann D, Meister G. Structural and functional insights into the fly microRNA biogenesis factor Loquacious. RNA (NEW YORK, N.Y.) 2016; 22:383-396. [PMID: 26769856 PMCID: PMC4748816 DOI: 10.1261/rna.055426.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/02/2015] [Indexed: 06/05/2023]
Abstract
In the microRNA (miRNA) pathway, Dicer processes precursors to mature miRNAs. For efficient processing, double-stranded RNA-binding proteins support Dicer proteins. In flies, Loquacious (Loqs) interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. Here, we have solved the structure of the third double-stranded RNA-binding domain (dsRBD) of Loqs and define specific structural elements that interact with dmDcr1. In addition, we show that the linker preceding dsRBD3 contributes significantly to dmDcr1 binding. Furthermore, our structural work demonstrates that the third dsRBD of Loqs forms homodimers. Mutations in the dimerization interface abrogate dmDcr1 interaction. Loqs, however, binds to dmDcr1 as a monomer using the identified dimerization surface, which suggests that Loqs might form dimers under conditions where dmDcr1 is absent or not accessible. Since critical sequence elements are conserved, we suggest that dimerization might be a general feature of dsRBD proteins in gene silencing.
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Affiliation(s)
- Leonhard Jakob
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Alexander Gust
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Kevin Kramm
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Kerrin Hansen
- Intana Bioscience GmbH, 82152 Planegg, Martinsried, Germany
| | - Mathias Stotz
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Ludwig Wankerl
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Franz Herzog
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany
| | - Stefan Hannus
- Intana Bioscience GmbH, 82152 Planegg, Martinsried, Germany
| | - Dina Grohmann
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
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11
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Herbert KM, Sarkar SK, Mills M, Delgado De la Herran HC, Neuman KC, Steitz JA. A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting. RNA (NEW YORK, N.Y.) 2016; 22:175-183. [PMID: 26683315 PMCID: PMC4712668 DOI: 10.1261/rna.054684.115] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/17/2015] [Indexed: 05/30/2023]
Abstract
During microRNA (miRNA) biogenesis, the Microprocessor complex (MC), composed minimally of Drosha, an RNaseIII enzyme, and DGCR8, a double-stranded RNA-binding protein, cleaves the primary-miRNA (pri-miRNA) to release the pre-miRNA stem-loop structure. Size-exclusion chromatography of the MC, isolated from mammalian cells, suggested multiple copies of one or both proteins in the complex. However, the exact stoichiometry was unknown. Initial experiments suggested that DGCR8 bound pri-miRNA substrates specifically, and given that Drosha could not be bound or cross-linked to RNA, a sequential model for binding was established in which DGCR8 bound first and recruited Drosha. Therefore, many laboratories have studied DGCR8 binding to RNA in the absence of Drosha and have shown that deletion constructs of DGCR8 can multimerize in the presence of RNA. More recently, it was demonstrated that Drosha can bind pri-miRNA substrates in the absence of DGCR8, casting doubt on the sequential model of binding. In the same study, using a single-molecule photobleaching assay, fluorescent protein-tagged deletion constructs of DGCR8 and Drosha assembled into a heterotrimeric complex on RNA, comprising two DGCR8 molecules and one Drosha molecule. To determine the stoichiometry of Drosha and DGCR8 within the MC in the absence of added RNA, we also used a single-molecule photobleaching assay and confirmed the heterotrimeric model of the human MC. We demonstrate that a heterotrimeric complex is likely preformed in the absence of RNA and exists even when full-length proteins are expressed and purified from human cells, and when hAGT-derived tags are used rather than fluorescent proteins.
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Affiliation(s)
- Kristina M Herbert
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California 22860, Mexico
| | - Susanta K Sarkar
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Maria Mills
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hilda C Delgado De la Herran
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California 22860, Mexico
| | - Keir C Neuman
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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12
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Gurianova V, Stroy D, Ciccocioppo R, Gasparova I, Petrovic D, Soucek M, Dosenko V, Kruzliak P. Stress response factors as hub-regulators of microRNA biogenesis: implication to the diseased heart. Cell Biochem Funct 2015; 33:509-18. [PMID: 26659949 DOI: 10.1002/cbf.3151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 09/21/2015] [Accepted: 10/02/2015] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are important regulators of heart function and then an intriguing therapeutic target for plenty of diseases. The problem raised is that many data in this area are contradictory, thus limiting the use of miRNA-based therapy. The goal of this review is to describe the hub-mechanisms regulating the biogenesis and function of miRNAs, which could help in clarifying some contradictions in the miRNA world. With this scope, we analyse an array of factors, including several known agents of stress response, mediators of epigenetic changes, regulators of alternative splicing, RNA editing, protein synthesis and folding and proteolytic systems. All these factors are important in cardiovascular function and most of them regulate miRNA biogenesis, but their influence on miRNAs was shown for non-cardiac cells or some specific cardiac pathologies. Finally, we consider that studying the stress response factors, which are upstream regulators of miRNA biogenesis, in the diseased heart could help in (1) explaining some contradictions concerning miRNAs in heart pathology, (2) making the role of miRNAs in pathogenesis of cardiovascular disease more clear, and therefore, (3) getting powerful targets for its molecular therapy.
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Affiliation(s)
- Veronika Gurianova
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Dmytro Stroy
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Rachele Ciccocioppo
- Clinica Medica I; Fondazione IRCCS Policlinico San Matteo, Università degli Studi di Pavia, Italy
| | - Iveta Gasparova
- Institute of Biology, Genetics and Medical Genetics, Faculty of Medicine, Comenius University and University Hospital, Bratislava, Slovak Republic
| | - Daniel Petrovic
- Institute of Histology and Embryology, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Miroslav Soucek
- Second Department of Internal Medicine, St. Anne's University Hospital and Masaryk University, Brno, Czech Republic
| | - Victor Dosenko
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Peter Kruzliak
- Second Department of Internal Medicine, St. Anne's University Hospital and Masaryk University, Brno, Czech Republic.,Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University, Bratislava, Slovak Republic.,Laboratory of Structural Biology and Proteomics, Faculty of Pharmacy, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
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13
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Barr I, Guo F. Pyridine Hemochromagen Assay for Determining the Concentration of Heme in Purified Protein Solutions. Bio Protoc 2015; 5:e1594. [PMID: 27390766 DOI: 10.21769/bioprotoc.1594] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Heme is a common cofactor in proteins, found in hemoglobin, myoglobin, cytochrome P450, DGCR8, and nitric oxide synthase, among others. This protocol describes a method for quantifying heme that works best in purified protein samples. This protocol might be used to, for example, determine whether a given heme-binding protein is fully occupied by heme, thus allowing correlation of heme content with activity. This requires the absolute heme concentration and an accurate protein concentration. Another use is to determine the extinction coefficients of a heme-bound protein. This assay is fast, easy, and reproducible if done correctly.
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Affiliation(s)
- Ian Barr
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, California, USA
| | - Feng Guo
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, California, USA
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14
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Quick-Cleveland J, Jacob JP, Weitz SH, Shoffner G, Senturia R, Guo F. The DGCR8 RNA-binding heme domain recognizes primary microRNAs by clamping the hairpin. Cell Rep 2014; 7:1994-2005. [PMID: 24910438 DOI: 10.1016/j.celrep.2014.05.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/03/2014] [Accepted: 05/06/2014] [Indexed: 01/09/2023] Open
Abstract
Canonical primary microRNA transcripts (pri-miRNAs) are characterized by a ∼30 bp hairpin flanked by single-stranded regions. These pri-miRNAs are recognized and cleaved by the Microprocessor complex consisting of the Drosha nuclease and its obligate RNA-binding partner DGCR8. It is not well understood how the Microprocessor specifically recognizes pri-miRNA substrates. Here, we show that in addition to the well-known double-stranded RNA-binding domains, DGCR8 uses a dimeric heme-binding domain to directly contact pri-miRNAs. This RNA-binding heme domain (Rhed) directs two DGCR8 dimers to bind each pri-miRNA hairpin. The two Rhed-binding sites are located at both ends of the hairpin. The Rhed and its RNA-binding surface are important for pri-miRNA processing activity. Additionally, the heme cofactor is required for formation of processing-competent DGCR8-pri-miRNA complexes. Our study reveals a unique protein-RNA interaction central to pri-miRNA recognition. We propose a unifying model in which two DGCR8 dimers clamp a pri-miRNA hairpin using their Rheds.
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Affiliation(s)
- Jen Quick-Cleveland
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jose P Jacob
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sara H Weitz
- Molecular, Cell and Integrative Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Grant Shoffner
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rachel Senturia
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Feng Guo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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15
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Huang JT, Wang J, Srivastava V, Sen S, Liu SM. MicroRNA Machinery Genes as Novel Biomarkers for Cancer. Front Oncol 2014; 4:113. [PMID: 24904827 PMCID: PMC4032885 DOI: 10.3389/fonc.2014.00113] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/01/2014] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) directly and indirectly affect tumorigenesis. To be able to perform their myriad roles, miRNA machinery genes, such as Drosha, DGCR8, Dicer1, XPO5, TRBP, and AGO2, must generate precise miRNAs. These genes have specific expression patterns, protein-binding partners, and biochemical capabilities in different cancers. Our preliminary analysis of data from The Cancer Genome Atlas consortium on multiple types of cancer revealed significant alterations in these miRNA machinery genes. Here, we review their biological structures and functions with an eye toward understanding how they could serve as cancer biomarkers.
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Affiliation(s)
- Jing-Tao Huang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University , Wuhan , China
| | - Jin Wang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center , Houston, TX , USA
| | - Vibhuti Srivastava
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center , Houston, TX , USA
| | - Subrata Sen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center , Houston, TX , USA
| | - Song-Mei Liu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University , Wuhan , China
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16
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Processing of microRNA primary transcripts requires heme in mammalian cells. Proc Natl Acad Sci U S A 2014; 111:1861-6. [PMID: 24449907 DOI: 10.1073/pnas.1309915111] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DiGeorge syndrome critical region gene 8 (DGCR8) is the RNA-binding partner protein of the nuclease Drosha. DGCR8 and Drosha recognize and cleave primary transcripts of microRNAs (pri-miRNAs) in the maturation of canonical microRNAs (miRNAs) in animals. We previously reported that human, frog, and starfish DGCR8 bind heme when expressed in Escherichia coli and that Fe(III) heme activates apoDGCR8 in reconstituted pri-miRNA processing assays. However, the physiological relevance of heme in miRNA maturation has not been clear. Here, we present a live-cell pri-miRNA processing assay that produces robust signals and faithfully indicates DGCR8 and Drosha activities. We demonstrate that all known heme-binding-deficient DGCR8 mutants are defective in pri-miRNA processing in HeLa cells. DGCR8 contains a previously uncharacterized heme-binding motif, "IPCL," that is also required for its activity. Heme availability and biosynthesis in HeLa cells positively affect pri-miRNA processing and production of mature miRNA. These results establish an essential function for heme in pri-miRNA processing in mammalian cells. Our study suggests that abnormal heme biosynthesis and degradation may contribute to diseases via miRNA-mediated gene regulation networks.
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Abstract
In animals, the Microprocessor complex cleaves primary transcripts of microRNAs (pri-miRNAs) to produce precursor microRNAs in the nucleus. The core components of Microprocessor include the Drosha ribonuclease and its RNA-binding partner protein DiGeorge critical region 8 (DGCR8). DGCR8 has been shown to tightly bind an Fe(III) heme cofactor, which activates its pri-miRNA processing activity. Here we describe how to reconstitute pri-miRNA processing using recombinant human Drosha and DGCR8 proteins. In particular, we present the procedures for expressing and purifying DGCR8 as an Fe(III) heme-bound dimer, the most active form of this protein, and for estimating its heme content.
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Phosphorylation of DGCR8 increases its intracellular stability and induces a progrowth miRNA profile. Cell Rep 2013; 5:1070-81. [PMID: 24239349 PMCID: PMC3892995 DOI: 10.1016/j.celrep.2013.10.017] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 07/03/2013] [Accepted: 10/09/2013] [Indexed: 02/07/2023] Open
Abstract
During miRNA biogenesis, the microprocessor complex (MC), which is composed minimally of Drosha, an RNase III enzyme, and DGCR8, a double-stranded RNA-binding protein, cleaves the primary miRNA (pri-miRNA) in order to release the pre-miRNA stem-loop structure. Using phosphoproteomics, we mapped 23 phosphorylation sites on full-length human DGCR8 expressed in insect or mammalian cells. DGCR8 can be phosphorylated by mitogenic ERK/MAPK, indicating that DGCR8 phosphorylation may respond to and integrate extracellular cues. The expression of phosphomimetic DGCR8 or inhibition of phosphatases increased the cellular levels of DGCR8 and Drosha proteins. Increased levels of phosphomimetic DGCR8 were not due to higher mRNA levels, altered DGCR8 localization, or DGCR8’s ability to self-associate, but rather to an increase in protein stability. MCs incorporating phosphomutant or phosphomimetic DGCR8 were not altered in specific processing activity. However, HeLa cells expressing phosphomimetic DGCR8 exhibited a progrowth miRNA expression profile and increased proliferation and scratch closure rates relative to cells expressing phosphomutant DGCR8.
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