1
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Štefanovie B, Jenner LP, Bozděchová L, Fajkus P, Sýkorová E, Fajkus J, Paleček JJ. Characterisation of the Arabidopsis thaliana telomerase TERT-TR complex. PLANT MOLECULAR BIOLOGY 2024; 114:56. [PMID: 38743198 PMCID: PMC11093817 DOI: 10.1007/s11103-024-01461-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024]
Abstract
Most eukaryotic organisms employ a telomerase complex for the maintenance of chromosome ends. The core of this complex is composed of telomerase reverse transcriptase (TERT) and telomerase RNA (TR) subunits. The TERT reverse transcriptase (RT) domain synthesises telomeric DNA using the TR template sequence. The other TERT domains contribute to this process in different ways. In particular, the TERT RNA-binding domain (TRBD) interacts with specific TR motif(s). Using a yeast 3-hybrid system, we show the critical role of Arabidopsis thaliana (At) TRBD and embryophyta-conserved KRxR motif in the unstructured linker preceding the TRBD domain for binding to the recently identified AtTR subunit. We also show the essential role of the predicted P4 stem and pseudoknot AtTR structures and provide evidence for the binding of AtTRBD to pseudoknot and KRxR motif stabilising interaction with the P4 stem structure. Our results thus provide the first insight into the core part of the plant telomerase complex.
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Affiliation(s)
- Barbora Štefanovie
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Leon P Jenner
- Institute of Biophysics, The Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Lucie Bozděchová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Petr Fajkus
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Institute of Biophysics, The Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, The Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Jiří Fajkus
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
- Institute of Biophysics, The Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic.
| | - Jan J Paleček
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
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2
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Cai J, He R, Zhang Y, Zhang P, Zhu Y, Wang D. Protocol for detecting lncRNA-protein interaction in vivo using the yeast three-hybrid assay. STAR Protoc 2024; 5:102856. [PMID: 38285736 PMCID: PMC10839528 DOI: 10.1016/j.xpro.2024.102856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/07/2023] [Accepted: 01/12/2024] [Indexed: 01/31/2024] Open
Abstract
Analyses of long non-coding RNA (lncRNA)-protein interactions provide key clues for understanding the molecular basis of lncRNA-modulated biological processes. Here, we detail a yeast three-hybrid assay to identify the lncRNA-interacting protein. We describe steps for lncRNA bait preparation, screening an RNA-binding proteins (RBPs) cDNA library, and validation of the lncRNA-RBP interaction. The assay can also be further applied to delineate the region of RBP that mediates the RNA-protein interaction. For complete details on the use and execution of this protocol, please refer to Zhang et al.1.
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Affiliation(s)
- Jingjing Cai
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Yongdi Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Pengxiang Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China.
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3
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Cai J, Zhang Y, He R, Jiang L, Qu Z, Gu J, Yang J, Legascue MF, Wang ZY, Ariel F, Adelson DL, Zhu Y, Wang D. LncRNA DANA1 promotes drought tolerance and histone deacetylation of drought responsive genes in Arabidopsis. EMBO Rep 2024; 25:796-812. [PMID: 38177920 PMCID: PMC10897447 DOI: 10.1038/s44319-023-00030-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Although many long noncoding RNAs have been discovered in plants, little is known about their biological function and mode of action. Here we show that the drought-induced long intergenic noncoding RNA DANA1 interacts with the L1p/L10e family member protein DANA1-INTERACTING PROTEIN 1 (DIP1) in the cell nucleus of Arabidopsis, and both DANA1 and DIP1 promote plant drought resistance. DANA1 and DIP1 increase histone deacetylase HDA9 binding to the CYP707A1 and CYP707A2 loci. DIP1 further interacts with PWWP3, a member of the PEAT complex that associates with HDA9 and has histone deacetylase activity. Mutation of DANA1 enhances CYP707A1 and CYP707A2 acetylation and expression resulting in impaired drought tolerance, in agreement with dip1 and pwwp3 mutant phenotypes. Our results demonstrate that DANA1 is a positive regulator of drought response and that DANA1 works jointly with the novel chromatin-related factor DIP1 on epigenetic reprogramming of the plant transcriptome during the response to drought.
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Affiliation(s)
- Jingjing Cai
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Yongdi Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Liyun Jiang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangdong, China
| | - Jun Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - María Florencia Legascue
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangdong, China
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
| | - David L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China.
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4
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Wharton TH, Marhabaie M, Wharton RP. Significant roles in RNA-binding for the amino-terminal domains of Drosophila Pumilio and Nanos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563753. [PMID: 37961211 PMCID: PMC10634786 DOI: 10.1101/2023.10.24.563753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The Drosophila Pumilio (Pum) and Nanos (Nos) RNA-binding proteins govern abdominal segmentation in the early embryo, as well as a variety of other events during development. They bind together to a compound Nanos Response Element (NRE) present in thousands of maternal mRNAs in the ovary and embryo, including hunchback ( hb ) mRNA, thereby regulating poly-adenylation, translation, and stability. Many studies support a model in which mRNA recognition and effector recruitment are achieved by distinct regions of each protein. The well-ordered Pum and Nos RNA-binding domains (RBDs) are sufficient to specifically recognize NREs; the relatively larger low-complexity N-terminal domains (NTDs) of each protein have been thought to act by recruiting mRNA regulators. Here we use yeast interaction assays to show that the NTDs also play a significant role in recognition of the NRE, acting via two mechanisms. First, the Pum and Nos NTDs interact in trans to promote assembly of the Pum/Nos/NRE ternary complex. Second, the Pum NTD acts via an unknown mechanism in cis, modifying base recognition by its RBD. These activities of the Pum NTD are important for its regulation of maternal hb mRNA in vivo.
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Su-Tobon Q, Fan J, Feeney K, Ren H, Autissier P, Wang P, Huang Y, Niu J. CRISPR-Hybrid: A CRISPR-Mediated Intracellular Directed Evolution Platform for RNA Aptamers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555185. [PMID: 37693461 PMCID: PMC10491168 DOI: 10.1101/2023.08.29.555185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Recent advances in gene editing and precise regulation of gene expression based on CRISPR technologies have provided powerful tools for the understanding and manipulation of gene functions. Fusing RNA aptamers to the sgRNA of CRISPR can recruit cognate RNA-binding protein (RBP) effectors to target genomic sites, and the expression of sgRNA containing different RNA aptamers permit simultaneous multiplexed and multifunctional gene regulations. Here, we report an intracellular directed evolution platform for RNA aptamers against intracellularly expressed RBPs. We optimized a bacterial CRISPR-hybrid system coupled with FACS, and identified novel high affinity RNA aptamers orthogonal to existing aptamer-RBP pairs. Application of orthogonal aptamer-RBP pairs in multiplexed CRISPR allowed effective simultaneous transcriptional activation and repression of endogenous genes in mammalian cells.
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6
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Zhang P, He R, Yang J, Cai J, Qu Z, Yang R, Gu J, Wang ZY, Adelson DL, Zhu Y, Cao X, Wang D. The long non-coding RNA DANA2 positively regulates drought tolerance by recruiting ERF84 to promote JMJ29-mediated histone demethylation. MOLECULAR PLANT 2023; 16:1339-1353. [PMID: 37553833 DOI: 10.1016/j.molp.2023.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 06/15/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023]
Abstract
Tens of thousands of long non-coding RNAs have been uncovered in plants, but few of them have been comprehensively studied for their biological function and molecular mechanism of their mode of action. Here, we show that the Arabidopsis long non-coding RNA DANA2 interacts with an AP2/ERF transcription factor ERF84 in the cell nucleus and then affects the transcription of JMJ29 that encodes a Jumonji C domain-containing histone H3K9 demethylase. Both RNA sequencing (RNA-seq) and genetic analyses demonstrate that DANA2 positively regulates drought stress responses through JMJ29. JMJ29 positively regulates the expression of ERF15 and GOLS2 by modulation of H3K9me2 demethylation. Accordingly, mutation of JMJ29 causes decreased ERF15 and GOLS2 expression, resulting in impaired drought tolerance, in agreement with drought-sensitive phenotypes of dana2 and erf84 mutants. Taken together, these results demonstrate that DANA2 is a positive regulator of drought response and works jointly with the transcriptional activator ERF84 to modulate JMJ29 expression in plant response to drought.
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Affiliation(s)
- Pengxiang Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Jun Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Jingjing Cai
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Rongxin Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China
| | - David L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China.
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7
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Watkin SAJ, Bennie RZ, Gilkes JM, Nock VM, Pearce FG, Dobson RCJ. On the utility of microfluidic systems to study protein interactions: advantages, challenges, and applications. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:459-471. [PMID: 36583735 PMCID: PMC9801160 DOI: 10.1007/s00249-022-01626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022]
Abstract
Within the complex milieu of a cell, which comprises a large number of different biomolecules, interactions are critical for function. In this post-reductionist era of biochemical research, the 'holy grail' for studying biomolecular interactions is to be able to characterize them in native environments. While there are a limited number of in situ experimental techniques currently available, there is a continuing need to develop new methods for the analysis of biomolecular complexes that can cope with the additional complexities introduced by native-like solutions. We think approaches that use microfluidics allow researchers to access native-like environments for studying biological problems. This review begins with a brief overview of the importance of studying biomolecular interactions and currently available methods for doing so. Basic principles of diffusion and microfluidics are introduced and this is followed by a review of previous studies that have used microfluidics to measure molecular diffusion and a discussion of the advantages and challenges of this technique.
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Affiliation(s)
- Serena A J Watkin
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel Z Bennie
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jenna M Gilkes
- Protein Science and Engineering Team, Callaghan Innovation, Christchurch, New Zealand
| | - Volker M Nock
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - F Grant Pearce
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia.
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8
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Yang J, He R, Qu Z, Gu J, Jiang L, Zhan X, Gao Y, Adelson DL, Li S, Wang ZY, Zhu Y, Wang D. Long noncoding RNA ARTA controls ABA response through MYB7 nuclear trafficking in Arabidopsis. Dev Cell 2023:S1534-5807(23)00236-8. [PMID: 37290444 DOI: 10.1016/j.devcel.2023.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/27/2023] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
In eukaryotes, transcription factors are a crucial element in the regulation of gene expression, and nuclear translocation is the key to the function of transcription factors. Here, we show that the long intergenic noncoding RNA ARTA interacts with an importin β-like protein, SAD2, through a long noncoding RNA-binding region embedded in the carboxyl terminal, and then it blocks the import of the transcription factor MYB7 into the nucleus. Abscisic acid (ABA)-induced ARTA expression can positively regulate ABI5 expression by fine-tuning MYB7 nuclear trafficking. Therefore, the mutation of arta represses ABI5 expression, resulting in desensitization to ABA, thereby reducing Arabidopsis drought tolerance. Our results demonstrate that lncRNA can hijack a nuclear trafficking receptor to modulate the nuclear import of a transcription factor during plant responses to environmental stimuli.
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Affiliation(s)
- Jun Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, the University of Adelaide, South Australia 5005, Australia
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences 510316, Guangdong, China
| | - Liyun Jiang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Ying Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - David L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, the University of Adelaide, South Australia 5005, Australia
| | - Sisi Li
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences 510316, Guangdong, China
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China.
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9
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Stockert OM, Gravel CM, Berry KE. A bacterial three-hybrid assay for forward and reverse genetic analysis of RNA-protein interactions. Nat Protoc 2022; 17:941-961. [PMID: 35197605 DOI: 10.1038/s41596-021-00657-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/03/2021] [Indexed: 11/09/2022]
Abstract
This protocol describes a bacterial three-hybrid (B3H) assay, an in vivo system that reports on RNA-protein interactions and can be implemented in both forward and reverse genetic experiments. The B3H assay connects the strength of an RNA-protein interaction inside of living Escherichia coli cells to the transcription of a reporter gene (here, lacZ). We present protocols to (1) insert RNA and protein sequences into appropriate vectors for B3H experiments, (2) detect putative RNA-protein interactions with both qualitative and quantitative readouts and (3) carry out forward genetic mutagenesis screens. The B3H assay builds on a well-established bacterial two-hybrid system for genetic analyses. As a result, protein-protein interactions can be assessed in tandem with RNA interactions with a bacterial two-hybrid assay to ensure that protein variants maintain their functionality. The B3H system is a powerful complement to traditional biochemical methods for dissecting RNA-protein interaction mechanisms: RNAs and proteins of interest do not need to be purified, and their interactions can be assessed under native conditions inside of a living bacterial cell. Once cloning has been completed, an assay can be completed in under a week and a screen in 1-2 weeks.
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Affiliation(s)
- Oliver M Stockert
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, USA.,Medical Scientist Training Program, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Chandra M Gravel
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, USA.,Department of Chemistry, Mount Holyoke College, South Hadley, MA, USA
| | - Katherine E Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, USA. .,Department of Chemistry, Mount Holyoke College, South Hadley, MA, USA.
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10
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Inferring protein function in an emerging virus: detection of the nucleoprotein in Tilapia Lake Virus. J Virol 2022; 96:e0175721. [PMID: 35107373 DOI: 10.1128/jvi.01757-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Emerging viruses impose global threats to animal and human populations and may bear novel genes with limited homology to known sequences, necessitating the development of novel approaches to infer and test protein functions. This challenge is dramatically evident in tilapia lake virus (TiLV), an emerging orthomyxo-like virus that threatens the global tilapia aquaculture and food security of millions of people. The majority of TiLV proteins have no homology to known sequences, impeding functionality assessments. Using a novel bioinformatics approach, we predicted that TiLV's Protein 4 encodes the nucleoprotein - a factor essential for viral RNA replication. Multiple methodologies revealed the expected properties of orthomyxoviral nucleoproteins. A modified yeast three-hybrid assay detected Protein 4-RNA interactions, which were independent of the RNA sequence, and identified specific positively charged residues involved. Protein 4-RNA interactions were uncovered by R-DeeP and XRNAX methodologies. Immunoelectron microscopy found that multiple Protein 4 copies localized along enriched ribonucleoproteins. TiLV RNA from cells and virions co-immunoprecipitated with Protein 4. Immunofluorescence microscopy detected Protein 4 in the cytoplasm and nuclei, and nuclear Protein 4 increased upon CRM1 inhibition, suggesting CRM1-dependent nuclear export of TiLV RNA. Together, these data reveal TiLV's nucleoprotein and highlight the ability to infer protein functionality, including novel RNA-binding proteins, in emerging pathogens. These are important in light of the expected discovery of many unknown viruses and the zoonotic potential of such pathogens. Importance Tilapia is an important source of dietary protein, especially in developing countries. Massive losses of tilapia were identified worldwide, risking the food security of millions of people. Tilapia lake virus (TiLV) is an emerging pathogen responsible for these disease outbreaks. TiLV's genome encodes ten major proteins, nine of which show no homology to other known viral or cellular proteins, hindering functionality assessment of these proteins. Here we describe a novel bioinformatics approach to infer the functionality of TiLV proteins, which predicted Protein 4 as the nucleoprotein - a factor essential for viral RNA replication. We provided experimental support for this prediction by applying multiple molecular, biochemical, and imaging approaches. Overall, we illustrate a strategy for functional analyses in viral discovery. The strategy is important in light of the expected discovery of many unknown viruses and the zoonotic potential of such pathogens.
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11
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Yu H, Yang L, Long H, Su X, Wang Y, Xing Q, Yao R, Zhang M, Chen L. Strigolactone signaling complex formation in yeast: A paradigm for studying hormone-induced receptor interaction with multiple downstream proteins. Methods Enzymol 2022; 674:519-541. [DOI: 10.1016/bs.mie.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Böttcher R, Schmidts I, Nitschko V, Duric P, Förstemann K. RNA polymerase II is recruited to DNA double-strand breaks for dilncRNA transcription in Drosophila. RNA Biol 2021; 19:68-77. [PMID: 34965182 PMCID: PMC8786327 DOI: 10.1080/15476286.2021.2014694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
DNA double-strand breaks are among the most toxic lesions that can occur in a genome and their faithful repair is thus of great importance. Recent findings have uncovered local transcription that initiates at the break and forms a non-coding transcript, called damage-induced long non-coding RNA (dilncRNA), which helps to coordinate the DNA transactions necessary for repair. We provide nascent RNA sequencing-based evidence that RNA polymerase II transcribes the dilncRNA in Drosophila and that this is more efficient for DNA breaks in an intron-containing gene, consistent with the higher damage-induced siRNA levels downstream of an intron. The spliceosome thus stimulates recruitment of RNA polymerase II to the break, rather than merely promoting the annealing of sense and antisense RNA to form the siRNA precursor. In contrast, RNA polymerase III nascent RNA libraries did not contain reads corresponding to the cleaved loci and selective inhibition of RNA polymerase III did not reduce the yield of damage-induced siRNAs. Finally, the damage-induced siRNA density was unchanged downstream of a T8 sequence, which terminates RNA polymerase III transcription. We thus found no evidence for a participation of RNA polymerase III in dilncRNA transcription in cultured Drosophila cells.
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Affiliation(s)
- Romy Böttcher
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Ines Schmidts
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Volker Nitschko
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Petar Duric
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Klaus Förstemann
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
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13
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Nguyen D, Buisine N, Fayol O, Michels AA, Bensaude O, Price DH, Uguen P. An alternative D. melanogaster 7SK snRNP. BMC Mol Cell Biol 2021; 22:43. [PMID: 34461828 PMCID: PMC8406779 DOI: 10.1186/s12860-021-00381-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The 7SK small nuclear RNA (snRNA) found in most metazoans is a key regulator of P-TEFb which in turn regulates RNA polymerase II elongation. Although its primary sequence varies in protostomes, its secondary structure and function are conserved across evolutionary distant taxa. RESULTS Here, we describe a novel ncRNA sharing many features characteristic of 7SK RNAs, in D. melanogaster. We examined the structure of the corresponding gene and determined the expression profiles of the encoded RNA, called snRNA:7SK:94F, during development. It is probably produced from the transcription of a lncRNA which is processed into a mature snRNA. We also addressed its biological function and we show that, like dm7SK, this alternative 7SK interacts in vivo with the different partners of the P-TEFb complex, i.e. HEXIM, LARP7 and Cyclin T. This novel RNA is widely expressed across tissues. CONCLUSION We propose that two distinct 7SK genes might contribute to the formation of the 7SK snRNP complex in D. melanogaster.
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Affiliation(s)
- Duy Nguyen
- Université Paris-Saclay, INSERM, CNRS, Interactions cellulaires et physiopathologie hépatique, Bât.440, 91405, Orsay, France
| | | | - Olivier Fayol
- Université Paris-Saclay, INSERM, CNRS, Interactions cellulaires et physiopathologie hépatique, Bât.440, 91405, Orsay, France
| | | | - Olivier Bensaude
- IBENS Paris, UMR CNRS 8197; UA INSERM 1024, 75005, Paris, France
| | - David H Price
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Patricia Uguen
- Université Paris-Saclay, INSERM, CNRS, Interactions cellulaires et physiopathologie hépatique, Bât.440, 91405, Orsay, France.
- Present address: Université Paris-Saclay, CNRS, INSERM, Institut Curie, Intégrité du Génome, ARN et cancer, Bât. 110, 91401, Orsay cedex, France.
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14
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Puf6 primes 60S pre-ribosome nuclear export at low temperature. Nat Commun 2021; 12:4696. [PMID: 34349113 PMCID: PMC8338941 DOI: 10.1038/s41467-021-24964-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Productive ribosomal RNA (rRNA) compaction during ribosome assembly necessitates establishing correct tertiary contacts between distant secondary structure elements. Here, we quantify the response of the yeast proteome to low temperature (LT), a condition where aberrant mis-paired RNA folding intermediates accumulate. We show that, at LT, yeast cells globally boost production of their ribosome assembly machinery. We find that the LT-induced assembly factor, Puf6, binds to the nascent catalytic RNA-rich subunit interface within the 60S pre-ribosome, at a site that eventually loads the nuclear export apparatus. Ensemble Förster resonance energy transfer studies show that Puf6 mimics the role of Mg2+ to usher a unique long-range tertiary contact to compact rRNA. At LT, puf6 mutants accumulate 60S pre-ribosomes in the nucleus, thus unveiling Puf6-mediated rRNA compaction as a critical temperature-regulated rescue mechanism that counters rRNA misfolding to prime export competence.
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15
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Asadzadeh H, Moosavi A, Alexandrakis G, Mofrad MRK. Atomic Scale Interactions between RNA and DNA Aptamers with the TNF- α Protein. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9926128. [PMID: 34327241 PMCID: PMC8310448 DOI: 10.1155/2021/9926128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/05/2021] [Indexed: 01/13/2023]
Abstract
Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for selecting the aptamer candidate with the highest binding strength to a target. We combine information from the binding free energy calculations, molecular docking, and molecular dynamics simulations to investigate the interactions of both aptamers with TNF-α. The results reveal that the RNA aptamer has a more stable structure relative to the DNA aptamer. Interaction of aptamers with TNF-α does not have any negative effect on its structure. The results of molecular docking and molecular dynamics simulations suggest that the RNA aptamer has a stronger interaction with the protein. Also, these findings illustrate that basic residues of TNF-α establish more atomic contacts with the aptamers compared to acidic or pH-neutral ones. Furthermore, binding energy calculations show that the interaction of the RNA aptamer with TNF-α is thermodynamically more favorable. In total, the findings of this study indicate that the RNA aptamer is a more suitable candidate for using as an apta-biosensor of TNF-α and, therefore, of greater potential use for the diagnosis of blood infections. Also, this study provides more information about aptamer-protein interactions and increases our understanding of this phenomenon.
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Affiliation(s)
- Homayoun Asadzadeh
- Center of Excellence in Energy Conversion (CEEC), School of Mechanical Engineering, Sharif University of Technology, Azadi Avenue, P.O. Box 11365-9567, Tehran 11365-9567, Iran
| | - Ali Moosavi
- Center of Excellence in Energy Conversion (CEEC), School of Mechanical Engineering, Sharif University of Technology, Azadi Avenue, P.O. Box 11365-9567, Tehran 11365-9567, Iran
| | - Georgios Alexandrakis
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Mohammad R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA, USA
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16
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Jansen S, Smlatic E, Copmans D, Debaveye S, Tangy F, Vidalain PO, Neyts J, Dallmeier K. Identification of host factors binding to dengue and Zika virus subgenomic RNA by efficient yeast three-hybrid screens of the human ORFeome. RNA Biol 2021; 18:732-744. [PMID: 33459164 PMCID: PMC8086697 DOI: 10.1080/15476286.2020.1868754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 10/26/2022] Open
Abstract
Flaviviruses such as the dengue (DENV) and the Zika virus (ZIKV) are important human pathogens causing around 100 million symptomatic infections each year. During infection, small subgenomic flavivirus RNAs (sfRNAs) are formed inside the infected host cell as a result of incomplete degradation of the viral RNA genome by cellular exoribonuclease XRN1. Although the full extent of sfRNA functions is to be revealed, these non-coding RNAs are key virulence factors and their detrimental effects on multiple cellular processes seem to consistently involve molecular interactions with RNA-binding proteins (RBPs). Discovery of such sfRNA-binding host-factors has followed established biochemical pull-down approaches skewed towards highly abundant proteins hampering proteome-wide coverage. Yeast three-hybrid (Y3H) systems represent an attractive alternative approach. To facilitate proteome-wide screens for RBP, we revisited and improved existing RNA-Y3H methodology by (1) implementing full-length ORF libraries in combination with (2) efficient yeast mating to increase screening depth and sensitivity, and (3) stringent negative controls to eliminate over-representation of non-specific RNA-binders. These improvements were validated employing the well-characterized interaction between DDX6 (DEAD-box helicase 6) and sfRNA of DENV as paradigm. Our advanced Y3H system was used to screen for human proteins binding to DENV and ZIKV sfRNA, resulting in a list of 69 putative sfRNA-binders, including several previously reported as well as numerous novel RBP host factors. Our methodology requiring no sophisticated infrastructure or analytic pipeline may be employed for the discovery of meaningful RNA-protein interactions at large scale in other fields.
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Affiliation(s)
- Sander Jansen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Enisa Smlatic
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
- Division of Paediatric Infectious Diseases, Ludwig-Maximilians-University Munich, Dr. Von Hauner Children’s Hospital, Munich, Germany
| | - Daniëlle Copmans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
- KU Leuven Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Biodiscovery, Leuven, Belgium
| | - Sarah Debaveye
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS, Paris, France
| | - Pierre-Olivier Vidalain
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS, Paris, France
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, Lyon, France
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
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17
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Wang CD, Mansky R, LeBlanc H, Gravel CM, Berry KE. Optimization of a bacterial three-hybrid assay through in vivo titration of an RNA-DNA adapter protein. RNA (NEW YORK, N.Y.) 2021; 27:513-526. [PMID: 33500316 PMCID: PMC7962490 DOI: 10.1261/rna.077404.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/19/2021] [Indexed: 05/25/2023]
Abstract
Noncoding RNAs regulate gene expression in every domain of life. In bacteria, small RNAs (sRNAs) regulate gene expression in response to stress and are often assisted by RNA-chaperone proteins, such as Hfq. We have recently developed a bacterial three-hybrid (B3H) assay that detects the strong binding interactions of certain E. coli sRNAs with proteins Hfq and ProQ. Despite the promise of this system, the signal-to-noise has made it challenging to detect weaker interactions. In this work, we use Hfq-sRNA interactions as a model system to optimize the B3H assay, so that weaker RNA-protein interactions can be more reliably detected. We find that the concentration of the RNA-DNA adapter is an important parameter in determining the signal in the system and have modified the plasmid expressing this component to tune its concentration to optimal levels. In addition, we have systematically perturbed the binding affinity of Hfq-RNA interactions to define, for the first time, the relationship between B3H signal and in vitro binding energetics. The new pAdapter construct presented here substantially expands the range of detectable interactions in the B3H assay, broadening its utility. This improved assay will increase the likelihood of identifying novel protein-RNA interactions with the B3H system and will facilitate exploration of the binding mechanisms of these interactions.
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Affiliation(s)
- Clara D Wang
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Rachel Mansky
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Hannah LeBlanc
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Chandra M Gravel
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Katherine E Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
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18
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Compendium of Methods to Uncover RNA-Protein Interactions In Vivo. Methods Protoc 2021; 4:mps4010022. [PMID: 33808611 PMCID: PMC8006020 DOI: 10.3390/mps4010022] [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: 02/10/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/01/2023] Open
Abstract
Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the nucleic acids. RNA–protein interactions play a significant role in co- and post-transcriptional regulation to control gene expression. RNA-binding proteins (RBPs) are a diverse group of macromolecules that bind to RNA and play an essential role in RNA biology by regulating pre-mRNA processing, maturation, nuclear transport, stability, and translation. Hence, the studies aimed at investigating RNA–protein interactions are essential to advance our knowledge in gene expression patterns associated with health and disease. Here we discuss the long-established and current technologies that are widely used to study RNA–protein interactions in vivo. We also present the advantages and disadvantages of each method discussed in the review.
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19
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Rosenblum SL, Lorenz DA, Garner AL. A live-cell assay for the detection of pre-microRNA-protein interactions. RSC Chem Biol 2021; 2:241-247. [PMID: 33817642 PMCID: PMC8006716 DOI: 10.1039/d0cb00055h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
Recent efforts in genome-wide sequencing and proteomics have revealed the fundamental roles that RNA-binding proteins (RBPs) play in the life cycle and function of coding and non-coding RNAs. While these methodologies provide a systems-level view of the networking of RNA and proteins, approaches to enable the cellular validation of discovered interactions are lacking. Leveraging the power of bioorthogonal chemistry- and split-luciferase-based assay technologies, we have devised a conceptually new assay for the live-cell detection of RNA-protein interactions (RPIs), RNA interaction with Protein-mediated Complementation Assay, or RiPCA. As proof-of-concept, we utilized the interaction of the pre-microRNA, pre-let-7, with its binding partner, Lin28. Using this system, we have demonstrated the selective detection of the pre-let-7-Lin28 RPI in both the cytoplasm and nucleus. Furthermore, we determined that this technology can be used to discern relative affinities for specific sequences as well as of individual RNA binding domains. Thus, RiPCA has the potential to serve as a useful tool in supporting the investigation of cellular RPIs.
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Affiliation(s)
- Sydney L Rosenblum
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , USA .
| | - Daniel A Lorenz
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , USA .
| | - Amanda L Garner
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , USA .
- Department of Medicinal Chemistry , College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109 , USA
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20
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Sharma S, Sourirajan A, Baumler DJ, Dev K. Saccharomyces cerevisiae ER membrane protein complex subunit 4 (EMC4) plays a crucial role in eIF2B-mediated translation regulation and survival under stress conditions. J Genet Eng Biotechnol 2020; 18:15. [PMID: 32476094 PMCID: PMC7261713 DOI: 10.1186/s43141-020-00029-7] [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: 02/25/2020] [Accepted: 04/22/2020] [Indexed: 11/10/2022]
Abstract
Background Eukaryotic initiation factor 2B (eIF2B) initiates and regulates translation initiation in eukaryotes. eIF2B gene mutations cause leukoencephalopathy called vanishing white matter disease (VWM) in humans and slow growth (Slg−) and general control derepression (Gcd−) phenotypes in Saccharomyces cerevisiae. Results To suppress eIF2B mutations, S. cerevisiae genomic DNA library was constructed in high-copy vector (YEp24) and transformed into eIF2B mutant S. cerevisiae strains. The library was screened for wild-type genes rescuing S. cerevisiae (Slg−) and (Gcd−) phenotypes. A genomic clone, Suppressor-I (Sup-I), rescued S. cerevisiae Slg− and Gcd− phenotypes (gcd7-201 gcn2∆). The YEp24/Sup-I construct contained truncated TAN1, full length EMC4, full length YGL230C, and truncated SAP4 genes. Full length EMC4 (chaperone protein) gene was sub-cloned into pEG (KG) yeast expression vector and overexpressed in gcd7-201 gcn2∆ strain which suppressed the Slg− and Gcd− phenotype. A GST-Emc4 fusion protein of 47 kDa was detected by western blotting using α-GST antibodies. Suppression was specific to gcd7-201 gcn2∆ mutation in eIF2Bβ and Gcd1-502 gcn2∆ in eIF2Bγ subunit. Emc4p overexpression also protected the wild type and mutant (gcd7-201 gcn2∆, GCD7 gcn2∆, and GCD7 GCN2∆) strains from H2O2, ethanol, and caffeine stress. Conclusions Our results suggest that Emc4p is involved in eIF2B-mediated translational regulation under stress and could provide an amenable tool to understand the eIF2B-mediated defects.
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21
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Pandey S, Gravel CM, Stockert OM, Wang CD, Hegner CL, LeBlanc H, Berry KE. Genetic identification of the functional surface for RNA binding by Escherichia coli ProQ. Nucleic Acids Res 2020; 48:4507-4520. [PMID: 32170306 PMCID: PMC7192607 DOI: 10.1093/nar/gkaa144] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/20/2020] [Accepted: 02/24/2020] [Indexed: 12/17/2022] Open
Abstract
The FinO-domain-protein ProQ is an RNA-binding protein that has been known to play a role in osmoregulation in proteobacteria. Recently, ProQ has been shown to act as a global RNA-binding protein in Salmonella and Escherichia coli, binding to dozens of small RNAs (sRNAs) and messenger RNAs (mRNAs) to regulate mRNA-expression levels through interactions with both 5′ and 3′ untranslated regions (UTRs). Despite excitement around ProQ as a novel global RNA-binding protein, and its potential to serve as a matchmaking RNA chaperone, significant gaps remain in our understanding of the molecular mechanisms ProQ uses to interact with RNA. In order to apply the tools of molecular genetics to this question, we have adapted a bacterial three-hybrid (B3H) assay to detect ProQ’s interactions with target RNAs. Using domain truncations, site-directed mutagenesis and an unbiased forward genetic screen, we have identified a group of highly conserved residues on ProQ’s NTD as the primary face for in vivo recognition of two RNAs, and propose that the NTD structure serves as an electrostatic scaffold to recognize the shape of an RNA duplex.
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Affiliation(s)
- Smriti Pandey
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Chandra M Gravel
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Oliver M Stockert
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Clara D Wang
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Courtney L Hegner
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Hannah LeBlanc
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Katherine E Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA.,Department of Chemistry, Mount Holyoke College, South Hadley, MA 01075, USA
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22
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Yeast Mitochondrial Translation Initiation Factor 3 Interacts with Pet111p to Promote COX2 mRNA Translation. Int J Mol Sci 2020; 21:ijms21103414. [PMID: 32408541 PMCID: PMC7279496 DOI: 10.3390/ijms21103414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genomes code for several core components of respiratory chain complexes. Thus, mitochondrial translation is of great importance for the organelle as well as for the whole cell. In yeast, mitochondrial translation initiation factor 3, Aim23p, is not essential for the organellar protein synthesis; however, its absence leads to a significant quantitative imbalance of the mitochondrial translation products. This fact points to a possible specific action of Aim23p on the biosynthesis of some mitochondrial protein species. In this work, we examined such peculiar effects of Aim23p in relation to yeast mitochondrial COX2 mRNA translation. We show that Aim23p is indispensable to this process. According to our data, this is mediated by Aimp23p interaction with the known specific factor of the COX2 mRNA translation, Pet111p. If there is no Aim23p in the yeast cells, an increased amount of Pet111p ensures proper COX2 mRNA translation. Our results demonstrate the additional non-canonical function of initiation factor 3 in yeast mitochondrial translation.
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23
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Lemmens I, Jansen S, de Rouck S, de Smet AS, Defever D, Neyts J, Dallmeier K, Tavernier J. The Development of RNA-KISS, a Mammalian Three-Hybrid Method to Detect RNA-Protein Interactions in Living Mammalian Cells. J Proteome Res 2020; 19:2529-2538. [PMID: 32216351 DOI: 10.1021/acs.jproteome.0c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA-protein interactions are essential for the regulation of mRNA and noncoding RNA functions and are implicated in many diseases, such as cancer and neurodegenerative disorders. A method that can detect RNA-protein interactions in living mammalian cells on a proteome-wide scale will be an important asset to identify and study these interactions. Here we show that a combination of the mammalian two-hybrid protein-protein detection method KISS (kinase substrate sensor) and the yeast RNA three-hybrid method, utilizing the specific interaction between the MS2 RNA and MS2 coat protein, is capable of detecting RNA-protein interactions in living mammalian cells. For conceptional proof we used the subgenomic flavivirus RNA (sfRNA) of the dengue virus (DENV), a highly structured noncoding RNA derived from the DENV genome known to target host cell proteins involved in innate immunity and antiviral defense, as bait. Using RNA-KISS, we could confirm the previously established interaction between the RNA-binding domain of DDX6 and the DENV sfRNA. Finally, we performed a human proteome-wide screen for DENV sfRNA-binding host factors, identifying several known flavivirus host factors such as DDX6 and PACT, further validating the RNA-KISS method as a robust and high-throughput cell-based RNA-protein interaction screening tool.
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Affiliation(s)
- Irma Lemmens
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Sander Jansen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Steffi de Rouck
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Anne-Sophie de Smet
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Dieter Defever
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Jan Tavernier
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium.,Orionis Biosciences, B-9052 Ghent, Belgium
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24
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Liu Y, Huang C, Zeng J, Yu H, Li Y, Yuan C. Identification of two additional plasmodesmata localization domains in the tobacco mosaic virus cell-to-cell-movement protein. Biochem Biophys Res Commun 2019; 521:145-151. [PMID: 31629470 DOI: 10.1016/j.bbrc.2019.10.093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 11/17/2022]
Abstract
Despite decades of intensive studies, the failure to identify plasmodesmata (PD) localization sequences has constrained our understanding of Tobacco mosaic virus (TMV) movement. Recently, we identified the first PD localization signal (major PLS) in the TMV movement protein (MP), which encompasses the first 50 amino acid residues of the MP. Although the major PLS is sufficient for PD targeting, the efficiency is lower than the full-length TMV MP. To address this efficiency gap, we identified two additional PLS domains encompassing amino acid residues 61 to 80, and 147 to 170 of the MP and showed that these two domains target to PD, but do not transit to adjacent cells. We also demonstrated that the MP61-80 fragment interacts with Arabidopsis synaptotagmin A, which was also shown to interact with the major TMV MP PLS. Therefore, our findings have provided new insights to more fully understand the mechanism underlying plasmodesmal targeting of TMV MP.
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Affiliation(s)
- Yong Liu
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Science, Kunming, Yunnan, 650201, China
| | - Changjun Huang
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Science, Kunming, Yunnan, 650201, China
| | - Jianmin Zeng
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Science, Kunming, Yunnan, 650201, China
| | - Haiqin Yu
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Science, Kunming, Yunnan, 650201, China
| | - Yongping Li
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Science, Kunming, Yunnan, 650201, China
| | - Cheng Yuan
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Science, Kunming, Yunnan, 650201, China.
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25
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rec-Y3H screening allows the detection of simultaneous RNA-protein interface mutations. Methods 2019; 178:19-32. [PMID: 31493518 DOI: 10.1016/j.ymeth.2019.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/16/2019] [Accepted: 09/01/2019] [Indexed: 12/20/2022] Open
Abstract
Understanding which proteins and RNAs directly interact is crucial for revealing cellular mechanisms of gene regulation. Efficient methods allowing to detect RNA-protein interactions and dissect the underlying molecular origin for RNA-binding protein (RBP) specificity are in high demand. The recently developed recombination-Y3H screening (rec-Y3H) enabled many-by-many detection of interactions between pools of proteins and RNA fragments for the first time. Here, we test different conditions for protein-RNA interaction selection during rec-Y3H screening and provide information on the screen performance in several selection media. We further show that rec-Y3H can detect the nucleotide and amino acid sequence determinants of protein-RNA interactions by mutating residues of interacting proteins and RNAs simultaneously. We envision that systematic RNA-protein interface mutation screening will be useful to understand the molecular origin of RBP selectivity and to engineer RBPs with targeted specificities in the future.
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Relevance of the iron-responsive element (IRE) pseudotriloop structure for IRP1/2 binding and validation of IRE-like structures using the yeast three-hybrid system. Gene 2019; 710:399-405. [DOI: 10.1016/j.gene.2019.06.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/16/2019] [Accepted: 06/06/2019] [Indexed: 01/28/2023]
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Gu J, Xia Z, Luo Y, Jiang X, Qian B, Xie H, Zhu JK, Xiong L, Zhu J, Wang ZY. Spliceosomal protein U1A is involved in alternative splicing and salt stress tolerance in Arabidopsis thaliana. Nucleic Acids Res 2019; 46:1777-1792. [PMID: 29228330 PMCID: PMC5829640 DOI: 10.1093/nar/gkx1229] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/30/2017] [Indexed: 12/14/2022] Open
Abstract
Soil salinity is a significant threat to sustainable agricultural production worldwide. Plants must adjust their developmental and physiological processes to cope with salt stress. Although the capacity for adaptation ultimately depends on the genome, the exceptional versatility in gene regulation provided by the spliceosome-mediated alternative splicing (AS) is essential in these adaptive processes. However, the functions of the spliceosome in plant stress responses are poorly understood. Here, we report the in-depth characterization of a U1 spliceosomal protein, AtU1A, in controlling AS of pre-mRNAs under salt stress and salt stress tolerance in Arabidopsis thaliana. The atu1a mutant was hypersensitive to salt stress and accumulated more reactive oxygen species (ROS) than the wild-type under salt stress. RNA-seq analysis revealed that AtU1A regulates AS of many genes, presumably through modulating recognition of 5′ splice sites. We showed that AtU1A is associated with the pre-mRNA of the ROS detoxification-related gene ACO1 and is necessary for the regulation of ACO1 AS. ACO1 is important for salt tolerance because ectopic expression of ACO1 in the atu1a mutant can partially rescue its salt hypersensitive phenotype. Our findings highlight the critical role of AtU1A as a regulator of pre-mRNA processing and salt tolerance in plants.
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Affiliation(s)
- Jinbao Gu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Zhiqiang Xia
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Yuehua Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Xingyu Jiang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Bilian Qian
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - He Xie
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA.,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Liming Xiong
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Jianhua Zhu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Zhen-Yu Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
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Preston MA, Porter DF, Chen F, Buter N, Lapointe CP, Keles S, Kimble J, Wickens M. Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase. Nat Methods 2019; 16:437-445. [PMID: 30988468 PMCID: PMC6613791 DOI: 10.1038/s41592-019-0370-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/24/2019] [Accepted: 03/05/2019] [Indexed: 12/22/2022]
Abstract
Ribonucleotidyl transferases (rNTases) add untemplated ribonucleotides to diverse RNAs. We have developed TRAID-seq, a screening strategy in Saccharomyces cerevisiae to identify sequences added to a reporter RNA at single-nucleotide resolution by overexpressed candidate enzymes from different organisms. The rNTase activities of 22 previously unexplored enzymes were determined. In addition to poly(A)- and poly(U)-adding enzymes, we identified a cytidine-adding enzyme that is likely to be part of a two-enzyme system that adds CCA to tRNAs in a eukaryote; a nucleotidyl transferase that adds nucleotides to RNA without apparent nucleotide preference; and a poly(UG) polymerase, Caenorhabditis elegans MUT-2, that adds alternating uridine and guanosine nucleotides to form poly(UG) tails. MUT-2 is known to be required for certain forms of RNA silencing, and mutants of the enzyme that result in defective silencing did not add poly(UG) tails in our assay. We propose that MUT-2 poly(UG) polymerase activity is required to promote genome integrity and RNA silencing.
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Affiliation(s)
- Melanie A Preston
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Promega Corporation, Madison, WI, USA
| | - Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Program in Epithelial Biology, Stanford University Medical School, Stanford, CA, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
| | - Natascha Buter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Promega Corporation, Madison, WI, USA
| | - Christopher P Lapointe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | - Sunduz Keles
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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29
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Stefanovic L, Stefanovic B. Technology for Discovery of Antifibrotic Drugs: Phenotypic Screening for LARP6 Inhibitors Using Inverted Yeast Three Hybrid System. Assay Drug Dev Technol 2019; 17:116-127. [PMID: 30901265 DOI: 10.1089/adt.2018.904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Fibrosis is defined by excessive production of type I collagen in various organs. Excessive type I collagen production in fibrosis is stimulated by binding of RNA protein LARP6 to the structural element of collagen mRNAs, the 5' stem loop (5'SL). The LARP6-dependent regulation is specific for type I collagen and critical for fibrosis development. Inhibitors of LARP6 binding have potential to be specific antifibrotic drugs, as evidenced by the discovery of one such inhibitor. To create technology for phenotypic screening of additional compounds we developed an inverted yeast three hybrid system. The system is based on expression of human LARP6 and a short RNA containing the 5'SL of human collagen α1(I) mRNA in Saccharomyces cerevisiae cells. The cells were engineered in such a way that when LARP6 is bound to 5'SL RNA they fail to grow in a specific synthetic medium. Dissociation of LARP6 from 5'SL RNA permits the cell growth, allowing identification of the inhibitors of LARP6 binding. The assay simply involves measuring optical density of cells growing in multiwall plates and is pertinent for high throughput applications. We describe the specificity of the system and its characteristics for high throughput screening. As a proof of principle, the result of one screen using collection of FDA approved drugs is also presented. This screen demonstrates that using this technology discovery of novel LARP6 inhibitors is possible.
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Affiliation(s)
- Lela Stefanovic
- 1 Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida
| | - Branko Stefanovic
- 1 Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida
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30
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Zhan ZH, Jia LN, Zhou Y, Li LP, Yi HC. BGFE: A Deep Learning Model for ncRNA-Protein Interaction Predictions Based on Improved Sequence Information. Int J Mol Sci 2019; 20:E978. [PMID: 30813451 PMCID: PMC6412311 DOI: 10.3390/ijms20040978] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 11/26/2022] Open
Abstract
The interactions between ncRNAs and proteins are critical for regulating various cellular processes in organisms, such as gene expression regulations. However, due to limitations, including financial and material consumptions in recent experimental methods for predicting ncRNA and protein interactions, it is essential to propose an innovative and practical approach with convincing performance of prediction accuracy. In this study, based on the protein sequences from a biological perspective, we put forward an effective deep learning method, named BGFE, to predict ncRNA and protein interactions. Protein sequences are represented by bi-gram probability feature extraction method from Position Specific Scoring Matrix (PSSM), and for ncRNA sequences, k-mers sparse matrices are employed to represent them. Furthermore, to extract hidden high-level feature information, a stacked auto-encoder network is employed with the stacked ensemble integration strategy. We evaluate the performance of the proposed method by using three datasets and a five-fold cross-validation after classifying the features through the random forest classifier. The experimental results clearly demonstrate the effectiveness and the prediction accuracy of our approach. In general, the proposed method is helpful for ncRNA and protein interacting predictions and it provides some serviceable guidance in future biological research.
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Affiliation(s)
- Zhao-Hui Zhan
- China University of Mining and Technology, Xuzhou 221116, China.
| | - Li-Na Jia
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, Shandong, China.
| | - Yong Zhou
- China University of Mining and Technology, Xuzhou 221116, China.
| | - Li-Ping Li
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China.
| | - Hai-Cheng Yi
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China.
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31
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2019; 58:1266-1279. [PMID: 30102012 PMCID: PMC6391945 DOI: 10.1002/anie.201806482] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 12/16/2022]
Abstract
The cellular functions of RNA are not limited to their role as blueprints for protein synthesis. In particular, noncoding RNA, such as, snRNAs, lncRNAs, miRNAs, play important roles. With increasing numbers of RNAs being identified, it is well known that the transcriptome outnumbers the proteome by far. This emphasizes the great importance of functional RNA characterization and the need to further develop tools for these investigations, many of which are still in their infancy. Fluorescent light-up aptamers (FLAPs) are RNA sequences that can bind nontoxic, cell-permeable small-molecule fluorogens and enhance their fluorescence over many orders of magnitude upon binding. FLAPs can be encoded on the DNA level using standard molecular biology tools and are subsequently transcribed into RNA by the cellular machinery, so that they can be used as fluorescent RNA tags (FLAP-tags). In this Minireview, we give a brief overview of the fluorogens that have been developed and their binding RNA aptamers, with a special focus on published crystal structures. A summary of current and future cellular FLAP applications with an emphasis on the study of RNA-RNA and RNA-protein interactions using split-FLAP and Förster resonance energy transfer (FRET) systems is given.
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Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
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32
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Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
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Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
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33
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Olgeiser L, Haag C, Boerner S, Ule J, Busch A, Koepke J, König J, Feldbrügge M, Zarnack K. The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. EMBO Rep 2018; 20:embr.201846588. [PMID: 30552148 DOI: 10.15252/embr.201846588] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 01/09/2023] Open
Abstract
RNA-binding proteins (RBPs) determine spatiotemporal gene expression by mediating active transport and local translation of cargo mRNAs. Here, we cast a transcriptome-wide view on the transported mRNAs and cognate RBP binding sites during endosomal messenger ribonucleoprotein (mRNP) transport in Ustilago maydis Using individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP), we compare the key transport RBP Rrm4 and the newly identified endosomal mRNP component Grp1 that is crucial to coordinate hyphal growth. Both RBPs bind predominantly in the 3' untranslated region of thousands of shared cargo mRNAs, often in close proximity. Intriguingly, Rrm4 precisely binds at stop codons, which constitute landmark sites of translation, suggesting an intimate connection of mRNA transport and translation. Towards uncovering the code of recognition, we identify UAUG as specific binding motif of Rrm4 that is bound by its third RRM domain. Altogether, we provide first insights into the positional organisation of co-localising RBPs on individual cargo mRNAs.
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Affiliation(s)
- Lilli Olgeiser
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Carl Haag
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Susan Boerner
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jernej Ule
- The Francis Crick Institute, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Anke Busch
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Janine Koepke
- Medical Clinic II (Molecular Pneumology), Excellence Cluster Cardio-Pulmonary System, Justus Liebig University of Gießen, Gießen, Germany
| | - Julian König
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
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34
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
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35
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Yang JS, Garriga-Canut M, Link N, Carolis C, Broadbent K, Beltran-Sastre V, Serrano L, Maurer SP. rec-YnH enables simultaneous many-by-many detection of direct protein-protein and protein-RNA interactions. Nat Commun 2018; 9:3747. [PMID: 30217970 PMCID: PMC6138660 DOI: 10.1038/s41467-018-06128-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 08/13/2018] [Indexed: 01/06/2023] Open
Abstract
Knowing which proteins and RNAs directly interact is essential for understanding cellular mechanisms. Unfortunately, discovering such interactions is costly and often unreliable. To overcome these limitations, we developed rec-YnH, a new yeast two and three-hybrid-based screening pipeline capable of detecting interactions within protein libraries or between protein libraries and RNA fragment pools. rec-YnH combines batch cloning and transformation with intracellular homologous recombination to generate bait-prey fusion libraries. By developing interaction selection in liquid-gels and using an ORF sequence-based readout of interactions via next-generation sequencing, we eliminate laborious plating and barcoding steps required by existing methods. We use rec-Y2H to simultaneously map interactions of protein domains and reveal novel putative interactors of PAR proteins. We further employ rec-Y2H to predict the architecture of published coprecipitated complexes. Finally, we use rec-Y3H to map interactions between multiple RNA-binding proteins and RNAs-the first time interactions between protein and RNA pools are simultaneously detected.
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Affiliation(s)
- Jae-Seong Yang
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Mireia Garriga-Canut
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Nele Link
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Carlo Carolis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Katrina Broadbent
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Violeta Beltran-Sastre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010, Barcelona, Spain
| | - Sebastian P Maurer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain.
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36
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Zhang L, Yu S, Wang C, Jia C, Lu Z, Chen J. Establishment of a non‑coding RNAomics screening platform for the regulation of KRAS in pancreatic cancer by RNA sequencing. Int J Oncol 2018; 53:2659-2670. [PMID: 30221677 DOI: 10.3892/ijo.2018.4560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/09/2018] [Indexed: 11/05/2022] Open
Affiliation(s)
- Li Zhang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Shuangni Yu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Cuiping Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Congwei Jia
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Zhaohui Lu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Jie Chen
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
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37
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Abstract
Plant viruses cross the barrier of the plant cell wall by moving through intercellular channels, termed plasmodesmata, to invade their hosts. They accomplish this by encoding movement proteins (MPs), which act to alter plasmodesmal gating. How MPs target to plasmodesmata is not well understood. Our recent characterization of the first plasmodesmal localization signal (PLS) identified in a viral MP, namely, the MP encoded by the Tobamovirus Tobacco mosaic virus (TMV), now provides the opportunity to identify host proteins that recognize this PLS and may be important for its plasmodesmal targeting. One such candidate protein is Arabidopsis synaptotagmin A (SYTA), which is required to form endoplasmic reticulum (ER)-plasma membrane contact sites and regulates the MP-mediated trafficking of begomoviruses, tobamoviruses, and potyviruses. In particular, SYTA interacts with, and regulates the cell-to-cell transport of, both TMV MP and the MP encoded by the Tobamovirus Turnip vein clearing virus (TVCV). Using in planta bimolecular fluorescence complementation (BiFC) and yeast two-hybrid assays, we show here that the TMV PLS interacted with SYTA. This PLS sequence was both necessary and sufficient for interaction with SYTA, and the plasmodesmal targeting activity of the TMV PLS was substantially reduced in an Arabidopsis syta knockdown line. Our findings show that SYTA is one host factor that can recognize the TMV PLS and suggest that this interaction may stabilize the association of TMV MP with plasmodesmata.IMPORTANCE Plant viruses use their movement proteins (MPs) to move through host intercellular connections, plasmodesmata. Perhaps one of the most intriguing, yet least studied, aspects of this transport is the MP signal sequences and their host recognition factors. Recently, we have described the plasmodesmal localization signal (PLS) of the Tobacco mosaic virus (TMV) MP. Here, we identified the Arabidopsis synaptotagmin A (SYTA) as a host factor that recognizes TMV MP PLS and promotes its association with the plasmodesmal membrane. The significance of these findings is two-fold: (i) we identified the TMV MP association with the cell membrane at plasmodesmata as an important PLS-dependent step in plasmodesmal targeting, and (ii) we identified the plant SYTA protein that specifically recognizes PLS as a host factor involved in this step.
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38
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Global pairwise RNA interaction landscapes reveal core features of protein recognition. Nat Commun 2018; 9:2511. [PMID: 29955037 PMCID: PMC6023938 DOI: 10.1038/s41467-018-04729-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/16/2018] [Indexed: 01/14/2023] Open
Abstract
RNA–protein interactions permeate biology. Transcription, translation, and splicing all hinge on the recognition of structured RNA elements by RNA-binding proteins. Models of RNA–protein interactions are generally limited to short linear motifs and structures because of the vast sequence sampling required to access longer elements. Here, we develop an integrated approach that calculates global pairwise interaction scores from in vitro selection and high-throughput sequencing. We examine four RNA-binding proteins of phage, viral, and human origin. Our approach reveals regulatory motifs, discriminates between regulated and non-regulated RNAs within their native genomic context, and correctly predicts the consequence of mutational events on binding activity. We design binding elements that improve binding activity in cells and infer mutational pathways that reveal permissive versus disruptive evolutionary trajectories between regulated motifs. These coupling landscapes are broadly applicable for the discovery and characterization of protein–RNA recognition at single nucleotide resolution. RNA–protein interactions often depend on the recognition of extended RNA elements but the identification of these motifs is challenging. Here, the authors present a global integrated approach to analyze RNA–protein binding landscapes, mapping extended RNA interaction motifs for four RNA-binding proteins.
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39
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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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40
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A modified yeast three-hybrid system enabling both positive and negative selections. Biotechnol Lett 2018; 40:1127-1134. [DOI: 10.1007/s10529-018-2567-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/15/2018] [Indexed: 10/16/2022]
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41
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Yang F, Lei Y, Zhou M, Yao Q, Han Y, Wu X, Zhong W, Zhu C, Xu W, Tao R, Chen X, Lin D, Rahman K, Tyagi R, Habib Z, Xiao S, Wang D, Yu Y, Chen H, Fu Z, Cao G. Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system. Nucleic Acids Res 2018; 46:e17. [PMID: 29165646 PMCID: PMC5815087 DOI: 10.1093/nar/gkx1173] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/13/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022] Open
Abstract
Protein-protein interaction (PPI) network maintains proper function of all organisms. Simple high-throughput technologies are desperately needed to delineate the landscape of PPI networks. While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still required. Here, we developed a recombination-based 'library vs library' Y2H system (RLL-Y2H), by which multi-library screening can be accomplished in a single pool without any individual treatment. This system is based on the phiC31 integrase-mediated integration between bait and prey plasmids. The integrated fragments were digested by MmeI and subjected to deep sequencing to decode the interaction matrix. We applied this system to decipher the trans-kingdom interactome between Mycobacterium tuberculosis and host cells and further identified Rv2427c interfering with the phagosome-lysosome fusion. This concept can also be applied to other systems to screen protein-RNA and protein-DNA interactions and delineate signaling landscape in cells.
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Affiliation(s)
- Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingying Lei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Meiling Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qili Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yichao Han
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Wanshun Zhong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenghang Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Weize Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ran Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Khaista Rahman
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Rohit Tyagi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zeshan Habib
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Yu
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS, Beijing 100101, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenfang Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Departments of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- Bio-Medical Center, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
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Berry KE, Hochschild A. A bacterial three-hybrid assay detects Escherichia coli Hfq-sRNA interactions in vivo. Nucleic Acids Res 2018; 46:e12. [PMID: 29140461 PMCID: PMC5778611 DOI: 10.1093/nar/gkx1086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/21/2017] [Accepted: 10/20/2017] [Indexed: 01/08/2023] Open
Abstract
The interaction of RNA molecules with proteins is a critical aspect of gene regulation across all domains of life. Here, we report the development of a bacterial three-hybrid (B3H) assay to genetically detect RNA-protein interactions. The basis for this three-hybrid assay is a transcription-based bacterial two-hybrid assay that has been used widely to detect and dissect protein-protein interactions. In the three-hybrid assay, a DNA-bound protein with a fused RNA-binding moiety (the coat protein of bacteriophage MS2 (MS2CP)) is used to recruit a hybrid RNA upstream of a test promoter. The hybrid RNA consists of a constant region that binds the tethered MS2CP and a variable region. Interaction between the variable region of the hybrid RNA and a target RNA-binding protein that is fused to a subunit of Escherichia coli RNA polymerase (RNAP) stabilizes the binding of RNAP to the test promoter, thereby activating transcription of a reporter gene. We demonstrate that this three-hybrid assay detects interaction between non-coding small RNAs (sRNAs) and the hexameric RNA chaperone Hfq from E. coli and enables the identification of Hfq mutants with sRNA-binding defects. Our findings suggest that this B3H assay will be broadly applicable for the study of RNA-protein interactions.
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Affiliation(s)
- Katherine E Berry
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ann Hochschild
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
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Abrhámová K, Nemčko F, Libus J, Převorovský M, Hálová M, Půta F, Folk P. Introns provide a platform for intergenic regulatory feedback of RPL22 paralogs in yeast. PLoS One 2018; 13:e0190685. [PMID: 29304067 PMCID: PMC5755908 DOI: 10.1371/journal.pone.0190685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 12/19/2017] [Indexed: 01/04/2023] Open
Abstract
Ribosomal protein genes (RPGs) in Saccharomyces cerevisiae are a remarkable regulatory group that may serve as a model for understanding genetic redundancy in evolutionary adaptations. Most RPGs exist as pairs of highly conserved functional paralogs with divergent untranslated regions and introns. We examined the roles of introns in strains with various combinations of intron and gene deletions in RPL22, RPL2, RPL16, RPL37, RPL17, RPS0, and RPS18 paralog pairs. We found that introns inhibited the expression of their genes in the RPL22 pair, with the RPL22B intron conferring a much stronger effect. While the WT RPL22A/RPL22B mRNA ratio was 93/7, the rpl22aΔi/RPL22B and RPL22A/rpl22bΔi ratios were >99/<1 and 60/40, respectively. The intron in RPL2A stimulated the expression of its own gene, but the removal of the other introns had little effect on expression of the corresponding gene pair. Rpl22 protein abundances corresponded to changes in mRNAs. Using splicing reporters containing endogenous intron sequences, we demonstrated that these effects were due to the inhibition of splicing by Rpl22 proteins but not by their RNA-binding mutant versions. Indeed, only WT Rpl22A/Rpl22B proteins (but not the mutants) interacted in a yeast three-hybrid system with an RPL22B intronic region between bp 165 and 236. Transcriptome analysis showed that both the total level of Rpl22 and the A/B ratio were important for maintaining the WT phenotype. The data presented here support the contention that the Rpl22B protein has a paralog-specific role. The RPL22 singleton of Kluyveromyces lactis, which did not undergo whole genome duplication, also responded to Rpl22-mediated inhibition in K. lactis cells. Vice versa, the overproduction of the K. lactis protein reduced the expression of RPL22A/B in S. cerevisiae. The extraribosomal function of of the K. lactis Rpl22 suggests that the loop regulating RPL22 paralogs of S. cerevisiae evolved from autoregulation.
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Affiliation(s)
- Kateřina Abrhámová
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Filip Nemčko
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiří Libus
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martina Hálová
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail:
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44
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Redder P. Molecular and genetic interactions of the RNA degradation machineries in Firmicute bacteria. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9. [PMID: 29314657 DOI: 10.1002/wrna.1460] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 09/10/2017] [Accepted: 11/10/2017] [Indexed: 12/12/2022]
Abstract
Correct balance between bacterial RNA degradation and synthesis is essential for controlling expression level of all RNAs. The RNA polymerase, which performs the RNA synthesis, is highly conserved across the bacterial domain. However, this is surprisingly not the case for the RNA degradation machinery, which is composed of different subunits and performs different enzymatic reactions, depending on the organism. In Escherichia coli, the RNA decay is performed by the degradosome complex, which forms around the membrane-associated endoribonuclease RNase E, and is stable enough to be purified without falling apart. In contrast, many Firmicutes, for example, Bacillus subtilis, Staphylococcus aureus, and Streptococcus pneumoniae, do not encode an RNase E homolog, but instead have the endoribonuclease RNase Y and the exo- and endo-ribonuclease RNase J complex. A wide range of experiments have been performed, mainly with B. subtilis and S. aureus, to determine which interactions exist between the various RNA decay enzymes in the Firmicutes, with the goal of understanding how RNA degradation (and thus gene expression homeostasis and regulation) is organized in these organisms. The in vivo and in vitro data is diverse, and does not always concur. This overview gathers the data on interactions between Firmicute RNA degradation factors, to highlight the similarities and differences between experimental data from different experiments and from different organisms. WIREs RNA 2018, 9:e1460. doi: 10.1002/wrna.1460 This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Peter Redder
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Integrative, Paul Sabatier University, Toulouse, France
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45
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Abstract
Comprehensive identification of direct, physical interactions between biological macromolecules, such as protein-protein, protein-DNA, and protein-RNA interactions, is critical for our understanding of the function of gene products as well as the global organization and interworkings of various molecular machines within the cell. The accurate and comprehensive detection of direct interactions, however, remains a huge challenge due to the inherent structural complexity arising from various post-transcriptional and translational modifications coupled with huge heterogeneity in concentration, affinity, and subcellular location differences existing for any interacting molecules. This has created a need for developing multiple orthogonal and complementary assays for detecting various types of biological interactions. In this introduction, we discuss the methods developed for measuring different types of molecular interactions with an emphasis on direct protein-protein interactions, critical issues for generating high-quality interactome datasets, and the insights into biological networks and human diseases that current interaction mapping efforts provide. Further, we will discuss what future might lie ahead for the continued evolution of two-hybrid methods and the role of interactomics for expanding the advancement of biomedical science.
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Affiliation(s)
- Soon Gang Choi
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Aaron Richardson
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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46
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Abstract
Yeast-hybrid methods have been successfully applied for screening interacting partners of DNAs or proteins. A yeast-based method, the yeast three-hybrid system, using a chimeric protein of a DNA-binding domain (LexA or GAL4BD) with a protein (MS2 coat protein or HIV Rev. M10) having a hybrid RNA at the 3' end of a target RNA sequence, has been developed for screening RNA-binding proteins. When the target RNA interacts with RNA-binding proteins fused with an activation domain (AD), yeast cells having all the interacting components can survive on selection media, and interacting reporters, HIS3 and LacZ, are activated. Based on this selection, interaction can be easily monitored and detected by simple biochemical assays. The in vivo screening strategy has been widely applied for characterizing and evaluating specific interactions between target RNAs and RNA-binding proteins. Here, we describe a library screening strategy for isolating RNA-binding proteins of select target RNAs using the yeast three-hybrid method. We also describe strategies to verify binding specificity using both a yeast-dependent reporter system and a yeast-independent method, in vivo RNA immunoprecipitation (RIP).
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Affiliation(s)
- Sung Ki Cho
- The Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, TN, USA
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47
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Vušurović J, Schneeberger E, Breuker K. Interactions of Protonated Guanidine and Guanidine Derivatives with Multiply Deprotonated RNA Probed by Electrospray Ionization and Collisionally Activated Dissociation. ChemistryOpen 2017; 6:739-750. [PMID: 29226062 PMCID: PMC5715244 DOI: 10.1002/open.201700143] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/06/2017] [Indexed: 11/25/2022] Open
Abstract
Interactions of ribonucleic acid (RNA) with guanidine and guanidine derivatives are important features in RNA-protein and RNA-drug binding. Here we have investigated noncovalently bound complexes of an 8-nucleotide RNA and six different ligands, all of which have a guanidinium moiety, by using electrospray ionization (ESI) and collisionally activated dissociation (CAD) mass spectrometry (MS). The order of complex stability correlated almost linearly with the number of ligand atoms that can potentially be involved in hydrogen-bond or salt-bridge interactions with the RNA, but not with the proton affinity of the ligands. However, ligand dissociation of the complex ions in CAD was generally accompanied by proton transfer from ligand to RNA, which indicated conversion of salt-bridge into hydrogen-bond interactions. The relative stabilities and dissociation pathways of [RNA+m L-n H] n- complexes with different stoichiometries (m=1-5) and net charge (n= 2-5) revealed both specific and unspecific ligand binding to the RNA.
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Affiliation(s)
- Jovana Vušurović
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Eva‐Maria Schneeberger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
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48
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Cook JM, Charlesworth A. Insertion of inter-domain linkers improves expression and bioactivity of Zygote arrest (Zar) fusion proteins. Protein Eng Des Sel 2017; 30:313-319. [PMID: 28130327 DOI: 10.1093/protein/gzx002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/10/2017] [Indexed: 11/12/2022] Open
Abstract
Developmentally important proteins that are crucial for fertilization and embryogenesis are synthesized through highly regulated translation of maternal mRNA. The Zygote arrest proteins, Zar1 and Zar2, are crucial for embryogenesis and have been implicated in binding mRNA and repressing mRNA translation. To investigate Zar1 and Zar2, the full-length proteins had been fused to glutathione-S-transferase (GST) or MS2 protein tags with minimal inter-domain linkers derived from multiple cloning sites; however, these fusion proteins expressed poorly and/or lacked robust function. Here, we tested the effect of inserting additional linkers between the fusion domains. Three linkers were tested, each 17 amino acids long with different physical and chemical properties: flexible hydrophilic, rigid extended or rigid helical. In the presence of any of the three linkers, GST-Zar1 and GST-Zar2 had fewer breakdown products. Moreover, in the presence of any of the linkers, MS2-Zar1 was expressed to higher levels, and in dual luciferase tethered assays, both MS2-Zar1 and MS2-Zar2 repressed luciferase translation to a greater extent. These data suggest that for Zar fusion proteins, increasing the length of linkers, regardless of their physical or chemical properties, improves stability, expression and bioactivity.
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Affiliation(s)
- Jonathan M Cook
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80204, USA
| | - Amanda Charlesworth
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80204, USA
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49
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Abstract
Alterations in regulatory networks contribute to evolutionary change. Transcriptional networks are reconfigured by changes in the binding specificity of transcription factors and their cognate sites. The evolution of RNA-protein regulatory networks is far less understood. The PUF (Pumilio and FBF) family of RNA regulatory proteins controls the translation, stability, and movements of hundreds of mRNAs in a single species. We probe the evolution of PUF-RNA networks by direct identification of the mRNAs bound to PUF proteins in budding and filamentous fungi and by computational analyses of orthologous RNAs from 62 fungal species. Our findings reveal that PUF proteins gain and lose mRNAs with related and emergent biological functions during evolution. We demonstrate at least two independent rewiring events for PUF3 orthologs, independent but convergent evolution of PUF4/5 binding specificity and the rewiring of the PUF4/5 regulons in different fungal lineages. These findings demonstrate plasticity in RNA regulatory networks and suggest ways in which their rewiring occurs.
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50
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Tamburino AM, Kaymak E, Shrestha S, Holdorf AD, Ryder SP, Walhout AJM. PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions. ACTA ACUST UNITED AC 2017; 5:e1295130. [PMID: 28702278 DOI: 10.1080/21690731.2017.1295130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/23/2017] [Accepted: 02/09/2017] [Indexed: 12/20/2022]
Abstract
Interactions between RNA binding proteins (RBPs) and mRNAs are critical to post-transcriptional gene regulation. Eukaryotic genomes encode thousands of mRNAs and hundreds of RBPs. However, in contrast to interactions between transcription factors (TFs) and DNA, the interactome between RBPs and RNA has been explored for only a small number of proteins and RNAs. This is largely because the focus has been on using 'protein-centered' (RBP-to-RNA) interaction mapping methods that identify the RNAs with which an individual RBP interacts. While powerful, these methods cannot as of yet be applied to the entire RBPome. Moreover, it may be desirable for a researcher to identify the repertoire of RBPs that can interact with an mRNA of interest-in a 'gene-centered' manner-yet few such techniques are available. Here, we present Protein-RNA Interaction Mapping Assay (PRIMA) with which an RNA 'bait' can be tested versus multiple RBP 'preys' in a single experiment. PRIMA is a translation-based assay that examines interactions in the yeast cytoplasm, the cellular location of mRNA translation. We show that PRIMA can be used with small RNA elements, as well as with full-length Caenorhabditis elegans 3' UTRs. PRIMA faithfully recapitulated numerous well-characterized RNA-RBP interactions and also identified novel interactions, some of which were confirmed in vivo. We envision that PRIMA will provide a complementary tool to expand the depth and scale with which the RNA-RBP interactome can be explored.
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Affiliation(s)
- Alex M Tamburino
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ebru Kaymak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shaleen Shrestha
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Amy D Holdorf
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sean P Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Albertha J M Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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