Recognition of polyadenosine RNA by zinc finger proteins

Kelly, Seth M.; Pabit, Suzette A.; Kitchen, Chad M.; Guo, Peng; Marfatia, Kavita A.; Murphy, Tamara C.; Corbett, Anita H.; Berland, Keith M.

doi:10.1073/pnas.0701244104

Cited by 79 publications

(130 citation statements)

References 52 publications

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“…Nevertheless, if we consider the results from both high-throughput sequencing and RT-PCR, we conclude that Nab2 is associated with the bulk of yeast mRNAs. This suggestion is consistent with the finding that Nab2 is a poly(A)-binding protein (29). However, our data do not support a model in which Nab2 is associated with specific subclasses of mRNAs (13).…”

Section: Discussionsupporting

confidence: 78%

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Purification of Nuclear Poly(A)-binding Protein Nab2 Reveals Association with the Yeast Transcriptome and a Messenger Ribonucleoprotein Core Structure

Batisse

Budd

et al. 2009

Journal of Biological Chemistry

104

107

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Nascent mRNAs produced by transcription in the nucleus are subsequently processed and packaged into mRNA ribonucleoprotein particles (messenger ribonucleoproteins (mRNPs)) before export to the cytoplasm. Here, we have used the poly(A)-binding protein Nab2 to isolate mRNPs from yeast under conditions that preserve mRNA integrity. Upon Nab2-tandem affinity purification, several mRNA export factors were co-enriched (Yra1, Mex67, THO-TREX) that were present in mRNPs of different size and mRNA length. High-throughput sequencing of the co-precipitated RNAs indicated that Nab2 is associated with the bulk of yeast transcripts with no specificity for different mRNA classes. Electron microscopy revealed that many of the mRNPs have a characteristic elongated structure. Our data suggest that mRNPs, although associated with different mRNAs, have a unifying core structure.Nucleocytoplasmic transport occurs via nuclear pore complexes, which are embedded into the nuclear membrane. For nuclear mRNA export, a conserved export receptor, Mex67-Mtr2, in yeast (TAP-p15 or NXF1-NXT1 in metazoans) and a number of export adaptor proteins were identified (for review, see Refs. 1 and 2).The TREX (transcription export) complex belongs to these adaptors and is composed of transcription elongation (THO complex) and export factors (Sub2 and Yra1). These proteins are loaded co-transcriptionally onto the pre-mRNA in yeast (3, 4), before recruitment of Mex67-Mtr2 occurs via an interaction with Yra1. A different assembly (Sac3-Thp1-Cdc31-Sus1 or TREX-2) is thought to facilitate the repositioning of transcribed genes to nuclear pore complexes and, thus, also helps to integrate transcription and export steps (2). Another adapter RNAbinding protein, Npl3, is recruited co-transcriptionally to the mRNA (5) and can interact with Mex67 in the nucleus when dephosphorylated (6).Finally, Nab2 is a poly(A) ϩ RNA-binding protein that shuttles between nucleus and cytoplasm and is required for mRNA export (1). Nab2 is mainly localized in the nucleus (7,8) and interacts with the poly(A)-binding protein (Pab1) to affect poly(A) tail length (9). Moreover, Nab2 interacts with Mlp1, a nuclear pore complex-associated protein at the nuclear basket involved in mRNP quality control (10), with Gfd1 and Gle1, factors involved in mRNA export (11), and with the Sac3-Thp1 complex, which plays a role in coupling transcription with mRNA metabolism (12). When the pools of mRNAs immuneprecipitated by Npl3, Nab2, and Nab4 were determined in microarrays and compared, it was suggested that distinct sets of mRNAs are bound to each of these proteins (13). In vitro, the RNA helicase Dbp5 was shown to dissociate Nab2 from the mRNP 3 (14) and because of its localization on the cytoplasmic side of the nuclear pore complex, it was suggested that Dbp5 could release Nab2 from mRNPs after the nuclear exit. In addition, the binding of the import receptor Kap104 to Nab2 after export of the Nab2-containing mRNP into the cytoplasm was suggested to trigger release of Nab2 from the mRNA cargo (15...

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Section: Discussionsupporting

confidence: 78%

“…It is not known whether in vivo Nab2 is restricted to the poly(A) tail, which so far is only an in vitro data (7,29). We speculate that in vivo, Nab2 and its binding partners (e.g.…”

Section: Discussionmentioning

confidence: 99%

Purification of Nuclear Poly(A)-binding Protein Nab2 Reveals Association with the Yeast Transcriptome and a Messenger Ribonucleoprotein Core Structure

Batisse

Budd

et al. 2009

Journal of Biological Chemistry

104

107

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“…Nuclear abundant poly(A) RNA-binding protein 2 (Nab2) shuttles between the nucleus and cytoplasm (31,32,35) and contains three key functional domains: an N-terminal domain (residues 1-97) involved in mRNA export (36), an RGG domain (residues 201-265) that acts as the nuclear import signal for Nab2 (37), and a C-terminal zinc finger domain (residues 262-477) that specifically binds polyadenosine RNA (31,34,36). A putative human orthologue of Nab2, ZC3H14, has a similar domain structure (34). The N-terminal domain of Nab2 (Nab2-N) is critical for Nab2 function in vivo and a Nab2 mutant that lacks the N-terminal domain (residues 4 -97), nab2-1/nab2 ⌬N, confers a severe growth defect and nuclear accumulation of poly(A) RNA when expressed as the sole cellular copy of Nab2 (36).…”

mentioning

confidence: 99%

“…Another potential mRNA export adaptor is the S. cerevisiae hnRNP, Nab2, which is a zinc finger protein essential for mRNA export in yeast (32)(33)(34). Nuclear abundant poly(A) RNA-binding protein 2 (Nab2) shuttles between the nucleus and cytoplasm (31,32,35) and contains three key functional domains: an N-terminal domain (residues 1-97) involved in mRNA export (36), an RGG domain (residues 201-265) that acts as the nuclear import signal for Nab2 (37), and a C-terminal zinc finger domain (residues 262-477) that specifically binds polyadenosine RNA (31,34,36).…”

mentioning

confidence: 99%

Functional Significance of the Interaction between the mRNA-binding Protein, Nab2, and the Nuclear Pore-associated Protein, Mlp1, in mRNA Export

Fasken

Stewart

Corbett

2008

Journal of Biological Chemistry

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Nuclear export of mRNA requires several key mRNA-binding proteins that recognize and remodel the mRNA and target it for export via interactions with the nuclear pore complex. In Saccharomyces cerevisiae, the shuttling heterogeneous nuclear ribonucleoprotein, Nab2, which is essential for mRNA export, specifically recognizes poly(A) RNA and binds to the nuclear pore-associated protein, myosin-like protein 1 (Mlp1), which functions in mRNA export and quality control. Specifically, the N-terminal domain of Nab2 (Nab2-N; residues 1-97) interacts directly with the C-terminal globular domain of Mlp1 (CTMlp1: residues 1490 -1875). Recent structural and binding studies focused on Nab2-N have shown that Nab2-N contains a hydrophobic patch centered on Phe 73 that is critical for interaction with Mlp1. Engineered amino acid changes within this patch disrupt the Nab2/Mlp1 interaction in vitro. Given the importance of Nab2 and Mlp1 to mRNA export, we have examined the Nab2/Mlp1 interaction in greater detail and analyzed the functional consequences of disrupting the interaction in vivo. We find that the Nab2-binding domain of Mlp1 (Mlp1-NBD) maps to a 183-residue region (residues 1586 -1768) within CT-Mlp1, binds directly to Nab2 with micromolar affinity, and confers nuclear accumulation of poly(A) RNA. Furthermore, we show that cells expressing a Nab2 F73D mutant that cannot interact with Mlp1 exhibit nuclear accumulation of poly(A) RNA and that this nab2 F73D mutant genetically interacts with alleles of two essential mRNA export genes, MEX67 and YRA1. These data provide in vivo evidence for a model of mRNA export in which Nab2 is important for targeting mRNAs to the nuclear pore for export.Production of mature mRNA for translation is a complex multistep process involving an array of RNA-binding proteins (1-3). From its transcriptional inception in the nucleus, pre-mRNA that emerges from RNA polymerase II must be bound by processing factors for 5Ј-end capping, splicing, and 3Ј-end cleavage and polyadenylation to reach maturation (4). Alongside these processing events, maturing mRNA must be co-transcriptionally loaded with heterogeneous nuclear ribonucleoproteins (hnRNPs), 2 mRNA export adaptors, and an mRNA export receptor to facilitate its active export from the nucleus to the cytoplasm through nuclear pore complexes (NPCs), large proteinaceous channels that perforate the nuclear membrane and mediate nucleocytoplasmic transport (1-3, 5). There are a number of nuclear quality controls that safeguard against improperly processed mRNA being exported and translated into deleterious proteins (6, 7). In particular, this quality control machinery likely monitors the state of processed mRNA by checking for the presence or absence of mRNA processing and export factors.One of the key players in mRNA export is the conserved heterodimeric mRNA export receptor, Mex67/Mtr2 (NXF1/ NXT1 or TAP/p15 in metazoans), which plays an essential role in bulk mRNA export in Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster...

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“…1A), and a C-terminal tandem CCCH ZnF domain which mediates binding to polyadenosine RNA 3,6,8,9 ( Fig. 1A).…”

Section: Members Of a Family Of Znf-containing Pabs Perform Conservedmentioning

confidence: 99%

New kid on the ID block

Kelly¹,

Pak²,

Garshasbi³

et al. 2012

RNA Biology

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Polyadenosine RNA binding proteins (Pabs) play critical roles in regulating the polyadenylation, nuclear export, stability and translation of cellular RNAs. Although most Pabs are ubiquitously expressed and are thought to play general roles in post-transcriptional regulation, mutations in genes encoding these factors have been linked to tissue-specific diseases including muscular dystrophy and now intellectual disability (ID). Our recent work defined this connection to ID, as we showed that mutations in the gene encoding the ubiquitously expressed Cys 3 His tandem zinc-finger (ZnF) Pab, ZC3H14 (Zinc finger protein, CCCH-type, number 14) are associated with non-syndromic autosomal recessive intellectual disability (NS-ARID). This study provided a first link between defects in Pab function and a brain disorder, suggesting that ZC3H14 plays a required role in regulating RNAs in nervous system cells. Here we highlight key questions raised by our study of ZC3H14 and its ortholog in the fruit fly Drosophila melanogaster, dNab2 and comment on future approaches that could provide insights into the cellular and molecular roles of this class of zinc fingercontaining Pabs. We propose a summary model depicting how ZC3H14-type Pabs might play particularly important roles in neuronal RNA metabolism.

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Recognition of polyadenosine RNA by zinc finger proteins

Cited by 79 publications

References 52 publications

Purification of Nuclear Poly(A)-binding Protein Nab2 Reveals Association with the Yeast Transcriptome and a Messenger Ribonucleoprotein Core Structure

Purification of Nuclear Poly(A)-binding Protein Nab2 Reveals Association with the Yeast Transcriptome and a Messenger Ribonucleoprotein Core Structure

Functional Significance of the Interaction between the mRNA-binding Protein, Nab2, and the Nuclear Pore-associated Protein, Mlp1, in mRNA Export

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