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Ormazábal A, Carletti MS, Saldaño TE, Gonzalez Buitron M, Marchetti J, Palopoli N, Bateman A. Expanding the repertoire of human tandem repeat RNA-binding proteins. PLoS One 2023; 18:e0290890. [PMID: 37729217 PMCID: PMC10511089 DOI: 10.1371/journal.pone.0290890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/15/2023] [Indexed: 09/22/2023] Open
Abstract
Protein regions consisting of arrays of tandem repeats are known to bind other molecular partners, including nucleic acid molecules. Although the interactions between repeat proteins and DNA are already widely explored, studies characterising tandem repeat RNA-binding proteins are lacking. We performed a large-scale analysis of human proteins devoted to expanding the knowledge about tandem repeat proteins experimentally reported as RNA-binding molecules. This work is timely because of the release of a full set of accurate structural models for the human proteome amenable to repeat detection using structural methods. The main goal of our analysis was to build a comprehensive set of human RNA-binding proteins that contain repeats at the sequence or structure level. Our results showed that the combination of sequence and structural methods finds significantly more tandem repeat proteins than either method alone. We identified 219 tandem repeat proteins that bind RNA molecules and characterised the overlap between repeat regions and RNA-binding regions as a first step towards assessing their functional relationship. We observed differences in the characteristics of repeat regions predicted by sequence-based or structure-based methods in terms of their sequence composition, their functions and their protein domains.
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Affiliation(s)
- Agustín Ormazábal
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Buenos Aires, Argentina
| | - Matías Sebastián Carletti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Buenos Aires, Argentina
| | - Tadeo Enrique Saldaño
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Buenos Aires, Argentina
- Departamento de Ciencias Básicas, Facultad de Agronomía, Universidad Nacional del Centro de la Provincia de Buenos Aires, Azul, Buenos Aires, Argentina
| | - Martín Gonzalez Buitron
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Buenos Aires, Argentina
| | - Julia Marchetti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Buenos Aires, Argentina
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
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2
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Albarqi MMY, Ryder SP. The role of RNA-binding proteins in orchestrating germline development in Caenorhabditis elegans. Front Cell Dev Biol 2023; 10:1094295. [PMID: 36684428 PMCID: PMC9846511 DOI: 10.3389/fcell.2022.1094295] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
RNA passed from parents to progeny controls several aspects of early development. The germline of the free-living nematode Caenorhabditis elegans contains many families of evolutionarily conserved RNA-binding proteins (RBPs) that target the untranslated regions of mRNA transcripts to regulate their translation and stability. In this review, we summarize what is known about the binding specificity of C. elegans germline RNA-binding proteins and the mechanisms of mRNA regulation that contribute to their function. We examine the emerging role of miRNAs in translational regulation of germline and embryo development. We also provide an overview of current technology that can be used to address the gaps in our understanding of RBP regulation of mRNAs. Finally, we present a hypothetical model wherein multiple 3'UTR-mediated regulatory processes contribute to pattern formation in the germline to ensure the proper and timely localization of germline proteins and thus a functional reproductive system.
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3
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Xia H, Kang Y, Ma Z, Hu C, Yang Q, Zhang X, Yang S, Dai J, Chen X. Evolutionary and reverse engineering in Saccharomyces cerevisiae reveals a Pdr1p mutation-dependent mechanism for 2-phenylethanol tolerance. Microb Cell Fact 2022; 21:269. [PMID: 36564756 PMCID: PMC9789650 DOI: 10.1186/s12934-022-01996-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND 2-Phenylethanol (2-PE), a higher alcohol with a rose-like odor, inhibits growth of the producer strains. However, the limited knowledge regarding 2-PE tolerance mechanisms renders our current knowledge base insufficient to inform rational design. RESULTS To improve the growth phenotype of Saccharomyces cerevisiae under a high 2-PE concentration, adaptive laboratory evolution (ALE) was used to generate an evolved 19-2 strain. Under 2-PE stress, its OD600 and growth rate increased by 86% and 22% than that of the parental strain, respectively. Through whole genome sequencing and reverse engineering, transcription factor Pdr1p mutation (C862R) was revealed as one of the main causes for increased 2-PE tolerance. Under 2-PE stress condition, Pdr1p mutation increased unsaturated fatty acid/saturated fatty acid ratio by 42%, and decreased cell membrane damage by 81%. Using STRING website, we identified Pdr1p interacted with some proteins, which were associated with intracellular ergosterol content, reactive oxygen species (ROS), and the ATP-binding cassette transporter. Also, the results of transcriptional analysis of genes encoded these proteins confirmed that Pdr1p mutation induced the expression of these genes. Compared with those of the reference strain, the ergosterol content of the PDR1_862 strain increased by 72%-101%, and the intracellular ROS concentration decreased by 38% under 2-PE stress. Furthermore, the Pdr1p mutation also increased the production of 2-PE (11% higher). CONCLUSIONS In the present work, we have demonstrated the use of ALE as a powerful tool to improve yeast tolerance to 2-PE. Based on the reverse engineering, transcriptional and physiological analysis, we concluded that Pdr1p mutation significantly enhanced the 2-PE tolerance of yeast by regulating the fatty acid proportion, intracellular ergosterol and ROS. It provides new insights on Pdr1p mediated 2-PE tolerance, which could help in the design of more robust yeasts for natural 2-PE synthesis.
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Affiliation(s)
- Huili Xia
- grid.411410.10000 0000 8822 034XKey Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei University of Technology, Wuhan, Hubei 430068 People’s Republic of China
| | - Yue Kang
- grid.411410.10000 0000 8822 034XKey Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei University of Technology, Wuhan, Hubei 430068 People’s Republic of China
| | - Zilin Ma
- grid.411410.10000 0000 8822 034XKey Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei University of Technology, Wuhan, Hubei 430068 People’s Republic of China
| | - Cuiyu Hu
- grid.411410.10000 0000 8822 034XKey Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei University of Technology, Wuhan, Hubei 430068 People’s Republic of China
| | - Qiao Yang
- grid.443668.b0000 0004 1804 4247ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316022 Zhejiang China
| | - Xiaoling Zhang
- grid.443668.b0000 0004 1804 4247ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316022 Zhejiang China
| | - Shihui Yang
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Jun Dai
- grid.411410.10000 0000 8822 034XKey Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei University of Technology, Wuhan, Hubei 430068 People’s Republic of China ,grid.443668.b0000 0004 1804 4247ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316022 Zhejiang China ,grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Xiong Chen
- grid.411410.10000 0000 8822 034XKey Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei University of Technology, Wuhan, Hubei 430068 People’s Republic of China
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4
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Han W, Huang W, Wei T, Ye Y, Mao M, Wang Z. Programmable RNA base editing with a single gRNA-free enzyme. Nucleic Acids Res 2022; 50:9580-9595. [PMID: 36029126 PMCID: PMC9458445 DOI: 10.1093/nar/gkac713] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 07/02/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
Programmable RNA editing enables rewriting gene expression without changing genome sequences. Current tools for specific RNA editing dependent on the assembly of guide RNA into an RNA/protein complex, causing delivery barrier and low editing efficiency. We report a new gRNA-free system, RNA editing with individual RNA-binding enzyme (REWIRE), to perform precise base editing with a single engineered protein. This artificial enzyme contains a human-originated programmable PUF domain to specifically recognize RNAs and different deaminase domains to achieve efficient A-to-I or C-to-U editing, which achieved 60-80% editing rate in human cells, with a few non-specific editing sites in the targeted region and a low level off-target effect globally. The RNA-binding domain in REWIREs was further optimized to improve editing efficiency and minimize off-target effects. We applied the REWIREs to correct disease-associated mutations and achieve both types of base editing in mice. As a single-component system originated from human proteins, REWIRE presents a precise and efficient RNA editing platform with broad applicability.
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Affiliation(s)
- Wenjian Han
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wendi Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Wei
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanwen Ye
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miaowei Mao
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zefeng Wang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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5
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Fan X, Yang Y, Chen C, Wang Z. Pervasive translation of circular RNAs driven by short IRES-like elements. Nat Commun 2022; 13:3751. [PMID: 35768398 PMCID: PMC9242994 DOI: 10.1038/s41467-022-31327-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 06/09/2022] [Indexed: 12/30/2022] Open
Abstract
Some circular RNAs (circRNAs) were found to be translated through IRES-driven mechanism, however the scope and functions of circRNA translation are unclear because endogenous IRESs are rare. To determine the prevalence and mechanism of circRNA translation, we develop a cell-based system to screen random sequences and identify 97 overrepresented hexamers that drive cap-independent circRNA translation. These IRES-like short elements are significantly enriched in endogenous circRNAs and sufficient to drive circRNA translation. We further identify multiple trans-acting factors that bind these IRES-like elements to initiate translation. Using mass-spectrometry data, hundreds of circRNA-coded peptides are identified, most of which have low abundance due to rapid degradation. As judged by mass-spectrometry, 50% of translatable endogenous circRNAs undergo rolling circle translation, several of which are experimentally validated. Consistently, mutations of the IRES-like element in one circRNA reduce its translation. Collectively, our findings suggest a pervasive translation of circRNAs, providing profound implications in translation control. Unbiased screen of random sequences identified many short IRES-like elements to drive circular RNA translation and hundreds of rolling circle translation events, suggesting a pervasive cap-independent translation in human transcriptome.
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Affiliation(s)
- Xiaojuan Fan
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yun Yang
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China.,CirCode BioMedicine, Pudong, Shanghai, China
| | - Chuyun Chen
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China
| | - Zefeng Wang
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China. .,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
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6
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Imanishi M. Mechanisms and Strategies for Determining m 6 A RNA Modification Sites by Natural and Engineered m 6 A Effector Proteins. Chem Asian J 2022; 17:e202200367. [PMID: 35750635 DOI: 10.1002/asia.202200367] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/17/2022] [Indexed: 12/13/2022]
Abstract
N6 -Methyladenosine (m6 A) is the most common internal RNA modification in the consensus sequence of 5'-RRACH-3'. The methyl mark is added by writer proteins (METTL3/METTL14 metyltransferase complex) and removed by eraser proteins (m6 A demethylases; FTO and ALKBH5). Recognition of this methyl mark by m6 A reader proteins leads to changes in RNA metabolism. How the writer and eraser proteins determine their targets is not well-understood, despite the importance of this information in understanding the regulatory mechanisms and physiological roles of m6 A. However, approaches for targeted manipulation of the methylation state at specific sites are being developed. In this review, I summarize the recent findings on the mechanisms of target identification of m6 A regulatory proteins, as well as recent approaches for targeted m6 A modifications.
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Affiliation(s)
- Miki Imanishi
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto, 611-0011, Japan
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7
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Nakamura K, Nakao T, Mori T, Ohno S, Fujita Y, Masaoka K, Sakabayashi K, Mori K, Tobimatsu T, Sera T. Necessity of Flanking Repeats R1' and R8' of Human Pumilio1 Protein for RNA Binding. Biochemistry 2021; 60:3007-3015. [PMID: 34541851 DOI: 10.1021/acs.biochem.1c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human Pumilio (hPUM) is a structurally well-analyzed RNA-binding protein that has been used recently for artificial RNA binding. Structural analysis revealed that amino acids at positions 12, 13, and 16 in the repeats from R1 to R8 each contact one specific RNA base in the eight-nucleotide RNA target. The functions of the N- and C-terminal flanking repeats R1' and R8', however, remain unclear. Here, we report how the repeats contribute to overall RNA binding. We first prepared three mutants in which R1' and/or R8' were deleted and then analyzed RNA binding using gel shift assays. The assays showed that all deletion mutants bound to their target less than the original hPUM, but that R1' contributed more than R8', unlike Drosophila PUM. We next investigated which amino acid residues of R1' or R8' were responsible for RNA binding. With detailed analysis of the protein tertiary structure, we found a hydrophobic core in each of the repeats. We therefore mutated all hydrophobic amino residues in each core to alanine. The gel shift assays with the resulting mutants revealed that both hydrophobic cores contributed to the RNA binding: especially the hydrophobic core of R1' had a significant influence. In the present study, we demonstrated that the flanking R1' and R8' repeats are indispensable for RNA binding of hPUM and suggest that hydrophobic R1'-R1 interactions may stabilize the whole hPUM structure.
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Affiliation(s)
- Kento Nakamura
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Taishu Nakao
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Tomoaki Mori
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Serika Ohno
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Yusuke Fujita
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Keisuke Masaoka
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Kazuki Sakabayashi
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Koichi Mori
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Takamasa Tobimatsu
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Takashi Sera
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
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8
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Xu Z, Zhao J, Hong M, Zeng C, Guang S, Shi Y. Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans. Nucleic Acids Res 2021; 49:10082-10097. [PMID: 34478557 PMCID: PMC8464079 DOI: 10.1093/nar/gkab754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 07/31/2021] [Accepted: 09/01/2021] [Indexed: 11/22/2022] Open
Abstract
The molecular mechanisms of aging are unsolved fundamental biological questions. Caenorhabditis elegans is an ideal model organism for investigating aging. PUF-8, a PUF (Pumilio and FBF) protein in C. elegans, is crucial for germline development through binding with the 3′ untranslated regions (3′ UTR) in the target mRNAs. Recently, PUF-8 was reported to alter mitochondrial dynamics and mitophagy by regulating MFF-1, a mitochondrial fission factor, and subsequently regulated longevity. Here, we determined the crystal structure of the PUF domain of PUF-8 with an RNA substrate. Mutagenesis experiments were performed to alter PUF-8 recognition of its target mRNAs. Those mutations reduced the fertility and extended the lifespan of C. elegans. Deep sequencing of total mRNAs from wild-type and puf-8 mutant worms as well as in vivo RNA Crosslinking and Immunoprecipitation (CLIP) experiments identified six PUF-8 regulated genes, which contain at least one PUF-binding element (PBE) at the 3′ UTR. One of the six genes, pqm-1, is crucial for lipid storage and aging process. Knockdown of pqm-1 could revert the lifespan extension of puf-8 mutant animals. We conclude that PUF-8 regulate the lifespan of C. elegans may not only via MFF but also via modulating pqm-1-related pathways.
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Affiliation(s)
- Zheng Xu
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Jie Zhao
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Minjie Hong
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Chenming Zeng
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Shouhong Guang
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yunyu Shi
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
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9
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Zhou W, Melamed D, Banyai G, Meyer C, Tuschl T, Wickens M, Cao J, Fields S. Expanding the binding specificity for RNA recognition by a PUF domain. Nat Commun 2021; 12:5107. [PMID: 34429425 PMCID: PMC8384837 DOI: 10.1038/s41467-021-25433-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/10/2021] [Indexed: 02/07/2023] Open
Abstract
The ability to design a protein to bind specifically to a target RNA enables numerous applications, with the modular architecture of the PUF domain lending itself to new RNA-binding specificities. For each repeat of the Pumilio-1 PUF domain, we generate a library that contains the 8,000 possible combinations of amino acid substitutions at residues critical for RNA contact. We carry out yeast three-hybrid selections with each library against the RNA recognition sequence for Pumilio-1, with any possible base present at the position recognized by the randomized repeat. We use sequencing to score the binding of each variant, identifying many variants with highly repeat-specific interactions. From these data, we generate an RNA binding code specific to each repeat and base. We use this code to design PUF domains against 16 RNAs, and find that some of these domains recognize RNAs with two, three or four changes from the wild type sequence.
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Affiliation(s)
- Wei Zhou
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, Washington, USA ,grid.34477.330000000122986657Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA ,grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Daniel Melamed
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, Washington, USA ,grid.18098.380000 0004 1937 0562Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel ,grid.18098.380000 0004 1937 0562Institute of Evolution, University of Haifa, Haifa, Israel
| | - Gabor Banyai
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Cindy Meyer
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Thomas Tuschl
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Marvin Wickens
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Junyue Cao
- grid.134907.80000 0001 2166 1519The Rockefeller University, New York, NY USA
| | - Stanley Fields
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, Washington, USA ,grid.34477.330000000122986657Department of Medicine, University of Washington, Seattle, Washington, USA
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10
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Pan X, Zhao J, Zhou Z, Chen J, Yang Z, Wu Y, Bai M, Jiao Y, Yang Y, Hu X, Cheng T, Lu Q, Wang B, Li CL, Lu YJ, Diao L, Zhong YQ, Pan J, Zhu J, Xiao HS, Qiu ZL, Li J, Wang Z, Hui J, Bao L, Zhang X. 5'-UTR SNP of FGF13 causes translational defect and intellectual disability. eLife 2021; 10:63021. [PMID: 34184986 PMCID: PMC8241442 DOI: 10.7554/elife.63021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 06/17/2021] [Indexed: 12/15/2022] Open
Abstract
The congenital intellectual disability (ID)-causing gene mutations remain largely unclear, although many genetic variations might relate to ID. We screened gene mutations in Chinese Han children suffering from severe ID and found a single-nucleotide polymorphism (SNP) in the 5′-untranslated region (5′-UTR) of fibroblast growth factor 13 (FGF13) mRNA (NM_001139500.1:c.-32c>G) shared by three male children. In both HEK293 cells and patient-derived induced pluripotent stem cells, this SNP reduced the translation of FGF13, which stabilizes microtubules in developing neurons. Mice carrying the homologous point mutation in 5′-UTR of Fgf13 showed delayed neuronal migration during cortical development, and weakened learning and memory. Furthermore, this SNP reduced the interaction between FGF13 5′-UTR and polypyrimidine-tract-binding protein 2 (PTBP2), which was required for FGF13 translation in cortical neurons. Thus, this 5′-UTR SNP of FGF13 interferes with the translational process of FGF13 and causes deficits in brain development and cognitive functions.
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Affiliation(s)
- Xingyu Pan
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Brain-Intelligence Project Center, Shanghai, China
| | - Jingrong Zhao
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhiying Zhou
- Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Jijun Chen
- Shanghai Brain-Intelligence Project Center, Shanghai, China
| | - Zhenxing Yang
- Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Yuxuan Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Meizhu Bai
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yang Jiao
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Yun Yang
- CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xuye Hu
- Shanghai Brain-Intelligence Project Center, Shanghai, China.,Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Tianling Cheng
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qianyun Lu
- CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Bin Wang
- Shanghai Brain-Intelligence Project Center, Shanghai, China.,State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Chang-Lin Li
- Shanghai Brain-Intelligence Project Center, Shanghai, China.,Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Ying-Jin Lu
- Shanghai Brain-Intelligence Project Center, Shanghai, China.,Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Lei Diao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yan-Qing Zhong
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jing Pan
- Shanghai Brain-Intelligence Project Center, Shanghai, China
| | - Jianmin Zhu
- Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Hua-Sheng Xiao
- Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China
| | - Zi-Long Qiu
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Zefeng Wang
- CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Lan Bao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Xu Zhang
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Brain-Intelligence Project Center, Shanghai, China.,Shanghai Clinical Center, Chinese Academy of Sciences/Xu-Hui Central Hospital, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.,Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
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11
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Bedi K, Magnuson BR, Narayanan I, Paulsen M, Wilson TE, Ljungman M. Co-transcriptional splicing efficiencies differ within genes and between cell types. RNA (NEW YORK, N.Y.) 2021; 27:rna.078662.120. [PMID: 33975916 PMCID: PMC8208053 DOI: 10.1261/rna.078662.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/05/2021] [Indexed: 06/01/2023]
Abstract
Pre-mRNA splicing is carried out by the spliceosome and involves splice site recognition, removal of introns, and ligation of exons. Components of the spliceosome have been shown to interact with the elongating RNA polymerase II (RNAPII) which is thought to allow splicing to occur concurrently with transcription. However, little is known about the regulation and efficiency of co-transcriptional splicing in human cells. In this study, we used Bru-seq and BruChase-seq to determine the co-transcriptional splicing efficiencies of 17,000 introns expressed across 6 human cell lines. We found that less than half of all introns across these 6 cell lines were co-transcriptionally spliced. Splicing efficiencies for individual introns showed variations across cell lines, suggesting that splicing may be regulated in a cell-type specific manner. Moreover, the splicing efficiency of introns varied within genes. The efficiency of co-transcriptional splicing did not correlate with gene length, intron position, splice site strengths, or the intron/neighboring exons GC content. However, we identified binding signals from multiple RNA binding proteins (RBPs) that correlated with splicing efficiency, including core spliceosomal machinery components-such as SF3B4, U2AF1 and U2AF2 showing higher binding signals in poorly spliced introns. In addition, multiple RBPs, such as BUD13, PUM1 and SND1, showed preferential binding in exons that flank introns with high splicing efficiencies. The nascent RNA splicing patterns presented here across multiple cell types add to our understanding of the complexity in RNA splicing, wherein RNA-binding proteins may play important roles in determining splicing outcomes in a cell type- and intron-specific manner.
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12
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Wolfe MB, Schagat TL, Paulsen MT, Magnuson B, Ljungman M, Park D, Zhang C, Campbell ZT, Goldstrohm AC, Freddolino PL. Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis. RNA (NEW YORK, N.Y.) 2020; 26:1680-1703. [PMID: 32753408 PMCID: PMC7566576 DOI: 10.1261/rna.077362.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/30/2020] [Indexed: 05/27/2023]
Abstract
The human PUF-family proteins, PUM1 and PUM2, posttranscriptionally regulate gene expression by binding to a PUM recognition element (PRE) in the 3'-UTR of target mRNAs. Hundreds of PUM1/2 targets have been identified from changes in steady-state RNA levels; however, prior studies could not differentiate between the contributions of changes in transcription and RNA decay rates. We applied metabolic labeling to measure changes in RNA turnover in response to depletion of PUM1/2, showing that human PUM proteins regulate expression almost exclusively by changing RNA stability. We also applied an in vitro selection workflow to precisely identify the binding preferences of PUM1 and PUM2. By integrating our results with prior knowledge, we developed a "rulebook" of key contextual features that differentiate functional versus nonfunctional PREs, allowing us to train machine learning models that accurately predict the functional regulation of RNA targets by the human PUM proteins.
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Affiliation(s)
- Michael B Wolfe
- Department of Biological Chemistry and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Brian Magnuson
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Daeyoon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Chi Zhang
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Peter L Freddolino
- Department of Biological Chemistry and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
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13
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Effective RNA Regulation by Combination of Multiple Programmable RNA-Binding Proteins. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10196803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNAs play important roles in gene expression through translation and RNA splicing. Regulation of specific RNAs is useful to understand and manipulate specific transcripts. Pumilio and fem-3 mRNA-binding factor (PUF) proteins, programmable RNA-binding proteins, are promising tools for regulating specific RNAs by fusing them with various functional domains. The key question is: How can PUF-based molecular tools efficiently regulate RNA functions? Here, we show that the combination of multiple PUF proteins, compared to using a single PUF protein, targeting independent RNA sequences at the 3′ untranslated region (UTR) of a target transcript caused cooperative effects to regulate the function of the target RNA by luciferase reporter assays. It is worth noting that a higher efficacy was achieved with smaller amounts of each PUF expression vector introduced into the cells compared to using a single PUF protein. This strategy not only efficiently regulates target RNA functions but would also be effective in reducing off-target effects due to the low doses of each expression vector.
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14
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Joshna CR, Saha P, Atugala D, Chua G, Muench DG. Plant PUF RNA-binding proteins: A wealth of diversity for post-transcriptional gene regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110505. [PMID: 32563454 DOI: 10.1016/j.plantsci.2020.110505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/30/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
PUF proteins are a conserved group of sequence-specific RNA-binding proteins that typically function to negatively regulate mRNA stability and translation. PUFs are well characterized at the molecular, structural and functional levels in Drosophila, Caenorhabditis elegans, budding yeast and human systems. Although usually encoded by small gene families, PUFs are over-represented in the plant genome, with up to 36 genes identified in a single species. PUF gene expansion in plants has resulted in extensive variability in gene expression patterns, diversity in predicted RNA-binding domain structure, and novel combinations of key amino acids involved in modular nucleotide binding. Reports on the characterization of plant PUF structure and function continue to expand, and include RNA target identification, subcellular distribution, crystal structure, and molecular mechanisms. Arabidopsis PUF mutant analysis has provided insight into biological function, and has identified roles related to development and environmental stress tolerance. The diversity of plant PUFs implies an extensive role for this family of proteins in post-transcriptional gene regulation. This diversity also holds the potential for providing novel RNA-binding domains that could be engineered to produce designer PUFs to alter the metabolism of target RNAs in the cell.
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Affiliation(s)
- Chris R Joshna
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Pritha Saha
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Dilini Atugala
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Gordon Chua
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada.
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15
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Shinoda K, Suda A, Otonari K, Futaki S, Imanishi M. Programmable RNA methylation and demethylation using PUF RNA binding proteins. Chem Commun (Camb) 2020; 56:1365-1368. [DOI: 10.1039/c9cc09298f] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A new method manipulating local RNA methylation was developed by fusing the programmable RNA binding protein and the m6A demethylase or methyltransferase.
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Affiliation(s)
- Kouki Shinoda
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Akiyo Suda
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Kenko Otonari
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Shiroh Futaki
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Miki Imanishi
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
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16
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Kilchert C, Sträßer K, Kunetsky V, Änkö ML. From parts lists to functional significance-RNA-protein interactions in gene regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1582. [PMID: 31883228 DOI: 10.1002/wrna.1582] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/03/2019] [Accepted: 12/07/2019] [Indexed: 12/17/2022]
Abstract
Hundreds of canonical RNA binding proteins facilitate diverse and essential RNA processing steps in cells forming a central regulatory point in gene expression. However, recent discoveries including the identification of a large number of noncanonical proteins bound to RNA have changed our view on RNA-protein interactions merely as necessary steps in RNA biogenesis. As the list of proteins interacting with RNA has expanded, so has the scope of regulation through RNA-protein interactions. In addition to facilitating RNA metabolism, RNA binding proteins help to form subcellular structures and membraneless organelles, and provide means to recruit components of macromolecular complexes to their sites of action. Moreover, RNA-protein interactions are not static in cells but the ribonucleoprotein (RNP) complexes are highly dynamic in response to cellular cues. The identification of novel proteins in complex with RNA and ways cells use these interactions to control cellular functions continues to broaden the scope of RNA regulation in cells and the current challenge is to move from cataloguing the components of RNPs into assigning them functions. This will not only facilitate our understanding of cellular homeostasis but may bring in key insights into human disease conditions where RNP components play a central role. This review brings together the classical view of regulation accomplished through RNA-protein interactions with the novel insights gained from the identification of RNA binding interactomes. We discuss the challenges in combining molecular mechanism with cellular functions on the journey towards a comprehensive understanding of the regulatory functions of RNA-protein interactions in cells. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications aRNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Cornelia Kilchert
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Katja Sträßer
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Vladislav Kunetsky
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Minna-Liisa Änkö
- Centre for Reproductive Health and Centre for Cancer Research, Hudson Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Molecular and Translational Science, School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
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17
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Wallis CP, Scott LH, Filipovska A, Rackham O. Manipulating and elucidating mitochondrial gene expression with engineered proteins. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190185. [PMID: 31787043 DOI: 10.1098/rstb.2019.0185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many conventional, modern genome engineering tools cannot be used to study mitochondrial genetics due to the unusual structure and physiology of the mitochondrial genome. Here, we review a number of newly developed, synthetic biology-based approaches for altering levels of mutant mammalian mitochondrial DNA and mitochondrial RNAs, including transcription activator-like effector nucleases, zinc finger nucleases and engineered RNA-binding proteins. These approaches allow researchers to manipulate and visualize mitochondrial processes and may provide future therapeutics. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Christopher P Wallis
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia
| | - Louis H Scott
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Western Australia 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
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18
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Pei Y, Lu M. Programmable RNA manipulation in living cells. Cell Mol Life Sci 2019; 76:4861-4867. [PMID: 31367845 PMCID: PMC11105762 DOI: 10.1007/s00018-019-03252-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/23/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023]
Abstract
RNAs are responsible for mediating genetic information flow within the cell. RNA splicing, modification, trafficking, translation, and stability are all controlled at the transcript level. However, biological tools to study and manipulate them in a programmable fashion are currently limited. In this review, we summarize recent advances regarding available RNA-targeting systems discovered so far, including CRISPR-based technologies-Cas9 and Cas13, and programmable RNA-binding proteins-PUF and PPR. These tools allow transcript-specific manipulation in gene expression.
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Affiliation(s)
- Yu Pei
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Mingxing Lu
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong.
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19
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Shotwell CR, Cleary JD, Berglund JA. The potential of engineered eukaryotic RNA-binding proteins as molecular tools and therapeutics. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1573. [PMID: 31680457 DOI: 10.1002/wrna.1573] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/21/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023]
Abstract
Eukaroytic RNA-binding proteins (RBPs) recognize and process RNAs through recognition of their sequence motifs via RNA-binding domains (RBDs). RBPs usually consist of one or more RBDs and can include additional functional domains that modify or cleave RNA. Engineered RBPs have been used to answer basic biology questions, control gene expression, locate viral RNA in vivo, as well as many other tasks. Given the growing number of diseases associated with RNA and RBPs, engineered RBPs also have the potential to serve as therapeutics. This review provides an in depth description of recent advances in engineered RBPs and discusses opportunities and challenges in the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Methods > RNA Nanotechnology RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Carl R Shotwell
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida
| | - John D Cleary
- RNA Institute, University at Albany, Albany, New York
| | - J Andrew Berglund
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York
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20
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Jarmoskaite I, Denny SK, Vaidyanathan PP, Becker WR, Andreasson JOL, Layton CJ, Kappel K, Shivashankar V, Sreenivasan R, Das R, Greenleaf WJ, Herschlag D. A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins. Mol Cell 2019; 74:966-981.e18. [PMID: 31078383 DOI: 10.1101/403006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/31/2019] [Accepted: 04/05/2019] [Indexed: 05/20/2023]
Abstract
High-throughput methodologies have enabled routine generation of RNA target sets and sequence motifs for RNA-binding proteins (RBPs). Nevertheless, quantitative approaches are needed to capture the landscape of RNA-RBP interactions responsible for cellular regulation. We have used the RNA-MaP platform to directly measure equilibrium binding for thousands of designed RNAs and to construct a predictive model for RNA recognition by the human Pumilio proteins PUM1 and PUM2. Despite prior findings of linear sequence motifs, our measurements revealed widespread residue flipping and instances of positional coupling. Application of our thermodynamic model to published in vivo crosslinking data reveals quantitative agreement between predicted affinities and in vivo occupancies. Our analyses suggest a thermodynamically driven, continuous Pumilio-binding landscape that is negligibly affected by RNA structure or kinetic factors, such as displacement by ribosomes. This work provides a quantitative foundation for dissecting the cellular behavior of RBPs and cellular features that impact their occupancies.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah K Denny
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Scribe Therapeutics, Berkeley, CA, 94704, USA
| | | | - Winston R Becker
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Johan O L Andreasson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Curtis J Layton
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Raashi Sreenivasan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
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21
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Wang F, Wang L, Zou X, Duan S, Li Z, Deng Z, Luo J, Lee SY, Chen S. Advances in CRISPR-Cas systems for RNA targeting, tracking and editing. Biotechnol Adv 2019; 37:708-729. [PMID: 30926472 DOI: 10.1016/j.biotechadv.2019.03.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/21/2022]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely used in gene/genome targeting. Modifications of Cas9 enable these systems to become platforms for precise DNA manipulations. However, the utilization of CRISPR-Cas systems in RNA targeting remains preliminary. The discovery of type VI CRISPR-Cas systems (Cas13) shed light on RNA-guided RNA targeting. Cas13d, the smallest Cas13 protein, with a length of only ~930 amino acids, is a promising platform for RNA targeting compatible with viral delivery systems. Much effort has also been made to develop Cas9, Cas13a and Cas13b applications for RNA-guided RNA targeting. The discovery of new RNA-targeting CRISPR-Cas systems as well as the development of RNA-targeting platforms with Cas9 and Cas13 will promote RNA-targeting technology substantially. Here, we review new advances in RNA-targeting CRISPR-Cas systems as well as advances in applications of these systems in RNA targeting, tracking and editing. We also compare these Cas protein-based technologies with traditional technologies for RNA targeting, tracking and editing. Finally, we discuss remaining questions and prospects for the future.
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Affiliation(s)
- Fei Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Xuan Zou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology, Yuseong-gu, 34141 Daejeon, Republic of Korea
| | - Suling Duan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Zhiqiang Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Jie Luo
- Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology, Yuseong-gu, 34141 Daejeon, Republic of Korea.
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China.
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22
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Bhat VD, McCann KL, Wang Y, Fonseca DR, Shukla T, Alexander JC, Qiu C, Wickens M, Lo TW, Tanaka Hall TM, Campbell ZT. Engineering a conserved RNA regulatory protein repurposes its biological function in vivo. eLife 2019; 8:43788. [PMID: 30652968 PMCID: PMC6351103 DOI: 10.7554/elife.43788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/15/2019] [Indexed: 12/18/2022] Open
Abstract
PUF (PUmilio/FBF) RNA-binding proteins recognize distinct elements. In C. elegans, PUF-8 binds to an 8-nt motif and restricts proliferation in the germline. Conversely, FBF-2 recognizes a 9-nt element and promotes mitosis. To understand how motif divergence relates to biological function, we first determined a crystal structure of PUF-8. Comparison of this structure to that of FBF-2 revealed a major difference in a central repeat. We devised a modified yeast 3-hybrid screen to identify mutations that confer recognition of an 8-nt element to FBF-2. We identified several such mutants and validated structurally and biochemically their binding to 8-nt RNA elements. Using genome engineering, we generated a mutant animal with a substitution in FBF-2 that confers preferential binding to the PUF-8 element. The mutant largely rescued overproliferation in animals that spontaneously generate tumors in the absence of puf-8. This work highlights the critical role of motif length in the specification of biological function.
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Affiliation(s)
- Vandita D Bhat
- Department of Biological Sciences, University of Texas Dallas, Richardson, United States
| | - Kathleen L McCann
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | - Yeming Wang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | | | - Tarjani Shukla
- Department of Biological Sciences, University of Texas Dallas, Richardson, United States
| | | | - Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | - Marv Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Te-Wen Lo
- Department of Biology, Ithaca College, Ithaca, United States
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas Dallas, Richardson, United States
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23
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Mao M, Hu Y, Yang Y, Qian Y, Wei H, Fan W, Yang Y, Li X, Wang Z. Modeling and Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning. Cell Syst 2018; 7:510-520.e4. [PMID: 30414922 DOI: 10.1016/j.cels.2018.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 05/10/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
Abstract
Alternative splicing (AS) is generally regulated by trans-splicing factors that specifically bind to cis-elements in pre-mRNAs. The human genome encodes ∼1,500 RNA binding proteins (RBPs) that potentially regulate AS, yet their functions remain largely unknown. To explore their potential activities, we fused the putative functional domains of RBPs to a sequence-specific RNA-binding domain and systemically analyzed how these engineered factors affect splicing. We discovered that ∼80% of low-complexity domains in endogenous RBPs displayed distinct context-dependent activities in regulating splicing, indicating that AS is under more extensive regulation than previously expected. We developed a machine learning approach to classify and predict the activities of RBPs based on their sequence compositions and further validated this model using endogenous RBPs and synthetic polypeptides. These results represent a systematic inspection, modeling, prediction, and validation of how RBP sequences affect their activities in controlling splicing, paving the way for de novo engineering of artificial splicing factors.
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Affiliation(s)
- Miaowei Mao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China; Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Yue Hu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yun Yang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yajie Qian
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Huanhuan Wei
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Fan
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
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24
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Goldstrohm AC, Hall TMT, McKenney KM. Post-transcriptional Regulatory Functions of Mammalian Pumilio Proteins. Trends Genet 2018; 34:972-990. [PMID: 30316580 DOI: 10.1016/j.tig.2018.09.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/10/2018] [Accepted: 09/19/2018] [Indexed: 01/18/2023]
Abstract
Mammalian Pumilio proteins, PUM1 and PUM2, are members of the PUF family of sequence-specific RNA-binding proteins. In this review, we explore their mechanisms, regulatory networks, biological functions, and relevance to diseases. Pumilio proteins bind an extensive network of mRNAs and repress protein expression by inhibiting translation and promoting mRNA decay. Opposingly, in certain contexts, they can activate protein expression. Pumilio proteins also regulate noncoding (nc)RNAs. The ncRNA, ncRNA activated by DNA damage (NORAD), can in turn modulate Pumilio activity. Genetic analysis provides new insights into Pumilio protein function. They are essential for growth and development. They control diverse processes, including stem cell fate, and neurological functions, such as behavior and memory formation. Novel findings show that their dysfunction contributes to neurodegeneration, epilepsy, movement disorders, intellectual disability, infertility, and cancer.
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Affiliation(s)
- Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Katherine M McKenney
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
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25
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Wallis CP, Richman TR, Filipovska A, Rackham O. Tighter Ligand Binding Can Compensate for Impaired Stability of an RNA-Binding Protein. ACS Chem Biol 2018; 13:1499-1505. [PMID: 29808990 DOI: 10.1021/acschembio.8b00424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
It has been widely shown that ligand-binding residues, by virtue of their orientation, charge, and solvent exposure, often have a net destabilizing effect on proteins that is offset by stability conferring residues elsewhere in the protein. This structure-function trade-off can constrain possible adaptive evolutionary changes of function and may hamper protein engineering efforts to design proteins with new functions. Here, we present evidence from a large randomized mutant library screen that, in the case of PUF RNA-binding proteins, this structural relationship may be inverted and that active-site mutations that increase protein activity are also able to compensate for impaired stability. We show that certain mutations in RNA-protein binding residues are not necessarily destabilizing and that increased ligand-binding can rescue an insoluble, unstable PUF protein. We hypothesize that these mutations restabilize the protein via thermodynamic coupling of protein folding and RNA binding.
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Affiliation(s)
- Christopher P. Wallis
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands 6009, Australia
| | - Tara R. Richman
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands 6009, Australia
- School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands 6009, Australia
- School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
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26
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Zhao YY, Mao MW, Zhang WJ, Wang J, Li HT, Yang Y, Wang Z, Wu JW. Expanding RNA binding specificity and affinity of engineered PUF domains. Nucleic Acids Res 2018; 46:4771-4782. [PMID: 29490074 PMCID: PMC5961129 DOI: 10.1093/nar/gky134] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/08/2018] [Accepted: 02/16/2018] [Indexed: 12/26/2022] Open
Abstract
Specific manipulation of RNA is necessary for the research in biotechnology and medicine. The RNA-binding domains of Pumilio/fem-3 mRNA binding factors (PUF domains) are programmable RNA binding scaffolds used to engineer artificial proteins that specifically modulate RNAs. However, the native PUF domains generally recognize 8-nt RNAs, limiting their applications. Here, we modify the PUF domain of human Pumilio1 to engineer PUFs that recognize RNA targets of different length. The engineered PUFs bind to their RNA targets specifically and PUFs with more repeats have higher binding affinity than the canonical eight-repeat domains; however, the binding affinity reaches the peak at those with 9 and 10 repeats. Structural analysis on PUF with nine repeats reveals a higher degree of curvature, and the RNA binding unexpectedly and dramatically opens the curved structure. Investigation of the residues positioned in between two RNA bases demonstrates that tyrosine and arginine have favored stacking interactions. Further tests on the availability of the engineered PUFs in vitro and in splicing function assays indicate that our engineered PUFs bind RNA targets with high affinity in a programmable way.
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Affiliation(s)
- Yang-Yang Zhao
- Center for Life Sciences, Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Miao-Wei Mao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biological Science, Shanghai 200031, China
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wen-Jing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Jue Wang
- Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu 215123, China
| | - Hai-Tao Li
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biological Science, Shanghai 200031, China
- Enzerna Biosciences, Inc., 125 South Road, 925B Kenan Labs, CB#3266, Chapel Hill, NC 27599, USA
| | - Jia-Wei Wu
- Center for Life Sciences, Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu 215123, China
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27
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Abstract
Epigenetic modifications of DNA and chromatin are long known to control stem cell differentiation and organ function but the role of similar modifications at the level or regulatory RNAs is just beginning to emerge. Over 160 RNA modifications have been identified but their abundance, distribution and functional significance are not known. The few available maps of RNA modifications indicated their dynamic regulation during somatic stem cell differentiation, brain development and function in adulthood suggesting a hitherto unsuspected layer of regulation both at the level of RNA metabolism and post-transcriptional control of gene expression. The advent of programmable, RNA-specific CRISPR-Cas editing platforms together with the identification of RNA modifying enzymes now offers the opportunity to investigate the functional role of these elusive epitranscriptome changes. Here, we discuss recent insights in studying the most abundant modifications in functional mRNAs and lncRNAs, N6-methyladenosine and 5-(hydroxy-)methylcytosine, and their role in regulating somatic stem cell differentiation with particular attention to neural stem cells during mammalian corticogenesis. An outlook on novel CRISPR-Cas based systems that allow stem cell reprogramming by epitranscriptome-editing will also be discussed.
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Affiliation(s)
- Florian Noack
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies, Dresden, Germany
| | - Federico Calegari
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies, Dresden, Germany
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28
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Mahas A, Neal Stewart C, Mahfouz MM. Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation. Biotechnol Adv 2018; 36:295-310. [DOI: 10.1016/j.biotechadv.2017.11.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/03/2017] [Accepted: 11/27/2017] [Indexed: 12/26/2022]
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29
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De Franco S, O'Connell MR, Vandevenne M. Engineering RNA-Binding Proteins by Modular Assembly of RanBP2-Type Zinc Fingers. Methods Mol Biol 2018; 1867:57-74. [PMID: 30155815 DOI: 10.1007/978-1-4939-8799-3_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Deciphering the function of the nonprotein-coding portion of genomes represents one of the major challenges that molecular biology is facing today. Numerous classes of RNAs have been discovered over the last past decade and appear to play important regulatory roles in gene expression and disease. The ability to study and manipulate these RNAs relies on the development of programmable RNA-binding molecules such as RNA-binding proteins. Most RNA-binding proteins have modular architectures and combine different RNA-binding domains that provide binding affinity toward a specific RNA sequence and/or structure. Herein, we describe a general strategy to design single-stranded RNA-binding proteins using RanBP2-type zinc-finger (ZF) domains that can recognize a given RNA sequence with high affinity and specificity.
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Affiliation(s)
- Simona De Franco
- Center for Protein Engineering, University of Liège, Liège, Belgium
| | - Mitchell R O'Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Center for RNA Biology, University of Rochester, Rochester, NY, USA
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30
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Shinoda K, Tsuji S, Futaki S, Imanishi M. Nested PUF Proteins: Extending Target RNA Elements for Gene Regulation. Chembiochem 2017; 19:171-176. [DOI: 10.1002/cbic.201700458] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Kouki Shinoda
- Institute for Chemical Research Kyoto University Uji Kyoto 611-0011 Japan
| | - Shogo Tsuji
- Institute for Chemical Research Kyoto University Uji Kyoto 611-0011 Japan
| | - Shiroh Futaki
- Institute for Chemical Research Kyoto University Uji Kyoto 611-0011 Japan
| | - Miki Imanishi
- Institute for Chemical Research Kyoto University Uji Kyoto 611-0011 Japan
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31
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Bao H, Wang N, Wang C, Jiang Y, Liu J, Xu L, Wu J, Shi Y. Structural basis for the specific recognition of 18S rRNA by APUM23. Nucleic Acids Res 2017; 45:12005-12014. [PMID: 29036323 PMCID: PMC5714250 DOI: 10.1093/nar/gkx872] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/19/2017] [Indexed: 01/26/2023] Open
Abstract
PUF (Pumilio/fem-3 mRNA binding factor) proteins, a conserved family of RNA-binding proteins, recognize specific single-strand RNA targets in a specific modular way. Although plants have a greater number of PUF protein members than do animal and fungal systems, they have been the subject of fewer structural and functional investigations. The aim of this study was to elucidate the involvement of APUM23, a nucleolar PUF protein in the plant Arabidopsis, in pre-rRNA processing. APUM23 is distinct from classical PUF family proteins, which are located in the cytoplasm and bind to 3'UTRs of mRNA to modulate mRNA expression and localization. We found that the complete RNA target sequence of APUM23 comprises 11 nt in 18S rRNA at positions 1141-1151. The complex structure shows that APUM23 has 10 PUF repeats; it assembles into a C-shape, with an insertion located within the inner concave surface. We found several different RNA recognition features. A notable structural feature of APUM23 is an insertion in the third PUF repeat that participates in nucleotide recognition and maintains the correct conformation of the target RNA. Our findings elucidate the mechanism for APUM23's-specific recognition of 18S rRNA.
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Affiliation(s)
- Hongyu Bao
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Na Wang
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chongyuan Wang
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Jiuyang Liu
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Li Xu
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Jihui Wu
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.,CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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32
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Yoshimura H. Live Cell Imaging of Endogenous RNAs Using Pumilio Homology Domain Mutants: Principles and Applications. Biochemistry 2017; 57:200-208. [PMID: 29164876 DOI: 10.1021/acs.biochem.7b00983] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recently, dynamic changes in the location of RNA in space and time in living cells have become a target of interest in biology because of their essential roles in controlling physiological phenomena. To visualize RNA, methods for the fluorescent labeling of RNA in living cells have been developed. For RNA labeling, oligonucleotide-based RNA probes have mainly been used because of their high selectivity for target RNAs. By contrast, protein-based RNA probes have not been used widely because of their lack of design flexibility, although they have various potential advantages compared with nucleotide-based probes, such as controllability of intracellular localization, high detectability, and ease of introduction into cells and transgenic organisms in a cell type and tissue specific manner by genetic engineering techniques. This Perspective focuses on a possible approach to the development of protein-based RNA probes using Pumilio homology domain (PUM-HD) mutants. The PUM-HD is a domain of an RNA binding protein that allows custom-made modifications to recognize a given eight-base RNA sequence. PUM-HD-based RNA probes have been applied to visualize various RNAs in living cells. Here, the techniques and RNA imaging results obtained using the PUM-HD are introduced.
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Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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33
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Shanmugam T, Abbasi N, Kim HS, Kim HB, Park NI, Park GT, Oh SA, Park SK, Muench DG, Choi Y, Park YI, Choi SB. An Arabidopsis divergent pumilio protein, APUM24, is essential for embryogenesis and required for faithful pre-rRNA processing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1092-1105. [PMID: 29031033 DOI: 10.1111/tpj.13745] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 09/28/2017] [Accepted: 10/03/2017] [Indexed: 05/06/2023]
Abstract
Pumilio RNA-binding proteins are largely involved in mRNA degradation and translation repression. However, a few evolutionarily divergent Pumilios are also responsible for proper pre-rRNA processing in human and yeast. Here, we describe an essential Arabidopsis nucleolar Pumilio, APUM24, that is expressed in tissues undergoing rapid proliferation and cell division. A T-DNA insertion for APUM24 did not affect the male and female gametogenesis, but instead resulted in a negative female gametophytic effect on zygotic cell division immediately after fertilization. Additionally, the mutant embryos displayed defects in cell patterning from pro-embryo through globular stages. The mutant embryos were marked by altered auxin maxima, which were substantiated by the mislocalization of PIN1 and PIN7 transporters in the defective embryos. Homozygous apum24 callus accumulates rRNA processing intermediates, including uridylated and adenylated 5.8S and 25S rRNA precursors. An RNA-protein interaction assay showed that the histidine-tagged recombinant APUM24 binds RNAin vitro with no apparent specificity. Overall, our results demonstrated that APUM24 is required for rRNA processing and early embryogenesis in Arabidopsis.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Nazia Abbasi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Hyung-Sae Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Ho Bang Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Nam-Il Park
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Guen Tae Park
- School of Biological Sciences, Seoul National University, Seoul, 151-747, South Korea
| | - Sung Aeong Oh
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Yeonhee Choi
- School of Biological Sciences, Seoul National University, Seoul, 151-747, South Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, South Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
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34
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Song X, Zeng Z, Wei H, Wang Z. Alternative splicing in cancers: From aberrant regulation to new therapeutics. Semin Cell Dev Biol 2017; 75:13-22. [PMID: 28919308 DOI: 10.1016/j.semcdb.2017.09.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/09/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022]
Abstract
Alternative splicing is one of the most common mechanisms for gene regulation in humans, and plays a vital role to increase the complexity of functional proteins. In this article, we seek to provide a general review on the relationships between alternative splicing and tumorigenesis. We briefly introduce the basic rules for regulation of alternative splicing, and discuss recent advances on dynamic regulation of alternative splicing in cancers by highlighting the roles of a variety of RNA splicing factors in tumorigenesis. We further discuss several important questions regarding the splicing of long noncoding RNAs and back-splicing of circular RNAs in cancers. Finally, we discuss the current technologies that can be used to manipulate alternative splicing and serve as potential cancer treatment.
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Affiliation(s)
- Xiaowei Song
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Department of Cardiology, Changhai Hospital, 168 Changhai Road, Shanghai 200433, China.
| | - Zhenyu Zeng
- Department of Cardiology, Changhai Hospital, 168 Changhai Road, Shanghai 200433, China
| | - Huanhuan Wei
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zefeng Wang
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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35
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Wang B, Ye K. Nop9 binds the central pseudoknot region of 18S rRNA. Nucleic Acids Res 2017; 45:3559-3567. [PMID: 28053123 PMCID: PMC5389560 DOI: 10.1093/nar/gkw1323] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023] Open
Abstract
The assembly of eukaryotic ribosomes requires numerous factors that transiently associate with evolving pre-ribosomal particles. The Pumilio repeat-containing protein Nop9 briefly associates with the 90S pre-ribosome during its co-transcriptional assembly. Here, we show that Nop9 specifically binds an 11-nucleotide sequence of 18S rRNA that forms the 3΄ side of the central pseudoknot and helix 28 in the mature subunit. Crystal structures of Nop9 in the free and RNA-bound states reveal a new type of Pumilio repeat protein with a distinct structure, target sequence and RNA-binding mode. Nop9 contains 10 Pumilio repeats arranged into a U-shaped scaffold. The target RNA is recognized by two stretches of repeats in a bipartite manner, and three central bases are unrecognized as a result of the degeneracy of repeats 6 and 7. Our data suggest that Nop9 regulates the folding of 18S rRNA at early assembly stages of 90S.
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Affiliation(s)
- Bing Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China.,National Institute of Biological Sciences, Beijing 102206, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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36
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Abil Z, Gumy LF, Zhao H, Hoogenraad CC. Inducible Control of mRNA Transport Using Reprogrammable RNA-Binding Proteins. ACS Synth Biol 2017; 6:950-956. [PMID: 28260376 PMCID: PMC5477001 DOI: 10.1021/acssynbio.7b00025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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Localization of mRNA is important
in a number of cellular processes
such as embryogenesis, cellular motility, polarity, and a variety
of neurological processes. A synthetic device that controls cellular
mRNA localization would facilitate investigations on the significance
of mRNA localization in cellular function and allow an additional
level of controlling gene expression. In this work, we developed the
PUF (Pumilio and FBF homology domain)-assisted localization of RNA
(PULR) system, which utilizes a eukaryotic cell’s cytoskeletal
transport machinery to reposition mRNA within a cell. Depending on
the cellular motor used, we show ligand-dependent transport of mRNA
toward either pole of the microtubular network of cultured cells.
In addition, implementation of the reprogrammable PUF domain allowed
the transport of untagged endogenous mRNA in primary neurons.
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Affiliation(s)
- Zhanar Abil
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Laura F. Gumy
- Cell
Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Huimin Zhao
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Department
of Chemical and Biomolecular Engineering, Department of Bioengineering,
Department of Chemistry, and Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Casper C. Hoogenraad
- Cell
Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
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37
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Wei HH, Liu Y, Wang Y, Lu Q, Yang X, Li J, Wang Z. Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells. J Vis Exp 2017. [PMID: 28518098 DOI: 10.3791/54967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The processing of most eukaryotic RNAs is mediated by RNA Binding Proteins (RBPs) with modular configurations, including an RNA recognition module, which specifically binds the pre-mRNA target and an effector domain. Previously, we have taken advantage of the unique RNA binding mode of the PUF domain in human Pumilio 1 to generate a programmable RNA binding scaffold, which was used to engineer various artificial RBPs to manipulate RNA metabolism. Here, a detailed protocol is described to construct Engineered Splicing Factors (ESFs) that are specifically designed to modulate the alternative splicing of target genes. The protocol includes how to design and construct a customized PUF scaffold for a specific RNA target, how to construct an ESF expression plasmid by fusing a designer PUF domain and an effector domain, and how to use ESFs to manipulate the splicing of target genes. In the representative results of this method, we have also described the common assays of ESF activities using splicing reporters, the application of ESF in cultured human cells, and the subsequent effect of splicing changes. By following the detailed protocols in this report, it is possible to design and generate ESFs for the regulation of different types of Alternative Splicing (AS), providing a new strategy to study splicing regulation and the function of different splicing isoforms. Moreover, by fusing different functional domains with a designed PUF domain, researchers can engineer artificial factors that target specific RNAs to manipulate various steps of RNA processing.
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Affiliation(s)
- Huan-Huan Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Yuanlong Liu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Yang Wang
- Institute of Cancer Stem Cell, Second Affiliated Hospital, Cancer Center, Dalian Medical University
| | - Qianyun Lu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Xuerong Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Jiefu Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Zefeng Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS);
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38
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Repression of the Internal Ribosome Entry Site-dependent Translation of Hepatitis C Virus by an Engineered PUF Protein. HEPATITIS MONTHLY 2017. [DOI: 10.5812/hepatmon.45022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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39
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Kellermann SJ, Rentmeister A. A FACS-based screening strategy to assess sequence-specific RNA-binding of Pumilio protein variants in E. coli. Biol Chem 2017; 398:69-75. [DOI: 10.1515/hsz-2016-0214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/15/2016] [Indexed: 12/22/2022]
Abstract
Abstract
Sequence-specific and programmable binding of proteins to RNA bears the potential to detect and manipulate target RNAs. Applications include analysis of subcellular RNA localization or post-transcriptional regulation but require sequence-specificity to be readily adjustable to any target RNA. The Pumilio homology domain binds an eight nucleotide target sequence in a predictable manner allowing for rational design of variants with new specificities. We describe a high-throughput system for screening Pumilio variants based on fluorescence-activated cell sorting of E. coli. Our approach should help optimizing variants obtained from rational design regarding folding and stability or identifying new variants with alternative binding modes.
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40
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Abil Z, Zhao H. Engineering reprogrammable RNA-binding proteins for study and manipulation of the transcriptome. MOLECULAR BIOSYSTEMS 2016; 11:2658-65. [PMID: 26166256 DOI: 10.1039/c5mb00289c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
With the expanding interest in RNA biology, interest in artificial RNA-binding proteins (RBPs) is likewise increasing. RBPs can be designed in a modular fashion, whereby effector and RNA-binding domains are combined in chimeric proteins that exhibit both functions and can be applied for regulation of a broad range of biological processes. The elucidation of the RNA recognition code for Pumilio and fem-3 mRNA-binding factor (PUF) homology proteins allowed engineering of artificial RBPs for targeting endogenous mRNAs. In this review, we will focus on the recent advances in elucidating and reprogramming PUF domain specificity, update on several promising applications of PUF-based designer RBPs, and discuss some other domains that hold the potential to be used as the RNA-binding scaffolds for designer RBP engineering.
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Affiliation(s)
- Zhanar Abil
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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41
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Kellermann SJ, Rentmeister A. A Genetically Encodable System for Sequence-Specific Detection of RNAs in Two Colors. Chembiochem 2016; 17:895-9. [PMID: 26919688 DOI: 10.1002/cbic.201500705] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Indexed: 12/28/2022]
Abstract
Multicolor readout is an important feature of RNA detection techniques aiming at the investigation of RNA localization. Several detection methods have been developed, however they require either transfection of cells with the probe or prior tagging of the target RNA. We report a fully genetically encodable system for simultaneous detection of two RNAs by using green and yellow fluorescence based on tetramolecular fluorescence complementation (TetFC). To obtain yellow fluorescent protein (YFP), substitution T203Y was introduced into one of the three non-fluorescent GFP fragments; this was fused to different variants of the Homo sapiens Pumilio homology domain. Using different sets of fusion proteins we were able to discriminate between two closely related target RNAs based on the fluorescence signals at the respective wavelengths.
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Affiliation(s)
- Stefanie J Kellermann
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany. .,Cells-in-Motion Cluster of Excellence (EXC 1003-CiM), University of Münster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.
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42
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De-coding and re-coding RNA recognition by PUF and PPR repeat proteins. Curr Opin Struct Biol 2016; 36:116-21. [PMID: 26874972 DOI: 10.1016/j.sbi.2016.01.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/14/2016] [Accepted: 01/15/2016] [Indexed: 11/22/2022]
Abstract
PUF and PPR proteins are two families of α-helical repeat proteins that recognize single-stranded RNA sequences. Both protein families hold promise as scaffolds for designed RNA-binding domains. A modular protein RNA recognition code was apparent from the first crystal structures of a PUF protein in complex with RNA, and recent studies continue to advance our understanding of natural PUF protein recognition (de-coding) and our ability to engineer specificity (re-coding). Degenerate recognition motifs make de-coding specificity of individual PPR proteins challenging. Nevertheless, re-coding PPR protein specificity using a consensus recognition code has been successful.
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43
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Hogan GJ, Brown PO, Herschlag D. Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. PLoS Biol 2015; 13:e1002307. [PMID: 26587879 PMCID: PMC4654594 DOI: 10.1371/journal.pbio.1002307] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 10/23/2015] [Indexed: 12/31/2022] Open
Abstract
Reprogramming of a gene’s expression pattern by acquisition and loss of sequences recognized by specific regulatory RNA binding proteins may be a major mechanism in the evolution of biological regulatory programs. We identified that RNA targets of Puf3 orthologs have been conserved over 100–500 million years of evolution in five eukaryotic lineages. Focusing on Puf proteins and their targets across 80 fungi, we constructed a parsimonious model for their evolutionary history. This model entails extensive and coordinated changes in the Puf targets as well as changes in the number of Puf genes and alterations of RNA binding specificity including that: 1) Binding of Puf3 to more than 200 RNAs whose protein products are predominantly involved in the production and organization of mitochondrial complexes predates the origin of budding yeasts and filamentous fungi and was maintained for 500 million years, throughout the evolution of budding yeast. 2) In filamentous fungi, remarkably, more than 150 of the ancestral Puf3 targets were gained by Puf4, with one lineage maintaining both Puf3 and Puf4 as regulators and a sister lineage losing Puf3 as a regulator of these RNAs. The decrease in gene expression of these mRNAs upon deletion of Puf4 in filamentous fungi (N. crassa) in contrast to the increase upon Puf3 deletion in budding yeast (S. cerevisiae) suggests that the output of the RNA regulatory network is different with Puf4 in filamentous fungi than with Puf3 in budding yeast. 3) The coregulated Puf4 target set in filamentous fungi expanded to include mitochondrial genes involved in the tricarboxylic acid (TCA) cycle and other nuclear-encoded RNAs with mitochondrial function not bound by Puf3 in budding yeast, observations that provide additional evidence for substantial rewiring of post-transcriptional regulation. 4) Puf3 also expanded and diversified its targets in filamentous fungi, gaining interactions with the mRNAs encoding the mitochondrial electron transport chain (ETC) complex I as well as hundreds of other mRNAs with nonmitochondrial functions. The many concerted and conserved changes in the RNA targets of Puf proteins strongly support an extensive role of RNA binding proteins in coordinating gene expression, as originally proposed by Keene. Rewiring of Puf-coordinated mRNA targets and transcriptional control of the same genes occurred at different points in evolution, suggesting that there have been distinct adaptations via RNA binding proteins and transcription factors. The changes in Puf targets and in the Puf proteins indicate an integral involvement of RNA binding proteins and their RNA targets in the adaptation, reprogramming, and function of gene expression. A map of the evolutionary history of Puf proteins and their RNA targets shows that reprogramming of global gene expression programs via adaptive mutations that affect protein-RNA interactions is an important source of biological diversity. We set out to trace the evolutionary history of an RNA binding protein and how its interactions with targets change over evolution. Identifying this natural history is a step toward understanding the critical differences between organisms and how gene expression programs are rewired during evolution. Using bioinformatics and experimental approaches, we broadly surveyed the evolution of binding targets of a particular family of RNA binding proteins—the Puf proteins, whose protein sequences and target RNA sequences are relatively well-characterized—across 99 eukaryotic species. We found five groups of species in which targets have been conserved for at least 100 million years and then took advantage of genome sequences from a large number of fungal species to deeply investigate the conservation and changes in Puf proteins and their RNA targets. Our analyses identified multiple and extensive reconfigurations during the natural history of fungi and suggest that RNA binding proteins and their RNA targets are profoundly involved in evolutionary reprogramming of gene expression and help define distinct programs unique to each organism. Continuing to uncover the natural history of RNA binding proteins and their interactions will provide a unique window into the gene expression programs of present day species and point to new ways to engineer gene expression programs.
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Affiliation(s)
- Gregory J. Hogan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Patrick O. Brown
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (POB); (DH)
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
- ChEM-H Institute, Stanford University, Stanford, California, United States of America
- * E-mail: (POB); (DH)
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44
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Zhang C, Muench DG. A Nucleolar PUF RNA-binding Protein with Specificity for a Unique RNA Sequence. J Biol Chem 2015; 290:30108-18. [PMID: 26487722 DOI: 10.1074/jbc.m115.691675] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Indexed: 12/21/2022] Open
Abstract
PUF proteins are a conserved group of sequence specific RNA-binding proteins that bind to RNA in a modular fashion. The RNA-binding domain of PUF proteins typically consists of eight clustered Puf repeats. Plant genomes code for large families of PUF proteins that show significant variability in their predicted Puf repeat number, organization, and amino acid sequence. Here we sought to determine whether the observed variability in the RNA-binding domains of four plant PUFs results in a preference for nonclassical PUF RNA target sequences. We report the identification of a novel RNA binding sequence for a nucleolar Arabidopsis PUF protein that contains an atypical RNA-binding domain. The Arabidopsis PUM23 (APUM23) binding sequence was 10 nucleotides in length, contained a centrally located UUGA core element, and had a preferred cytosine at nucleotide position 8. These RNA sequence characteristics differ from those of other PUF proteins, because all natural PUFs studied to date bind to RNAs that contain a conserved UGU sequence at their 5' end and lack specificity for cytosine. Gel mobility shift assays validated the identity of the APUM23 binding sequence and supported the location of 3 of the 10 predicted Puf repeats in APUM23, including the cytosine-binding repeat. The preferred 10-nucleotide sequence bound by APUM23 is present within the 18S rRNA sequence, supporting the known role of APUM23 in 18S rRNA maturation. This work also reveals that APUM23, an ortholog of yeast Nop9, could provide an advanced structural backbone for Puf repeat engineering and target-specific regulation of cellular RNAs.
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Affiliation(s)
- Chi Zhang
- From the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Douglas G Muench
- From the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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45
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Abstract
Pumilio is an RNA-binding protein originally identified in Drosophila, with a Puf domain made up of eight Puf repeats, three helix bundles arranged in a rainbow architecture, where each repeat recognizes a single base of the RNA-binding sequence. The eight-base recognition sequence can therefore be modified simply via mutation of the repeat that recognizes the base to be changed and this is understood in detail via high-resolution crystal structures. The binding mechanism is also altered in a variety of homologues from different species, with bases flipped out from the binding site to regenerate a consensus sequence. Thus Pumilios can be designed with bespoke RNA recognition sequences and can be fused to nucleases, split GFP, etc. as tools in vitro and in cells.
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46
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Szempruch AJ, Choudhury R, Wang Z, Hajduk SL. In vivo analysis of trypanosome mitochondrial RNA function by artificial site-specific RNA endonuclease-mediated knockdown. RNA (NEW YORK, N.Y.) 2015; 21:1781-1789. [PMID: 26264591 PMCID: PMC4574754 DOI: 10.1261/rna.052084.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/08/2015] [Indexed: 05/29/2023]
Abstract
Trypanosomes possess a unique mitochondrial genome called the kinetoplast DNA (kDNA). Many kDNA genes encode pre-mRNAs that must undergo guide RNA-directed editing. In addition, alternative mRNA editing gives rise to diverse mRNAs and several kDNA genes encode open reading frames of unknown function. To better understand the mechanism of RNA editing and the function of mitochondrial RNAs in trypanosomes, we have developed a reverse genetic approach using artificial site-specific RNA endonucleases (ASREs) to directly silence kDNA-encoded genes. The RNA-binding domain of an ASRE can be programmed to recognize unique 8-nucleotide sequences, allowing the design of ASREs to cleave any target RNA. Utilizing an ASRE containing a mitochondrial localization signal, we targeted the extensively edited mitochondrial mRNA for the subunit A6 of the F0F1 ATP synthase (A6) in the procyclic stage of Trypanosoma brucei. This developmental stage, found in the midgut of the insect vector, relies on mitochondrial oxidative phosphorylation for ATP production with A6 forming the critical proton half channel across the inner mitochondrial membrane. Expression of an A6-targeted ASRE in procyclic trypanosomes resulted in a 50% reduction in A6 mRNA levels after 24 h, a time-dependent decrease in mitochondrial membrane potential (ΔΨm), and growth arrest. Expression of the A6-ASRE, lacking the mitochondrial localization signal, showed no significant growth defect. The development of the A6-ASRE allowed the first in vivo functional analysis of an edited mitochondrial mRNA in T. brucei and provides a critical new tool to study mitochondrial RNA biology in trypanosomes.
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Affiliation(s)
- Anthony J Szempruch
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Rajarshi Choudhury
- Department of Pharmacology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Zefeng Wang
- Department of Pharmacology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Stephen L Hajduk
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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47
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Wei H, Wang Z. Engineering RNA-binding proteins with diverse activities. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:597-613. [DOI: 10.1002/wrna.1296] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/09/2015] [Accepted: 07/20/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Huanhuan Wei
- Key Laboratory of Computational Biology; MPG-CAS Partner Institute of Computational Biology; Shanghai China
| | - Zefeng Wang
- Key Laboratory of Computational Biology; MPG-CAS Partner Institute of Computational Biology; Shanghai China
- Department of Pharmacology; University of North Carolina at Chapel Hill; Chapel Hill NC USA
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48
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Genetically encoded tools for RNA imaging in living cells. Curr Opin Biotechnol 2015; 31:42-9. [DOI: 10.1016/j.copbio.2014.07.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 07/30/2014] [Indexed: 12/11/2022]
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49
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Campbell ZT, Wickens M. Probing RNA-protein networks: biochemistry meets genomics. Trends Biochem Sci 2015; 40:157-64. [PMID: 25636997 DOI: 10.1016/j.tibs.2015.01.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/05/2015] [Accepted: 01/06/2015] [Indexed: 12/26/2022]
Abstract
RNA-protein interactions are pervasive. The specificity of these interactions dictates which RNAs are controlled by what protein. Here we describe a class of revolutionary new methods that enable global views of RNA-binding specificity in vitro, for both single proteins and multiprotein complexes. These methods provide insight into central issues in RNA regulation in living cells, including understanding the balance between free and bound components, the basis for exclusion of binding sites, detection of binding events in the absence of discernible regulatory elements, and new approaches to targeting endogenous transcripts by design. Comparisons of in vitro and in vivo binding provide a foundation for comprehensive understanding of the biochemistry of protein-mediated RNA regulatory networks.
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Affiliation(s)
- Zachary T Campbell
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
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50
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Abstract
Subcellular, sequence-specific detection of RNA in vivo is a powerful tool to study the macromolecular transport that occurs through plasmodesmata. The RNA-binding domain of Pumilio proteins can be engineered to bind RNA sequences of choice and fused to fluorescent proteins for RNA imaging. This chapter describes the construction of a Pumilio-based imaging system to track the RNA of Tobacco mosaic virus in vivo, and practical aspects of RNA live-cell imaging.
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Affiliation(s)
- Jens Tilsner
- Biomedical Sciences Research Complex, University of St Andrews, BMS Building, North Haugh, St Andrews, Fife, KY16 9ST, UK,
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