1
|
Raad NG, Ghattas IR, Amano R, Watanabe N, Sakamoto T, Smith CA. Altered‐specificity mutants of the HIV Rev arginine‐rich motif‐RRE IIB interaction. J Mol Recognit 2020; 33:e2833. [DOI: 10.1002/jmr.2833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/08/2019] [Accepted: 12/20/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Nicole G. Raad
- Department of BiologyAmerican University of Beirut Beirut Lebanon
| | | | - Ryo Amano
- Department of Life ScienceChiba Institute of Technology Chiba Japan
| | - Natsuki Watanabe
- Department of Life ScienceChiba Institute of Technology Chiba Japan
| | - Taiichi Sakamoto
- Department of Life ScienceChiba Institute of Technology Chiba Japan
| | - Colin A. Smith
- Department of BiologyAmerican University of Beirut Beirut Lebanon
| |
Collapse
|
2
|
Banerjee S, Wu Q, Ying Y, Li Y, Shirota M, Neculai D, Li C. In silico predicted structural and functional insights of all missense mutations on 2B domain of K1/K10 causing genodermatoses. Oncotarget 2016; 7:52766-52780. [PMID: 27421141 PMCID: PMC5288147 DOI: 10.18632/oncotarget.10599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/17/2016] [Indexed: 12/02/2022] Open
Abstract
The K1 and K10 associated genodermatoses are characterized by clinical symptoms of mild to severe redness, blistering and hypertrophy of the skin. In this paper, we set out to computationally investigate the structural and functional effects of missense mutations on the 2B domain of K1/K10 heterodimer and its consequences in disease phenotype. We modeled the structure of the K1/K10 heterodimer based on crystal structures for the human homolog K5/K14 heterodimer, and identified that the missense mutations exert their effects on stability and assembly competence of the heterodimer by altering physico-chemical properties, interatomic interactions, and inter-residue atomic contacts. Comparative structural analysis between all the missense mutations and SNPs showed that the location and physico-chemical properties of the substituted amino acid are significantly correlated with phenotypic variations. In particular, we find evidence that a particular SNP (K10, p.E443K) is a pathogenic nsSNP which disrupts formation of the hydrophobic core and destabilizes the heterodimer through the loss of interatomic interactions. Our study is the first comprehensive report analyzing the mutations located on 2B domain of K1/K10 heterodimeric coiled-coil complex.
Collapse
Affiliation(s)
- Santasree Banerjee
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
- BGI-Shenzhen, Shenzhen, China
| | - Qian Wu
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuyi Ying
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yanni Li
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Matsuyuki Shirota
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Dante Neculai
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chen Li
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
3
|
Tanamura S, Terakado H, Harada K. Cooperative dimerization of a stably folded protein directed by a flexible RNA in the assembly of the HIV Rev dimer-RRE stem II complex. J Mol Recognit 2015; 29:199-209. [PMID: 26620599 DOI: 10.1002/jmr.2518] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/13/2015] [Accepted: 10/17/2015] [Indexed: 11/08/2022]
Abstract
The binding of the HIV-1 Rev protein as an oligomer to a viral RNA element, the Rev-response element (RRE), mediates nuclear export of genomic RNA. Assembly of the Rev-RRE ribonucleoprotein (RNP) complex is nucleated by the binding of the first Rev molecule to stem IIB of the RRE. This is followed by stepwise addition of a total of ~six Rev molecules along the RRE through a combination of RNA-protein and protein-protein interactions. RRE stem II, which forms a three-way junction consisting of stems IIA, IIB and IIC, has been shown to bind to two Rev molecules in a cooperative manner, with the second Rev molecule binding to the junction region of stem II. The results of base substitutions at the stem II junction, and characterization of stem II junction variants selected from a randomized library showed that an "open" flexible structure is preferred for binding of the second Rev molecule, and that binding of the second Rev molecule to the junction region is not sequence-specific. Alanine substitutions of a number of Rev amino acid residues implicated to be important for Rev folding in previous structural studies were found to result in a dramatic decrease in the binding of the second Rev molecule. These results support the model that proper folding of Rev is critical in ensuring that the flexible RRE is able to correctly position Rev molecules for specific RNP assembly, and suggests that targeting Rev folding may be effective in the inhibition of Rev function.
Collapse
Affiliation(s)
- Satoshi Tanamura
- Department of Life Sciences, Tokyo Gakugei University, Koganei, Tokyo, 184-8501, Japan
| | - Hiroto Terakado
- Department of Life Sciences, Tokyo Gakugei University, Koganei, Tokyo, 184-8501, Japan
| | - Kazuo Harada
- Department of Life Sciences, Tokyo Gakugei University, Koganei, Tokyo, 184-8501, Japan
| |
Collapse
|
4
|
Abdallah EY, Smith CA. Diverse mutants of HIV RRE IIB recognize wild-type Rev ARM or Rev ARM R35G-N40V. J Mol Recognit 2015; 28:710-21. [PMID: 26130028 DOI: 10.1002/jmr.2485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 05/07/2015] [Accepted: 05/23/2015] [Indexed: 01/22/2023]
Abstract
The binding of human immunodeficiency virus Rev protein via its arginine-rich motif (ARM) to an internal loop in the Rev-response element region IIB (RRE IIB) is necessary for viral replication. Many variant RNAs and ARMs that bind Rev and RRE IIB have been found. Despite the essential role of Rev asparagine 40 in recognition, the Rev ARM double-mutant R35G-N40V functions well in a Rev-RRE IIB reporter assay, indicating R35G-N40V uses a distinct recognition strategy. To examine how RRE IIB may evolve specificity to wild-type Rev ARM and R35G-N40V, 10 RRE IIB libraries, each completely randomized in overlapping regions, were screened with wild-type Rev ARM and R35G-N40V using a reporter system based on bacteriophage λ N antitermination. Consistent with previous studies, a core element of RRE IIB did not vary, and substitutions occurred at conserved residues only in the presence of other substitutions. Notably, the groove-widening, non-canonical base-pair G48:G71 was mutable to U48:G71 without strong loss of binding to wild-type Rev ARM, suggesting U48:G71 performs the same role by adopting the nearly isosteric, reverse wobble base pair. Originating from RRE IIB, as few as one or two substitutions are sufficient to confer specificity to wild-type Rev or Rev R35G-N40. The diversity of RRE IIB mutants that maintain binding to wild-type Rev ARM and R35G-N40V supports neutral theories of evolution and illustrates paths by which viral RNA-protein interactions can evolve new specificities. Rev-RRE offers an excellent model with which to study the fine structure of how specificity evolves.
Collapse
Affiliation(s)
- Emane Y Abdallah
- Department of Biology, American University of Beirut, Beirut, Lebanon
| | - Colin A Smith
- Department of Biology, American University of Beirut, Beirut, Lebanon
| |
Collapse
|
5
|
Casu F, Duggan BM, Hennig M. The arginine-rich RNA-binding motif of HIV-1 Rev is intrinsically disordered and folds upon RRE binding. Biophys J 2014; 105:1004-17. [PMID: 23972852 DOI: 10.1016/j.bpj.2013.07.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/19/2013] [Accepted: 07/02/2013] [Indexed: 11/17/2022] Open
Abstract
Arginine-rich motifs (ARMs) capable of binding diverse RNA structures play critical roles in transcription, translation, RNA trafficking, and RNA packaging. The regulatory HIV-1 protein Rev is essential for viral replication and belongs to the ARM family of RNA-binding proteins. During the early stages of the HIV-1 life cycle, incompletely spliced and full-length viral mRNAs are very inefficiently recognized by the splicing machinery of the host cell and are subject to degradation in the cell nucleus. These transcripts harbor the Rev Response Element (RRE), which orchestrates the interaction with the Rev ARM and the successive Rev-dependent mRNA export pathway. Based on established criteria for predicting intrinsic disorder, such as hydropathy, combined with significant net charge, the very basic primary sequences of ARMs are expected to adopt coil-like structures. Thus, we initiated this study to investigate the conformational changes of the Rev ARM associated with RNA binding. We used multidimensional NMR and circular dichroism spectroscopy to monitor the observed structural transitions, and described the conformational landscapes using statistical ensemble and molecular-dynamics simulations. The combined spectroscopic and simulated results imply that the Rev ARM is intrinsically disordered not only as an isolated peptide but also when it is embedded into an oligomerization-deficient Rev mutant. RRE recognition triggers a crucial coil-to-helix transition employing an induced-fit mechanism.
Collapse
Affiliation(s)
- Fabio Casu
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | | | | |
Collapse
|
6
|
Possik EJ, Bou Sleiman MS, Ghattas IR, Smith CA. Randomized codon mutagenesis reveals that the HIV Rev arginine-rich motif is robust to substitutions and that double substitution of two critical residues alters specificity. J Mol Recognit 2013; 26:286-96. [PMID: 23595810 DOI: 10.1002/jmr.2272] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 02/09/2013] [Accepted: 02/10/2013] [Indexed: 02/05/2023]
Abstract
The binding of the arginine-rich motif (ARM) of HIV Rev protein to its high-affinity site in stem IIB in the Rev response element (RRE) initiates assembly of a ribonucleoprotein complex that mediates the export of essential, incompletely spliced viral transcripts. Many biochemical, genetic, and structural studies of Rev-RRE IIB have been published, yet the roles of many peptide residues in Rev ARM are unconfirmed by mutagenesis. Rev aptamer I (RAI) is an optimized RRE IIB that binds Rev with higher affinity and for which mutational data are sparse. Randomized-codon libraries of Rev ARM were assayed for their ability to bind RRE IIB and RAI using a bacterial reporter system based on bacteriophage λ N-nut antitermination. Most Rev ARM residues tolerated substitutions without strong loss of binding to RRE IIB, and all except arginine 39 tolerated substitution without strong loss of binding to RAI. The pattern of critical Rev residues is not the same for RRE IIB and RAI, suggesting important differences between the interactions. The results support and aid the interpretation of existing structural models. Observed clinical variation is consistent with additional constraints on Rev mutation. By chance, we found double mutants of two highly critical residues, arginine 35 (to glycine) and asparagine 40 (to valine or lysine), that bind RRE IIB well, but not RAI. That an apparently distinct binding mode occurs with only two mutations highlights the ability of ARMs to evolve new recognition strategies and supports the application of neutral theories of evolution to protein-RNA recognition.
Collapse
Affiliation(s)
- Elite J Possik
- McGill Cancer Centre and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | | | | | | |
Collapse
|
7
|
Choate KA, Lu Y, Zhou J, Choi M, Elias PM, Farhi A, Nelson-Williams C, Crumrine D, Williams ML, Nopper AJ, Bree A, Milstone LM, Lifton RP. Mitotic recombination in patients with ichthyosis causes reversion of dominant mutations in KRT10. Science 2010; 330:94-7. [PMID: 20798280 DOI: 10.1126/science.1192280] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Somatic loss of wild-type alleles can produce disease traits such as neoplasia. Conversely, somatic loss of disease-causing mutations can revert phenotypes; however, these events are infrequently observed. Here we show that ichthyosis with confetti, a severe, sporadic skin disease in humans, is associated with thousands of revertant clones of normal skin that arise from loss of heterozygosity on chromosome 17q via mitotic recombination. This allowed us to map and identify disease-causing mutations in the gene encoding keratin 10 (KRT10); all result in frameshifts into the same alternative reading frame, producing an arginine-rich C-terminal peptide that redirects keratin 10 from the cytokeratin filament network to the nucleolus. The high frequency of somatic reversion in ichthyosis with confetti suggests that revertant stem cell clones are under strong positive selection and/or that the rate of mitotic recombination is elevated in individuals with this disorder.
Collapse
Affiliation(s)
- Keith A Choate
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06510, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Yano A, Horiya S, Minami T, Haneda E, Ikeda M, Harada K. Identification of antisense RNA stem-loops that inhibit RNA-protein interactions using a bacterial reporter system. Nucleic Acids Res 2010; 38:3489-501. [PMID: 20156995 PMCID: PMC2879510 DOI: 10.1093/nar/gkq027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many well-characterized examples of antisense RNAs from prokaryotic systems involve hybridization of the looped regions of stem–loop RNAs, presumably due to the high thermodynamic stability of the resulting loop–loop and loop–linear interactions. In this study, the identification of RNA stem–loops that inhibit U1A protein binding to the hpII RNA through RNA–RNA interactions was attempted using a bacterial reporter system based on phage λ N-mediated antitermination. As a result, loop sequences possessing 7–8 base complementarity to the 5′ region of the boxA element important for functional antitermination complex formation, but not the U1 hpII loop, were identified. In vitro and in vivo mutational analysis strongly suggested that the selected loop sequences were binding to the boxA region, and that the structure of the antisense stem–loop was important for optimal inhibitory activity. Next, in an attempt to demonstrate the ability to inhibit the interaction between the U1A protein and the hpII RNA, the rational design of an RNA stem–loop that inhibits U1A-binding to a modified hpII was carried out. Moderate inhibitory activity was observed, showing that it is possible to design and select antisense RNA stem–loops that disrupt various types of RNA–protein interactions.
Collapse
Affiliation(s)
- Akiko Yano
- Department of Life Sciences, Tokyo Gakugei University, Koganei, Tokyo 184-8501, Japan
| | | | | | | | | | | |
Collapse
|
9
|
Horiya S, Inaba M, Koh CS, Uehara H, Masui N, Mizuguchi M, Ishibashi M, Matsufuji S, Harada K. Replacement of the λ boxB RNA-N peptide with heterologous RNA-peptide interactions relaxes the strict spatial requirements for the formation of a transcription anti-termination complex. Mol Microbiol 2009; 74:85-97. [DOI: 10.1111/j.1365-2958.2009.06852.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
10
|
Sugaya M, Saito R, Matsumura Y, Harada K, Katoh A. Facile detection of specific RNA-polypeptide interactions by MALDI-TOF mass spectrometry. J Pept Sci 2008; 14:978-83. [DOI: 10.1002/psc.1021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|