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Nichols PJ, Welty R, Krall JB, Henen MA, Vicens Q, Vögeli B. Zα Domain of ADAR1 Binds to an A-Form-like Nucleic Acid Duplex with Low Micromolar Affinity. Biochemistry 2024; 63:777-787. [PMID: 38437710 PMCID: PMC11168418 DOI: 10.1021/acs.biochem.3c00636] [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] [Indexed: 03/06/2024]
Abstract
The left-handed Z-conformation of nucleic acids can be adopted by both DNA and RNA when bound by Zα domains found within a variety of viral and innate immune response proteins. While Z-form adoption is preferred by certain sequences, such as the commonly studied (CpG)n repeats, Zα has been reported to bind to a wide range of sequence contexts. Studying how Zα interacts with B-/A-form helices prior to their conversion to the Z-conformation is challenging as binding coincides with Z-form adoption. Here, we studied the binding of Zα fromHomo sapiens ADAR1 to a locked "A-type" version of the (CpG)3 construct (LNA (CpG)3) where the sugar pucker is locked into the C3'-endo/C2'-exo conformation, which prevents the duplex from adopting the alternating C2'/C3'-endo sugar puckers found in the Z-conformation. Using NMR and other biophysical techniques, we find that ZαADAR1 binds to the LNA (CpG)3 using a similar interface as for Z-form binding, with a dissociation constant (KD) of ∼4 μM. In contrast to Z-DNA/Z-RNA, where two ZαADAR1 bind to every 6 bp stretch, our data suggests that ZαADAR1 binds to multiple LNA molecules, indicating a completely different binding mode. Because ZαADAR1 binds relatively tightly to a non-Z-form model, its binding to B/A-form helices may need to be considered when experiments are carried out which attempt to identify the Z-form targets of Zα domains. The use of LNA constructs may be beneficial in experiments where negative controls for Z-form adoption are needed.
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Affiliation(s)
- Parker J. Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045, USA
| | - Robb Welty
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045, USA
| | - Jeffrey B. Krall
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045, USA
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045, USA
- Present address: Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX 77204, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045, USA
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Nichols PJ, Krall JB, Henen MA, Vögeli B, Vicens Q. Z-RNA biology: a central role in the innate immune response? RNA (NEW YORK, N.Y.) 2023; 29:273-281. [PMID: 36596670 PMCID: PMC9945438 DOI: 10.1261/rna.079429.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Z-RNA is a higher-energy, left-handed conformation of RNA, whose function has remained elusive. A growing body of work alludes to regulatory roles for Z-RNA in the immune response. Here, we review how Z-RNA features present in cellular RNAs-especially containing retroelements-could be recognized by a family of winged helix proteins, with an impact on host defense. We also discuss how mutations to specific Z-contacting amino acids disrupt their ability to stabilize Z-RNA, resulting in functional losses. We end by highlighting knowledge gaps in the field, which, if addressed, would significantly advance this active area of research.
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Affiliation(s)
- Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Jeffrey B Krall
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
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3
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Z-DNA and Z-RNA: Methods-Past and Future. Methods Mol Biol 2023; 2651:295-329. [PMID: 36892776 DOI: 10.1007/978-1-0716-3084-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
A quote attributed to Yogi Berra makes the observation that "It's tough to make predictions, especially about the future," highlighting the difficulties posed to an author writing a manuscript like the present. The history of Z-DNA shows that earlier postulates about its biology have failed the test of time, both those from proponents who were wildly enthusiastic in enunciating roles that till this day still remain elusive to experimental validation and those from skeptics within the larger community who considered the field a folly, presumably because of the limitations in the methods available at that time. If anything, the biological roles we now know for Z-DNA and Z-RNA were not anticipated by anyone, even when those early predictions are interpreted in the most favorable way possible. The breakthroughs in the field were made using a combination of methods, especially those based on human and mouse genetic approaches informed by the biochemical and biophysical characterization of the Zα family of proteins. The first success was with the p150 Zα isoform of ADAR1 (adenosine deaminase RNA specific), with insights into the functions of ZBP1 (Z-DNA-binding protein 1) following soon after from the cell death community. Just as the replacement of mechanical clocks by more accurate designs changed expectations about navigation, the discovery of the roles assigned by nature to alternative conformations like Z-DNA has forever altered our view of how the genome operates. These recent advances have been driven by better methodology and by better analytical approaches. This article will briefly describe the methods that were key to these discoveries and highlight areas where new method development is likely to further advance our knowledge.
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Chiang DC, Li Y, Ng SK. The Role of the Z-DNA Binding Domain in Innate Immunity and Stress Granules. Front Immunol 2021; 11:625504. [PMID: 33613567 PMCID: PMC7886975 DOI: 10.3389/fimmu.2020.625504] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Both DNA and RNA can maintain left-handed double helical Z-conformation under physiological condition, but only when stabilized by Z-DNA binding domain (ZDBD). After initial discovery in RNA editing enzyme ADAR1, ZDBD has also been described in pathogen-sensing proteins ZBP1 and PKZ in host, as well as virulence proteins E3L and ORF112 in viruses. The host-virus antagonism immediately highlights the importance of ZDBD in antiviral innate immunity. Furthermore, Z-RNA binding has been shown to be responsible for the localization of these ZDBD-containing proteins to cytoplasmic stress granules that play central role in coordinating cellular response to stresses. This review sought to consolidate current understanding of Z-RNA sensing in innate immunity and implore possible roles of Z-RNA binding within cytoplasmic stress granules.
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Affiliation(s)
- De Chen Chiang
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
| | - Yan Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Siew Kit Ng
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
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5
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Jin HS, Kim NH, Choi SR, Oh KI, Lee JH. Protein-induced B-Z transition of DNA duplex containing a 2'-OMe guanosine. Biochem Biophys Res Commun 2020; 533:417-423. [PMID: 32972754 DOI: 10.1016/j.bbrc.2020.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023]
Abstract
Structural transformation of the canonical right-handed helix, B-DNA, to the non-canonical left-handed helix, Z-DNA, can be induced by the Zα domain of the human RNA editing enzyme ADAR1 (hZαADAR1). To characterize the site-specific preferences of binding and structural changes in DNA containing the 2'-O-methyl guanosine derivative (mG), titration of the imino proton spectra and chemical shift perturbations were performed on hZαADAR1 upon binding to Z-DNA. The structural transition between B-Z conformation as the changing ratio between DNA and protein showed a binding affinity of the modified DNA onto the Z-DNA binding protein similar to wild-type DNA or RNA. The chemical shift perturbation results showed that the overall structure and environment of the modified DNA revealed DNA-like properties rather than RNA-like characteristics. Moreover, we found evidence for two distinct regimes, "Z-DNA Sensing" and "Modification Sensing", based on the site-specific chemical shift perturbation between the DNA (or RNA) binding complex and the modified DNA-hZαADAR1 complex. Thus, we propose that modification of the sugar backbone of DNA with 2'-O-methyl guanosine promotes the changes in the surrounding α3 helical structural segment as well as the non-perturbed feature of the β-hairpin region.
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Affiliation(s)
- Ho-Seong Jin
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Na-Hyun Kim
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Seo-Ree Choi
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea.
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea.
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6
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Lee AR, Hwang J, Hur JH, Ryu KS, Kim KK, Choi BS, Kim NK, Lee JH. NMR Dynamics Study Reveals the Zα Domain of Human ADAR1 Associates with and Dissociates from Z-RNA More Slowly than Z-DNA. ACS Chem Biol 2019; 14:245-255. [PMID: 30592616 DOI: 10.1021/acschembio.8b00914] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human RNA editing enzyme ADAR1 deaminates adenosine in pre-mRNA to yield inosine. The Zα domain of human ADAR1 (hZαADAR1) binds specifically to left-handed Z-RNA as well as Z-DNA and stabilizes the Z-conformation. To answer the question of how hZαADAR1 can induce both the B-Z transition of DNA and the A-Z transition of RNA, we investigated the structure and dynamics of hZαADAR1 in complex with 6-base-pair Z-DNA or Z-RNA. We performed chemical shift perturbation and relaxation dispersion experiments on hZαADAR1 upon binding to Z-DNA as well as Z-RNA. Our study demonstrates the unique dynamics of hZαADAR1 during the A-Z transition of RNA, in which the hZαADAR1 protein forms a thermodynamically stable complex with Z-RNA, similar to Z-DNA, but kinetically converts RNA to the Z-form more slowly than DNA. We also discovered some distinct structural features of hZαADAR1 in the Z-RNA binding conformation. Our results suggest that the A-Z transition of RNA facilitated by hZαADAR1 displays unique structural and dynamic features that may be involved in targeting ADAR1 for a role in recognition of RNA substrates.
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Affiliation(s)
- Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, South Korea
| | - Jihyun Hwang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jeong Hwan Hur
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Gyeonggi 16419, South Korea
| | - Kyoung-Seok Ryu
- Protein Structure Research Team, Korea Basic Science Institute, Chungbuk 28119, South Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Gyeonggi 16419, South Korea
| | - Byong-Seok Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, South Korea
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7
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Abstract
Left-handed Z-DNA/Z-RNA is bound with high affinity by the Zα domain protein family that includes ADAR (a double-stranded RNA editing enzyme), ZBP1 and viral orthologs regulating innate immunity. Loss-of-function mutations in ADAR p150 allow persistent activation of the interferon system by Alu dsRNAs and are causal for Aicardi-Goutières Syndrome. Heterodimers of ADAR and DICER1 regulate the switch from RNA- to protein-centric immunity. Loss of DICER1 function produces age-related macular degeneration, a different type of Alu-mediated disease. The overlap of Z-forming sites with those for the signal recognition particle likely limits invasion of primate genomes by Alu retrotransposons.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, 42, 8th Street, Unit 3412, Charlestown, MA 02129 USA
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Tajaddod M, Jantsch MF, Licht K. The dynamic epitranscriptome: A to I editing modulates genetic information. Chromosoma 2015; 125:51-63. [PMID: 26148686 PMCID: PMC4761006 DOI: 10.1007/s00412-015-0526-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 02/03/2023]
Abstract
Adenosine to inosine editing (A to I editing) is a cotranscriptional process that contributes to transcriptome complexity by deamination of adenosines to inosines. Initially, the impact of A to I editing has been described for coding targets in the nervous system. Here, A to I editing leads to recoding and changes of single amino acids since inosine is normally interpreted as guanosine by cellular machines. However, more recently, new roles for A to I editing have emerged: Editing was shown to influence splicing and is found massively in Alu elements. Moreover, A to I editing is required to modulate innate immunity. We summarize the multiple ways in which A to I editing generates transcriptome variability and highlight recent findings in the field.
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Affiliation(s)
- Mansoureh Tajaddod
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria
| | - Michael F Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria. .,Department of Cell Biology, Center of Cell Biology and Anatomy, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090, Vienna, Austria.
| | - Konstantin Licht
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria.
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9
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Lu P, Deng S, Wu C, Zhu Y, Liu Y, Lin G, Yan Y, Hu C. The Zα domain of fish PKZ converts DNA hairpin with d(GC)(n) inserts to Z-conformation. Acta Biochim Biophys Sin (Shanghai) 2013; 45:1062-8. [PMID: 24113090 DOI: 10.1093/abbs/gmt114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
PKZ, protein kinase containing Z-DNA domains, is a novel member of the vertebrate eIF2α kinase family. Containing a catalytic domain in C-terminus and two Z-DNA binding domains (Zα1 and Zα2) in N-terminus, PKZ can be activated through the binding of Zα to Z-DNA. However, the regulatory function of PKZ Zα remains to be established. Here, to understand the impact of PKZ Zα on DNA conformational transition, wild-type Zα1Zα2 and 11 mutant proteins were expressed and purified. At the same time, several different lengths of DNA hairpins-d(GC)nT4(GC)n (n = 2-6) and an RNA hairpin-r(GC)6T4(GC)6 were synthesized. The effects of Zα1Zα2 and mutant proteins on the conformation of these synthetic DNA or RNA hairpins were investigated by using circular dichroism spectrum and gel mobility shift assays. The results showed that DNA hairpins retained a conventional B-DNA conformation in the absence of Zα1Zα2, while some of the DNA hairpins (n≥3) were converted to Z-conformation under Zα1Zα2 induction. The tendency was proportionally associated with the increasing amount of GC repeat. In comparison with Zα1Zα2, Zα1Zα1 rather than Zα2Zα2 displayed a higher ability in converting d(GC)6T4(GC)6 from B- to Z-DNA. These results demonstrated that Zα1 sub-domain played a more essential role in the process of B-Z conformational transition than Zα2 sub-domain did. Mutant proteins (K34A, N38A, R39A, Y42A, P57A, P58A, and W60A) could not convert d(GC)6T4(GC)6 into Z-DNA, whereas S35A or K56A retained some partial activities. Interestingly, Zα1Zα2 was also able to induce r(GC)6T4(GC)6 RNA from A-conformation to Z-conformation under appropriate conditions.
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MESH Headings
- Animals
- Base Sequence
- Circular Dichroism
- DNA, A-Form/chemistry
- DNA, A-Form/genetics
- DNA, A-Form/metabolism
- DNA, B-Form/chemistry
- DNA, B-Form/genetics
- DNA, B-Form/metabolism
- DNA, Z-Form/chemistry
- DNA, Z-Form/genetics
- DNA, Z-Form/metabolism
- Fish Proteins/chemistry
- Fish Proteins/genetics
- Fish Proteins/metabolism
- Goldfish
- Mutation
- Nucleic Acid Conformation
- Oligodeoxyribonucleotides/chemistry
- Oligodeoxyribonucleotides/metabolism
- Oligoribonucleotides/chemistry
- Oligoribonucleotides/metabolism
- Protein Binding
- Protein Structure, Tertiary
- eIF-2 Kinase/chemistry
- eIF-2 Kinase/genetics
- eIF-2 Kinase/metabolism
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Affiliation(s)
- Puzhong Lu
- Department of Bioscience, College of Life Science and Food Engineering, Nanchang University, Nanchang 330031, China
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10
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Lu P, Deng S, Zhu Y, Yan Y, Liu Y, Hu C. The Zα domain of fish PKZ facilitates the B-Z conformational transition of oligonucleotide DNAs with d(GC)(n) inserts. Acta Biochim Biophys Sin (Shanghai) 2012; 44:957-63. [PMID: 23034482 DOI: 10.1093/abbs/gms081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
PKZ (PKR-like) was discovered as a member of elF2α kinase family in fish, which possesses a conserved catalytic domain of an eIF2α kinase in C-terminal and also two Z-DNA-binding domains (Zα1 and Zα2) in N-terminal. PKZ can be activated through binding of Zα to Z-DNA. However, the regulatory function of PKZ Zα still remains unclear. To investigate a molecular mechanism of how PKZ Zα interacts with Z-DNA, we expressed Zα polypeptide Zα1α2 in Escherichia coli Rosetta strain and purified by affinity chromatography on Ni-NTA resin. Different lengths of oligonucleotide DNAs with various inserts, namely d(GC)(n) (n = 6, 8, 10, 13), d(TA)(n) (n = 6, 10), non-d(GC), and non-d(TA), were designed and synthesized. Circular dichroism spectrum and gel mobility shift assays were used to investigate the effects of Zα1α2 on the conformational transition of different oligonucleotide DNAs. Results showed that oligonucleotide DNAs retained a conventional B-DNA conformation in the absence of Zα1α2. With the increasing amount of Zα1α2 titration, d(GC)(n) were recognized and converted to Z-DNA conformation to some degree. With increasing the repeat number (from n = 6 to n = 13), the tendency of conformational transition became more obvious. However, the conformation of oligonucleotides with d(TA)(n) inserts changed a little in the presence of Zα1α2, and Zα1α2 had no effect on conformational transition of oligonucleotides with non-d(GC) or non-d(TA) inserts. Gel mobility shift assays further showed that Zα1α2 could bind to oligonucleotide with d(GC)(10). In other words, Zα1α2 can turn oligonucleotides with d(GC)(n) inserts into Z-DNA conformation and bind to it with high affinity.
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Affiliation(s)
- Puzhong Lu
- Department of Bioscience, College of Life Science and Food Engineering, Nanchang University, Nanchang 330031, China
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11
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Gallo A, Locatelli F. ADARs: allies or enemies? The importance of A-to-I RNA editing in human disease: from cancer to HIV-1. Biol Rev Camb Philos Soc 2011; 87:95-110. [PMID: 21682836 DOI: 10.1111/j.1469-185x.2011.00186.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Adenosine deaminases acting on RNA (ADARs) are enzymes that convert adenosine (A) to inosine (I) in nuclear-encoded RNAs and viral RNAs. The activity of ADARs has been demonstrated to be essential in mammals and serves to fine-tune different proteins and modulate many molecular pathways. Recent findings have shown that ADAR activity is altered in many pathological tissues. Moreover, it has been shown that modulation of RNA editing is important for cell proliferation and migration, and has a protective effect on ischaemic insults. This review summarises available recent knowledge on A-to-I RNA editing and ADAR enzymes, with particular attention given to the emerging role played by these enzymes in cancer, some infectious diseases and immune-mediated disorders.
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Affiliation(s)
- Angela Gallo
- RNA Editing Laboratory, Oncohaematology Department, IRCCS, Ospedale Pediatrico "Bambino Gesù", Rome, Italy.
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12
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Alternate rRNA secondary structures as regulators of translation. Nat Struct Mol Biol 2011; 18:169-76. [PMID: 21217697 DOI: 10.1038/nsmb.1962] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 10/22/2010] [Indexed: 11/08/2022]
Abstract
Structural dynamics of large molecular assemblies are intricately linked to function. For ribosomes, macromolecular changes occur especially during mRNA translation and involve participation of ribosomal RNA. Without suitable probes specific to RNA secondary structure, however, elucidation of more subtle dynamic ribosome structure-function relationships, especially in vivo, remains challenging. Here we report that the Z-DNA- and Z-RNA-binding domain Zα, derived from the human RNA editing enzyme ADAR1-L, binds with high stability to specific rRNA segments of Escherichia coli and human ribosomes. Zα impaired in Z-RNA recognition does not associate with ribosomes. Notably, Zα(ADAR1)-ribosome interaction blocks translation in vitro and in vivo, with substantial physiological consequences. Our study shows that ribosomes can be targeted by a protein that specifically recognizes an alternate rRNA secondary structure, and suggests a new mechanism of translational regulation on the ribosome.
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Fujimoto K, Aizawa S, Oota I, Chiba J, Inouye M. Specific Induced Circular Dichroism and Enhanced B to Z Transitions of Duplexes Stabilized by Chromophore-Linked Alkynylnucleoside Residues. Chemistry 2010; 16:2401-6. [DOI: 10.1002/chem.200902882] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Wood DO, Lee JS. Investigation of pH-dependent DNA-metal ion interactions by surface plasmon resonance. J Inorg Biochem 2005; 99:566-74. [PMID: 15621291 DOI: 10.1016/j.jinorgbio.2004.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2004] [Revised: 10/22/2004] [Accepted: 11/01/2004] [Indexed: 11/16/2022]
Abstract
Ni(II) and Zn(II) M-DNA formation and denaturation of double-stranded DNA (dsDNA) by Cd(2+) were monitored by surface plasmon resonance (SPR). When exposed to immobilized 30 bp 50% GC dsDNA, Zn(2+) and Ni(2+) were found to give signals indicative of a conformational change at pH 8.5 but not 7.5, while Mg(2+) and Ca(2+) caused small changes at both pHs. The concentrations that gave 50% of the maximum responses were 0.06 and 0.50 mM for Zn(2+) and Ni(2+), respectively. At pH 8.5, Cd(2+) denatured over 40% of the dsDNA, while other metals denatured less than 5% of the DNA. Smaller pH-dependent signals were induced by Zn(2+), Ni(2+) or Cd(2+) with 50% GC single-stranded DNA (ssDNA), and with a homopolymer of d(T)30. Homopolymers d(A)30 and d(C)30 showed small signals that were largely independent of pH in the presence of Zn(2+) or Ni(2+).
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Affiliation(s)
- David O Wood
- Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Canada S7N 5E5
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15
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Kahmann JD, Wecking DA, Putter V, Lowenhaupt K, Kim YG, Schmieder P, Oschkinat H, Rich A, Schade M. The solution structure of the N-terminal domain of E3L shows a tyrosine conformation that may explain its reduced affinity to Z-DNA in vitro. Proc Natl Acad Sci U S A 2004; 101:2712-7. [PMID: 14981270 PMCID: PMC365686 DOI: 10.1073/pnas.0308612100] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The N-terminal domain of the vaccinia virus protein E3L (Z alpha(E3L)) is essential for full viral pathogenicity in mice. It has sequence similarity to the high-affinity human Z-DNA-binding domains Z alpha(ADAR1) and Z alpha(DLM1). Here, we report the solution structure of Z alpha(E3L) and the chemical shift map of its interaction surface with Z-DNA. The global structure and the Z-DNA interaction surface of Z alpha(E3L) are very similar to the high-affinity Z-DNA-binding domains Z alpha(ADAR1) and Z alpha(DLM1). However, the key Z-DNA contacting residue Y48 of Z alpha(E3L) adopts a different side chain conformation in unbound Z alpha(E3L), which requires rearrangement for binding to Z-DNA. This difference suggests a molecular basis for the significantly lower in vitro affinity of Z alpha(E3L) to Z-DNA compared with its homologues.
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Affiliation(s)
- Jan D Kahmann
- Combinature Biopharm AG, Robert-Rössle-Strasse 10, D-13125 Berlin, Germany
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Hohaus A, Person V, Behlke J, Schaper J, Morano I, Haase H. The carboxyl-terminal region of ahnak provides a link between cardiac L-type Ca2+ channels and the actin-based cytoskeleton. FASEB J 2002; 16:1205-16. [PMID: 12153988 DOI: 10.1096/fj.01-0855com] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Ahnak is a ubiquitously expressed giant protein of 5643 amino acids implicated in cell differentiation and signal transduction. In a recent study, we demonstrated the association of ahnak with the regulatory beta2 subunit of the cardiac L-type Ca2+ channel. Here we identify the most carboxyl-terminal ahnak region (aa 5262-5643) to interact with recombinant beta2a as well as with beta2 and beta1a isoforms of native muscle Ca2+ channels using a panel of GST fusion proteins. Equilibrium sedimentation analysis revealed Kd values of 55 +/- 11 nM and 328 +/- 24 nM for carboxyl-terminal (aa 195-606) and amino-terminal (aa 1-200) truncates of the beta2a subunit, respectively. The same carboxyl-terminal ahnak region (aa 5262-5643) bound to G-actin and cosedimented with F-actin. Confocal microscopy of human left ventricular tissue localized the carboxyl-terminal ahnak portion to the sarcolemma including the T-tubular system and the intercalated disks of cardiomyocytes. These results suggest that ahnak provides a structural basis for the subsarcolemmal cytoarchitecture and confers the regulatory role of the actin-based cytoskeleton to the L-type Ca2+ channel.
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Affiliation(s)
- Annette Hohaus
- Max Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
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Brown BA, Lowenhaupt K, Wilbert CM, Hanlon EB, Rich A. The zalpha domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA. Proc Natl Acad Sci U S A 2000; 97:13532-6. [PMID: 11087828 PMCID: PMC17610 DOI: 10.1073/pnas.240464097] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Zalpha domain of human double-stranded RNA adenosine deaminase 1 binds specifically to left-handed Z-DNA and stabilizes the Z-conformation. Here we report spectroscopic and analytical results that demonstrate that Zalpha can also stabilize the left-handed Z-conformation in double-stranded RNA. Zalpha induces a slow transition from the right-handed A-conformation to the Z-form in duplex r(CG)(6), with an activation energy of 38 kcal mol(-1). We conclude that Z-RNA as well as Z-DNA can be accommodated in the tailored binding site of Zalpha. The specific binding of Z-RNA by Zalpha may be involved in targeting double-stranded RNA adenosine deaminase 1 for a role in hypermutation of RNA viruses.
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Affiliation(s)
- B A Brown
- Department of Biology and George R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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18
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Abstract
The application of surface plasmon resonance biosensors in life sciences and pharmaceutical research continues to increase. This review provides a comprehensive list of the commercial 1999 SPR biosensor literature and highlights emerging applications that are of general interest to users of the technology. Given the variability in the quality of published biosensor data, we present some general guidelines to help increase confidence in the results reported from biosensor analyses.
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Affiliation(s)
- R L Rich
- Center for Biomolecular Interaction Analysis, University of Utah School of Medicine, Salt Lake City 84132, USA
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19
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Xu H, Frank J, Holzwarth JF, Saenger W, Behlke J. Interaction of different oligomeric states of hexameric DNA-helicase RepA with single-stranded DNA studied by analytical ultracentrifugation. FEBS Lett 2000; 482:180-4. [PMID: 11024456 DOI: 10.1016/s0014-5793(00)02026-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Analytical ultracentrifugation was used to determine the molecular mass, M, of hexameric DNA-helicase RepA at pH 5.8 and 7.6. At pH 7.6, a molecular mass of 179.5+/-2.6 kDa was found, consistent with the known hexameric state of RepA, (RepA)(6). At pH 5.8, (RepA)(6) associates to form a dimer with a molecular mass of 366.2+/-4.1 kDa. Analytical ultracentrifugation was also applied to characterize the interaction of single-stranded DNA (ssDNA) with the two different oligomeric states of (RepA)(6) at pH 5.8 and 7.6. The dissociation constants, K(d), for the equilibrium binding of (dA)(30) to the (RepA)(6) dimer at pH 5.8 and to (RepA)(6) at pH 7.6 were determined at 10 degrees C in the presence of 0.5 mM ATPgammaS, 10 mM MgCl(2) and 60 mM NaCl as K(d5.8)=0.94+/-0.13 microM at pH 5.8 and K(d7. 6)=25.4+/-6.4 microM at pH 7.6. The stoichiometries, n, for the two complexes (dA)(30)/(RepA)(6) dimer and (dA)(30)/(RepA)(6) at pH 5.8 and 7.6 were calculated from the corresponding binding curves. At pH 5.8 one (dA)(30) molecule was bound per (RepA)(6) dimer, while at pH 7.6 one (dA)(30) molecule was bound to one (RepA)(6). Binding curves were compatible with a single ssDNA binding site present on the (RepA)(6) dimer and on (RepA)(6), respectively, with no indication of cooperativity. (RepA)(6) tends to form larger aggregates under acidic conditions (pH<6.0) which are optimal for ssDNA binding. In contrast, at pH 5.8 in the presence of 60 mM NaCl, only the (RepA)(6) dimer was observed both in the absence and presence of (dA)(30).
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Affiliation(s)
- H Xu
- Institut für Kristallographie, Freie Universität Berlin, Berlin, Germany
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Kim YG, Lowenhaupt K, Maas S, Herbert A, Schwartz T, Rich A. The Zab Domain of the Human RNA Editing Enzyme ADAR1 Recognizes Z-DNA When Surrounded by B-DNA. J Biol Chem 2000. [DOI: 10.1016/s0021-9258(19)61450-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Schade M, Turner CJ, Kühne R, Schmieder P, Lowenhaupt K, Herbert A, Rich A, Oschkinat H. The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA. Proc Natl Acad Sci U S A 1999; 96:12465-70. [PMID: 10535945 PMCID: PMC22950 DOI: 10.1073/pnas.96.22.12465] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Double-stranded RNA deaminase I (ADAR1) contains the Z-DNA binding domain Zalpha. Here we report the solution structure of free Zalpha and map the interaction surface with Z-DNA, confirming roles previously assigned to residues by mutagenesis. Comparison with the crystal structure of the (Zalpha)(2)/Z-DNA complex shows that most Z-DNA contacting residues in free Zalpha are prepositioned to bind Z-DNA, thus minimizing the entropic cost of binding. Comparison with homologous (alpha+beta)helix-turn-helix/B-DNA complexes suggests that binding of Zalpha to B-DNA is disfavored by steric hindrance, but does not eliminate the possibility that related domains may bind to both B- and Z-DNA.
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Affiliation(s)
- M Schade
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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