The double‐stranded RNA‐binding domains of <i>Xenopus laevis</i> ADAR1 exhibit different RNA‐binding behaviors

Brooks, Roman; Eckmann, Christian R.; Jantsch, Michael F.

doi:10.1016/s0014-5793(98)00963-6

Cited by 13 publications

(17 citation statements)

References 33 publications

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“…The results shown herein that the wild-type ADAR1-a, -b, and -c variants and the dsRBM motif mutants of the ADAR1-b variant differ in their ability to edit the natural cellular GluR-B RNA substrate, together with the finding that the Xenopus ADAR1 dsRBM motifs exhibit different RNA-binding behaviors (48), support the notion that functionally distinct dsRNA-binding domains of ADAR1 (32,36) reflect the occurrence of different structures among potential RNA substrates that are bound and edited by ADAR1 isoforms. Our results indicate that changes in the region between the dsRBD domain and the catalytic domain of ADAR1 affects the editing efficiency of GluR-B RNA in a site-specific fashion but without altering site-selectivity per se.…”

Section: Discussionmentioning

confidence: 55%

Editing of Glutamate Receptor Subunit B Pre-mRNA by Splice-site Variants of Interferon-inducible Double-stranded RNA-specific Adenosine Deaminase ADAR1

Liu

Samuel

1999

Journal of Biological Chemistry

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The interferon-inducible RNA-specific adenosine deaminase (ADAR1) is an RNA-editing enzyme that catalyzes the deamination of adenosine in double-stranded RNA structures. Three alternative splice-site variants of ADAR1 (ADAR1-a, -b, and -c) occur that possess functionally distinct double-stranded RNA-binding motifs as measured with synthetic double-stranded RNA substrates. The pre-mRNA transcript encoding the B subunit of glutamate receptor (GluR-B) has two functionally important editing sites (Q/R and R/G sites) that undergo selective A-to-I conversions. We have examined the ability of the three ADAR1 splice-site variants to catalyze the editing of GluR-B pre-mRNA at the Q/R and R/G sites as well as an intron hotspot (؉60) of unknown function. Measurement of GluR-B pre-mRNA editing in vitro revealed different site-specific deamination catalyzed by the three ADAR1 variants. The ADAR1-a, -b, and -c splice variants all efficiently edited the R/G site and the intron ؉60 hotspot but exhibited little editing activity at the Q/R site. ADAR1-b and -c showed higher editing activity than ADAR1-a for the R/G site, whereas the intron ؉60 site was edited with comparable efficiency by all three ADAR1 splice variants. Mutational analysis revealed that the functional importance of each of the three RNA-binding motifs of ADAR1 varied with the specific target editing site in GluR-B RNA. Quantitative reverse transcription-polymerase chain reaction analyses of GluR-B RNA from dissected regions of rat brain showed significant expression and editing at the R/G site in all brain regions examined except the choroid plexus. The relative levels of the alternatively spliced flip and flop isoforms of GluR-B RNA varied among the choroid plexus, cortex, hippocampus, olfactory bulb, and striatum, but in all regions of rat brain the editing of the flip isoform was greater than that of the flop isoform.

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Section: Discussionmentioning

confidence: 55%

Editing of Glutamate Receptor Subunit B Pre-mRNA by Splice-site Variants of Interferon-inducible Double-stranded RNA-specific Adenosine Deaminase ADAR1

Liu

Samuel

1999

Journal of Biological Chemistry

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“…The second dsRBDs of either xlADAR1 or Xlrbpa, two proteins of different RNA-binding specificities, were chosen. These dsRBDs proved to be the strongest binders in the respective proteins as judged by Northwestern assays, and thus seemed the ideal candidates for initial target recognition (Brooks et al 1998). Interestingly, our results indicate that binding sites on the RNA clones obtained by SELEX show structural similarities, but share no common motif or sequence homology.…”

Section: Mimicking Coevolution Of Rnas With Dsrbds By Applying Selexmentioning

confidence: 78%

“…Moreover, Xlrbpa exhibits RNA chaperonin activity (Hitti et al 1998). The second dsRBD chosen for these experiments has the strongest RNA-binding activity in vitro and displays no apparent binding preference (Brooks et al 1998). On the other hand, the second dsRBD of Xenopus (xl) ADAR1, which also showed the strongest in vitro RNA-binding activity in this protein, was chosen.…”

Section: Resultsmentioning

confidence: 99%

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RNA aptamers binding the double-stranded RNA-binding domain

Hallegger

Taschner²,

Jantsch³

2006

RNA

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Specific RNA recognition of proteins containing the double-strand RNA-binding domain (dsRBD) is essential for several biological pathways such as ADAR-mediated adenosine deamination, localization of RNAs by Staufen, or RNA cleavage by RNAse III. Structural analysis has demonstrated the lack of base-specific interactions of dsRBDs with either a perfect RNA duplex or an RNA hairpin. We therefore asked whether in vitro selections performed in parallel with individual dsRBDs could yield RNAs that are specifically recognized by the dsRBD on which they were selected . To this end, SELEX experiments were performed using either the second dsRBD of the RNA-editing enzyme ADAR1 or the second dsRBD of Xlrbpa, a homolog of TRBP that is involved in RISC formation. Several RNA families with high binding capacities for dsRBDs were isolated from either SELEX experiment, but no discrimination of these RNAs by different dsRBDs could be detected. The selected RNAs are highly structured, and binding regions map to two neighboring stem-loops that presumably form stacked helices and are interrupted by mismatches and bulges. Despite the lack of selective binding of SELEX RNAs to individual dsRBDS, selected RNAs can efficiently interfere with RNA editing in vivo.

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“…The search results showed that the HYL1 protein contains two regions with marked similarities to dsRNA binding motifs (St. Johnston et al, 1992;Bass et al, 1994). The highest scoring segment pairs were those matching the dsRNA binding domains of the human interferon-induced RNA-dependent protein kinase P68, Escherichia coli ribonuclease III, and Xenopus dsRNA adenosine deaminase (Burd and Dreyfuss, 1994;Kharrat et al, 1995;Brooks et al, 1998). The two dsRNA binding motifs of the HYL1 protein are shown aligned with those of other proteins in Figure 7B.…”

mentioning

confidence: 96%

A Mutation in the Arabidopsis HYL1 Gene Encoding a dsRNA Binding Protein Affects Responses to Abscisic Acid, Auxin, and Cytokinin

2000

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Both physiological and genetic evidence indicate interconnections among plant responses to different hormones. We describe a pleiotropic recessive Arabidopsis transposon insertion mutation, designated hyponastic leaves ( hyl1 ), that alters the plant's responses to several hormones. The mutant is characterized by shorter stature, delayed flowering, leaf hyponasty, reduced fertility, decreased rate of root growth, and an altered root gravitropic response. It also exhibits less sensitivity to auxin and cytokinin and hypersensitivity to abscisic acid (ABA). The auxin transport inhibitor 2,3,5-triiodobenzoic acid normalizes the mutant phenotype somewhat, whereas another auxin transport inhibitor, N -(1-naphthyl)phthalamic acid, exacerbates the phenotype. The gene, designated HYL1 , encodes a 419-amino acid protein that contains two double-stranded RNA (dsRNA) binding motifs, a nuclear localization motif, and a C-terminal repeat structure suggestive of a protein-protein interaction domain. We present evidence that the HYL1 gene is ABA-regulated and encodes a nuclear dsRNA binding protein. We hypothesize that the HYL1 protein is a regulatory protein functioning at the transcriptional or post-transcriptional level. INTRODUCTIONThe development, growth, and survival of plants under a wide range of environmental conditions reflect an intricate interplay of physical and chemical conditions with the highly integrated sensing and response networks in plants. The growth habit and physiological properties of plants can differ markedly under different regimes of light, gravity, temperature, humidity, and salinity, among others. Hormones have long been known to be important internal mediating signals in plants, but the components of the underlying cellular machinery are just beginning to be identified and characterized (Trewavas and Malho, 1997; Grill and Himmelbach, 1998;Solano and Ecker, 1998;D'Agostino and Kieber, 1999). The range of proteins involved in receiving, transmitting, and responding to external signals includes receptorlike and other kinds of protein kinases, phosphatases, and transcription factors, as well as enzymes such as thioredoxin and farnesyltransferase, which influence protein structure or localization through mechanisms other than phosphorylation (Mulligan et al., 1997; Becraft, 1998;Bonetta and McCourt, 1998; Hooley, 1998;Bleecker, 1999;Thornton et al., 1999; Hirt, 2000;Urao et al., 2000).Ample physiological evidence supports the presence of interconnections among plant responses to different environmental stimuli; moreover, evidence is accumulating that certain mutations can simultaneously influence the response to more than one hormone or altered physical parameter (Wilson et al., 1990;Clouse et al., 1996;Nemeth et al., 1998;Ephritikhine et al., 1999a; Beaudoin et al., 2000; Ghassemian et al., 2000). The implication is that individual proteins can be responsible for such interconnections, either transmitting multiple signals or participating in distinct complexes that transmit different signals (Elio...

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The double‐stranded RNA‐binding domains of Xenopus laevis ADAR1 exhibit different RNA‐binding behaviors

Cited by 13 publications

References 33 publications

Editing of Glutamate Receptor Subunit B Pre-mRNA by Splice-site Variants of Interferon-inducible Double-stranded RNA-specific Adenosine Deaminase ADAR1

Editing of Glutamate Receptor Subunit B Pre-mRNA by Splice-site Variants of Interferon-inducible Double-stranded RNA-specific Adenosine Deaminase ADAR1

RNA aptamers binding the double-stranded RNA-binding domain

A Mutation in the Arabidopsis HYL1 Gene Encoding a dsRNA Binding Protein Affects Responses to Abscisic Acid, Auxin, and Cytokinin

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