Structural Characterization of Interactions between the Double-Stranded RNA-Binding Zinc Finger Protein JAZ and Nucleic Acids

Burge, Russell G.; Martinez-Yamout, Maria A.; Dyson, H. Jane; Wright, Peter E.

doi:10.1021/bi401675h

Cited by 21 publications

(24 citation statements)

References 57 publications

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“…above than the mean. In comparison, individual classical ZFs of the double-stranded RNA-binding proteins JAZ and ZFa exhibit perturbations of less than 0.6 ppm (12). This disparity is attributable to hydrogen bonding to RNA bases by sequence-specific ssRNA-binding proteins, which induces larger changes in environment for participating amide groups, and also to closer proximity of the protein to the aromatic ring currents of the bases.…”

Section: Discussionmentioning

confidence: 99%

The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity

et al. 2016

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Classical zinc fingers (ZFs) are traditionally considered to act as sequence-specific DNA-binding domains. More recently, classical ZFs have been recognised as potential RNA-binding modules, raising the intriguing possibility that classical-ZF transcription factors are involved in post-transcriptional gene regulation via direct RNA binding. To date, however, only one classical ZF-RNA complex, that involving TFIIIA, has been structurally characterised. Yin Yang-1 (YY1) is a multi-functional transcription factor involved in many regulatory processes, and binds DNA via four classical ZFs. Recent evidence suggests that YY1 also interacts with RNA, but the molecular nature of the interaction remains unknown. In the present work, we directly assess the ability of YY1 to bind RNA using in vitro assays. Systematic Evolution of Ligands by EXponential enrichment (SELEX) was used to identify preferred RNA sequences bound by the YY1 ZFs from a randomised library over multiple rounds of selection. However, a strong motif was not consistently recovered, suggesting that the RNA sequence selectivity of these domains is modest. YY1 ZF residues involved in binding to single-stranded RNA were identified by NMR spectroscopy and found to be largely distinct from the set of residues involved in DNA binding, suggesting that interactions between YY1 and ssRNA constitute a separate mode of nucleic acid binding. Our data are consistent with recent reports that YY1 can bind to RNA in a low-specificity, yet physiologically relevant manner.

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Section: Discussionmentioning

confidence: 99%

The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity

et al. 2016

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“…3 and data not shown). A search for conserved domains (36) identified Znf5 as a dsRNA-binding domain (pfam12171; E value, 7.05e-03) originally reported in JAZ dsRNA-binding Znf proteins (48). The conserved domain database search predicted Znf6 -8.…”

Section: Subunits Of the Novel Reh2-associated Subcomplex (Reh2c)-mentioning

confidence: 99%

“…Several dsRNA-binding Znf proteins (dsRBZFPs) play important roles in cellular localization and apoptosis (48). These proteins have several domains, each containing zinc finger motifs, and each is capable of binding dsRNA.…”

Section: Reh2cmentioning

confidence: 99%

REH2C Helicase and GRBC Subcomplexes May Base Pair through mRNA and Small Guide RNA in Kinetoplastid Editosomes

Kumar

Madina

Gulati

et al. 2016

Journal of Biological Chemistry

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Mitochondrial mRNAs in Trypanosoma brucei undergo extensive insertion and deletion of uridylates that are catalyzed by the RNA editing core complex (RECC) and directed by hundreds of small guide RNAs (gRNAs) that base pair with mRNA. RECC is largely RNA-free, and accessory mitochondrial RNAbinding complex 1 (MRB1) variants serve as scaffolds for the assembly of mRNA-gRNA hybrids and RECC. However, the molecular steps that create higher-order holoenzymes ("editosomes") are unknown. Previously, we identified an RNA editing helicase 2-associated subcomplex (REH2C) and showed that REH2 binds RNA. Here we showed that REH2C is an mRNA-associated ribonucleoprotein (mRNP) subcomplex with editing substrates, intermediates, and products. We isolated this mRNP from mitochondria lacking gRNA-bound RNP (gRNP) subcomplexes and identified REH2-associated cofactors 1 and 2 ( H2 F1 and H2 F2). H2 F1 is an octa-zinc finger protein required for mRNP-gRNP docking, pre-mRNA and RECC loading, and RNP formation with a short synthetic RNA duplex. REH2 and other eukaryotic DEAH/RHA-type helicases share a conserved regulatory C-terminal domain cluster that includes an oligonucleotide-binding fold. Recombinant REH2 and H2 F1 constructs associate in a purified complex in vitro. We propose a model of stepwise editosome assembly that entails controlled docking of mRNP and gRNP modules via specific base pairing between their respective mRNA and gRNA cargo and regulatory REH2 and H2 F1 subunits of the novel mRNP that may control specificity checkpoints in the editing pathway.RNA editing by uridylate insertion and deletion in Trypanosoma brucei modifies over 3000 sites in mitochondrial mRNAs in a gradual process directed by hundreds of small guide RNAs (gRNAs) 4 (1-3). The basic regulatory mechanisms of substrate specificity and developmental control in RNA editing remain unknown. The uridylate changes are catalyzed by the RECC enzyme from 3Ј to 5Ј in discrete blocks. Each gRNA directs editing of one mRNA block. Surprisingly, RECC has little or no RNA and lacks the processivity found in vivo, as established in early purifications of this multiprotein enzyme (4 -6). So, accessory components of the editing apparatus must facilitate substrate recruitment and editing catalysis. There are many non-RECC proteins that affect editing. Most of these proteins (Ͼ25 proteins) are components of the MRB1 complex in T. brucei, also termed gRNA-binding complex (GRBC) in Leishmania, that binds and stabilizes gRNA. MRB1 interacts transiently with the RECC enzyme and mitoribosomes (1,7,8). It has also been found that MRB1 contains all three classes of mRNA in editing: unedited pre-mRNAs, partially edited intermediates, and fully edited transcripts. This indicates that MRB1 complexes serve as scaffolds for the assembly of hybrid substrates and the RECC enzyme (9 -11). Transient addition of RECC to these scaffolds would establish higher-order editing holoenzymes or editosomes. MRB1 was first considered a single dynamic complex, but the reason of its variable compos...

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“…Thus, we propose that this domain suppresses the ability of ZLD to activate transcription. While ZnF2 has the canonical architecture of the JAZ-like C 2 H 2 zinc finger, it lacks a positively charged lysine residues that is conserved in double-strand RNA-binding zinc fingers and is thought to be required for RNA binding [38]. Therefore, it is unlikely that this domain functions through interaction with doublestranded RNA.…”

Section: The Jaz-like Zinc Finger Domain Regulates Zld Transcriptionamentioning

confidence: 99%

A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis inDrosophila melanogaster

Hamm

Larson

Nevil

et al. 2017

Preprint

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In nearly all metazoans, the earliest stages of development are controlled by maternally deposited mRNAs and proteins. The zygotic genome becomes transcriptionally active hours after fertilization. Transcriptional activation during this maternal-to-zygotic transition (MZT) is tightly coordinated with the degradation of maternally provided mRNAs. In Drosophila melanogaster, the transcription factor Zelda plays an essential role in widespread activation of the zygotic genome. While Zelda expression is required both maternally and zygotically, the mechanisms by which it functions to remodel the embryonic genome and prepare the embryo for development remain unclear. Using Cas9-mediated genome editing to generate targeted mutations in the endogenous zelda locus, we determined the functional relevance of protein domains conserved amongst Zelda orthologs. We showed that neither a conserved N-terminal zinc finger nor an acidic patch were required for activity. Similarly, a previously identified splice isoform of zelda is dispensable for viability. By contrast, we identified a highly conserved zincfinger domain that is essential for the maternal, but not zygotic functions of Zelda. Animals homozygous for mutations in this domain survived to adulthood, but embryos inheriting these loss-off-function alleles from their mothers died late in embryogenesis. These mutations did not interfere with the capacity of Zelda to activate transcription. Unexpectedly, these mutations generated a hyperactive form of the protein and enhanced Zelda-dependent gene expression.

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Structural Characterization of Interactions between the Double-Stranded RNA-Binding Zinc Finger Protein JAZ and Nucleic Acids

Cited by 21 publications

References 57 publications

The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity

The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity

REH2C Helicase and GRBC Subcomplexes May Base Pair through mRNA and Small Guide RNA in Kinetoplastid Editosomes

A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis inDrosophila melanogaster

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