1
|
McDowell R, Small I, Bond CS. Synthetic PPR proteins as tools for sequence-specific targeting of RNA. Methods 2022; 208:19-26. [DOI: 10.1016/j.ymeth.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/29/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
|
2
|
Rösner L, Reichert D, Rau K, Muthmann N, Rentmeister A. Sequence-specific targeting of RNA. Methods 2022; 205:73-82. [PMID: 35764247 DOI: 10.1016/j.ymeth.2022.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/10/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Post-transcriptional modifications play an important role in several processes, including translation, splicing, and RNA degradation in eukaryotic cells. To investigate the function of specific modifications it is of high interest to develop tools for sequence-specific RNA-targeting. This work focuses on two abundant modifications of eukaryotic mRNA, namely methylation of the guanine-N7 position of the 5'-cap and internal N6-methyladenosine (m6A). We describe the sequence-specific targeting of model RNA transcripts via RNA-binding proteins, such as nuclease-deficient RNA-targeting Cas9 (RCas9) and the Pumilio homology domain (PumHD) fused to two different effector enzymes, the dioxygenase FTO and the guanine-N7 methyltransferase Ecm1. With this tool, we were able to install and remove the methylation at the respective positions with high specificity.
Collapse
Affiliation(s)
- Lukas Rösner
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Dennis Reichert
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Kristina Rau
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Nils Muthmann
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Andrea Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, 48149 Münster, Germany
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Dedow LK, Bailey-Serres J. Searching for a Match: Structure, Function and Application of Sequence-Specific RNA-Binding Proteins. PLANT & CELL PHYSIOLOGY 2019; 60:1927-1938. [PMID: 31329953 DOI: 10.1093/pcp/pcz072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/11/2019] [Indexed: 05/21/2023]
Abstract
Plants encode over 1800 RNA-binding proteins (RBPs) that modulate a myriad of steps in gene regulation from chromatin organization to translation, yet only a small number of these proteins and their target transcripts have been functionally characterized. Two classes of eukaryotic RBPs, pentatricopeptide repeat (PPR) and pumilio/fem-3 binding factors (PUF), recognize and bind to specific sequential RNA sequences through protein-RNA interactions. These modular proteins possess helical structural units containing key residues with high affinity for specific nucleotides, whose sequential order determines binding to a specific target RNA sequence. PPR proteins are nucleus-encoded, but largely regulate post-transcriptional gene regulation within plastids and mitochondria, including splicing, translation and RNA editing. Plant PUFs are involved in gene regulatory processes within the cell nucleus and cytoplasm. The modular structures of PPRs and PUFs that determine sequence specificity has facilitated identification of their RNA targets and biological functions. The protein-based RNA-targeting of PPRs and PUFs contrasts to the prokaryotic cluster regularly interspaced short palindromic repeats (CRISPR)-associated proteins (Cas) that target RNAs in prokaryotes. Together the PPR, PUF and CRISPR-Cas systems provide varied opportunities for RNA-targeted engineering applications.
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Atitey K, Loskot P, Rees P. Inferring distributions from observed mRNA and protein copy counts in genetic circuits. Biomed Phys Eng Express 2018. [DOI: 10.1088/2057-1976/aaef5c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
7
|
Jin C, Luo T, Fu Z, Jin Y. Chronic exposure of mice to low doses of imazalil induces hepatotoxicity at the physiological, biochemical, and transcriptomic levels. ENVIRONMENTAL TOXICOLOGY 2018; 33:650-658. [PMID: 29451352 DOI: 10.1002/tox.22550] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/24/2018] [Accepted: 02/03/2018] [Indexed: 06/08/2023]
Abstract
Imazalil (IMZ), which is a widely used fungicide, can accumulate in the body and threaten an animal's health. However, this fungicide has adverse effects on aquatic organisms and ultimately affects human health when it leaches into the environment. Our research tried to determine that if IMZ might cause liver damage and its potential to cause-related diseases. In this study, male adult C57BL/6 mice were exposed to 0.1, 0.5, or 2.5 mg/kg body weight IMZ in drinking water for 15 weeks. Then, we evaluated the liver damage at the physiological, biochemical, and transcriptome levels in mice after chronic IMZ exposure. We observed serious ballooning degeneration of hepatocytes in the IMZ-treated groups. And IMZ induced oxidative stress and caused the disorders of bile acid metabolism in mice. In addition, the transcriptome data showed that IMZ has substantial influence on several pathways, including metabolic pathways for drug metabolism, RNA transport, and bile secretion. We further confirmed that the mRNA expression of the key genes involved in oxidative stress and bile acid metabolism were changed of mice exposed to IMZ. Our data suggested that chronic IMZ exposure could induce hepatotoxicity in mice at the physiological, biochemical, and transcriptome levels.
Collapse
Affiliation(s)
- Cuiyuan Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Ting Luo
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| |
Collapse
|