The A form RNA double helix can be transformed to a left-handed helix, called Z-RNA. Currently, little is known about the detailed structural features of Z-RNA or its involvement in cellular processes. The discovery that certain interferon-response proteins have domains that can stabilize Z-RNA as well as Z-DNA opens the way for the study of Z-RNA. Here, we present the 2.25 A crystal structure of the Zalpha domain of the RNA-editing enzyme ADAR1 (double-stranded RNA adenosine deaminase) complexed to a dUr(CG)(3) duplex RNA. The Z-RNA helix is associated with a unique solvent pattern that distinguishes it from the otherwise similar conformation of Z-DNA. Based on the structure, we propose a model suggesting how differences in solvation lead to two types of Z-RNA structures. The interaction of Zalpha with Z-RNA demonstrates how the interferon-induced isoform of ADAR1 could be targeted toward selected dsRNAs containing purine-pyrimidine repeats, possibly of viral origin.
The translational recoding of UGA as selenocysteine (Sec) is directed by a SECIS element in the 3' untranslated region (UTR) of eukaryotic selenoprotein mRNAs. The selenocysteine insertion sequence (SECIS) contains two essential tandem sheared G.A pairs that bind SECIS-binding protein 2 (SBP2), which recruits a selenocysteine-specific elongation factor and Sec-tRNA(Sec) to the ribosome. Here we show that ribosomal protein L30 is a component of the eukaryotic selenocysteine recoding machinery. L30 binds SECIS elements in vitro and in vivo, stimulates UGA recoding in transfected cells and competes with SBP2 for SECIS binding. Magnesium, known to induce a kink-turn in RNAs that contain two tandem G.A pairs, decreases the SBP2-SECIS complex in favor of the L30-SECIS interaction. We propose a model in which SBP2 and L30 carry out different functions in the UGA recoding mechanism, with the SECIS acting as a molecular switch upon protein binding.
Methylation of ribosomal RNA (rRNA) is required for optimal protein synthesis. Multiple 2'-O-ribose methylations are carried out by small (nucleolar) box C/D guide ribonucleoproteins (s(no)RNPs), which are ubiquitous in nature from archaea to eukaryotes. Each site of methylation is dictated by base pairing between the specific guide s(no)RNA component of the s(no)RNP and the target rRNA. Here we present the first structure of a reconstituted and catalytically active box C/D sRNP from the archaeon Methanocaldococcus jannaschii determined by single-particle electron microscopy. Our results reveal that archaeal box C/D sRNPs unexpectedly form a dimeric structure with a novel organization of their RNA and protein components, challenging the conventional view of box C/D s(no)RNP architecture. Mutational analysis demonstrates that the di-sRNP structure is relevant for the function of archaeal box C/D sRNPs as RNP enzymes.
The Z␣ 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 Z␣ can also stabilize the left-handed Z-conformation in double-stranded RNA. Z␣ 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 Z␣. The specific binding of Z-RNA by Z␣ may be involved in targeting double-stranded RNA adenosine deaminase 1 for a role in hypermutation of RNA viruses. D ouble-stranded RNA (dsRNA) adenosine deaminase (ADAR1) is an enzyme that modifies the genetic message by deaminating adenosine in pre-mRNAs; the resulting inosine acts like guanosine in translation. ADAR1 requires a dsRNA substrate, which often is provided by the pairing of exons with introns (1); therefore, editing must take place before the removal of introns from pre-mRNAs. In addition to a deaminase domain and three dsRNA binding domains, ADAR1 contains a Z-DNA binding domain, Zab, at its N terminus (2, 3). The Z␣ subdomain of Zab has been isolated and binds left-handed Z-DNA with a low nanomolar dissociation constant (4, 5). Recently, Z␣ has been crystallized with a segment of left-handed Z-DNA, and the resulting structure reveals the tailored fitting of the Z␣ domain to a number of specific geometrical and electrostatic features of the left-handed nucleic acid conformation (6). Z-DNA is stabilized in vivo by negative supercoiling of DNA, which occurs upstream of a moving RNA polymerase (7). This stabilization by supercoiling has given rise to the suggestion that the Z-DNA binding domain of ADAR1 may target the enzyme to actively transcribing genes, thereby ensuring that editing can precede splicing (8).When an RNA virus such as measles infects a cell, the antiviral interferon response leads to increased activity of interferoninducible genes, including the ADAR1 gene, which is strongly up-regulated and produces the full-length protein, including the Z␣ domain (9). In addition, the distribution of ADAR1 changes from primarily nuclear localization to both nuclear and cytoplasmic localization. The measles virus replicates in the cytoplasm (as do most RNA viruses), and late in infection it has been observed that the viral RNA has been subjected to hypermutation in which a significant fraction of adenines have been changed to guanines, and uracil residues to cytosines (10). Such mutations are the expected result of the action of ADAR1 on the viral RNA replication system and may be an attempt on the part of the host cell to disable the virus. Hypermutation similar to that found in the measles virus has also been found in the RNA of vesicular stomatitis virus, respiratory syncytial virus, and parainfluenza virus 3 (11, 12).RNA viruses generally use a double-stranded intermediate during some period of their life cycle (13). Little is known abo...
Z␣ is a peptide motif that binds to Z-DNA with high affinity. This motif binds to alternating dC-dG sequences stabilized in the Z-conformation by means of bromination or supercoiling, but not to B-DNA. Z␣ is part of the N-terminal region of double-stranded RNA adenosine deaminase (ADAR1) , a candidate enzyme for nuclear pre-mRNA editing in mammals. Z␣ is conserved in ADAR1 from many species; in each case, there is a second similar motif, Z, separated from Z␣ by a more divergent linker. To investigate the structure-function relationship of Z␣, its domain structure was studied by limited proteolysis. Proteolytic profiles indicated that Z␣ is part of a domain, Zab, of 229 amino acids (residues 133-361 in human ADAR1). This domain contains both Z␣ and Z as well as a tandem repeat of a 49-amino acid linker module. Prolonged proteolysis revealed a minimal core domain of 77 amino acids (positions 133-209), containing only Z␣, which is sufficient to bind lefthanded Z-DNA; however, the substrate binding is strikingly different from that of Zab. The second motif, Z, retains its structural integrity only in the context of Zab and does not bind Z-DNA as a separate entity. These results suggest that Z␣ and Z act as a single bipartite domain. In the presence of substrate DNA, Zab becomes more resistant to proteases, suggesting that it adopts a more rigid structure when bound to its substrate, possibly with conformational changes in parts of the protein.Many protein domains that recognize DNA in both sequenceand conformation-specific manners have been characterized (for a review, see Ref. 1). These studies have resulted in an understanding of the variety of ways in which protein-DNA interactions can result in function. Identification of a peptide motif, Z␣, which binds specifically to Z-DNA, opens up a new vista and invites the investigation of the similarities and differences between domains that bind right-and left-handed DNAs. The conformation specificity of Z␣ binding has been characterized in many ways. Peptides including this motif bind to alternating dC-dG that has been stabilized in the Z-conformation using bromination or supercoiling, as shown by band shift assays, competition experiments, and BIAcore measurements (2). When linked to the nuclease domain from FokI, the resulting chimeric nuclease cuts supercoiled plasmid DNA to bracket a d(C-G) 13 in the Z-conformation (3). The protein also binds to short oligonucleotides of suitable sequence and converts them from the B-to the Z-conformation, as detected by CD and Raman spectroscopy (4, 5). The binding of Z-DNA by Z␣ occurs even in the presence of a 10 5 -fold excess of B-DNA (6). Z␣ binds poly(dC-dG), stabilized in the Z-conformation by bromination, with an equilibrium dissociation constant (K d ) in the lower nanomolar range, as shown by BIAcore measurements (2).Although many properties of Z␣ have been studied, its biological function in the context of ADAR1 remains unknown. The Z-DNA binding activity of Z␣ was first identified in proteolytic fragments of double...
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.