scholarly journals The polypyrimidine tract binding protein, PTBP1, regulates selenium homeostasis via the Selenoprotein P 3′ untranslated region

2020 ◽  
Author(s):  
Sumangala P. Shetty ◽  
Nora T. Kiledjian ◽  
Paul R. Copeland
Keyword(s):  
Untranslated Region ◽  
Insertion Sequence ◽  
Rna Binding ◽  
Binding Protein ◽  
Selenoprotein P ◽  
Polypyrimidine Tract ◽  
Secis Element ◽  
Polypyrimidine Tract Binding Protein ◽  
Considerable Length ◽  
Selenoprotein Mrnas

AbstractSelenoproteins contain the 21st amino acid, selenocysteine (Sec), which is incorporated at select UGA codons when the encoding mRNA contains a specialized hairpin sequence in its 3′ UTR. This hairpin, the so-called Sec insertion sequence (SECIS) element, is found in all selenoprotein mRNAs, but the sequence surrounding these elements is widely variable and in many cases of considerable length. In order to determine the function of one such SECIS context, we chose to focus on the plasma selenoprotein, SELENOP, that is required to maintain selenium homeostasis. It is unique in that its mRNA contains two SECIS elements that lie in the context of a highly conserved 843-nucleotide 3′ UTR. Prior work has attempted to examine the functions of the SECIS context but none were identified. Here we have used CRISPR/Cas9 genome editing to delete the region between the two SECIS elements. We found that this sequence is required to mediate an increase in SELENOP synthesis under conditions of peroxide stress. Using RNA affinity chromatography, we have identified PTBP1 as the major RNA binding protein that specifically interacts with this region.

A High Affinity Binding Site for the Polypyrimidine Tract Binding Protein (PTB) Is Located in the 5'-Untranslated Region of the Rat Proteinase α1-Inhibitor 3 Variant I Gene

1999 ◽  
Vol 380 (10) ◽  
pp. 1217-1223 ◽  
Author(s):  
Stefan Sickinger ◽  
Michael Schweizer
Keyword(s):  
Untranslated Region ◽  
Binding Protein ◽  
Upstream Region ◽  
Polypyrimidine Tract ◽  
Complementary Sequence ◽  
Polypyrimidine Tract Binding ◽  
High Affinity ◽  
Polypyrimidine Tract Binding Protein ◽  
Sense Strand ◽  
I Gene

Abstract As a first step towards understanding the mechanism underlying the differential gene expression of the two variants of the rat proteinase-inhibitor α1-Inhibitor 3 (α1I3) corresponding genomic clones were isolated. The 100% similarity between the sequence of one genomic clone and that of the α1-I3 variant I cDNA strongly suggested that its 5′-sequence represented the upstream region of the corresponding gene. Several putative cis-regulatory elements were identified as well as a polypyrimidine tract located between the transcription start site of the α1-I3 variant I mRNA and the AUG codon. The polypyrimidine tract functions as a positive cis-element in a heterologous promoter. By electrophoretic mobility shift assays (EMSA) we have shown that a GST (glutathione S-transferase) fusion of the rat polypyrimidine tract binding protein (PTB) has a high affinity for the pyrimidine-rich sense strand but not for the complementary sequence of the 5′-untranslated region of the α1-I3 variant I gene.

scholarly journals Nucleocytoplasmic Shuttling of Polypyrimidine Tract-binding Protein Is Uncoupled from RNA Export

2001 ◽  
Vol 12 (12) ◽  
pp. 3808-3820 ◽  
Author(s):  
Rajesh V. Kamath ◽  
Daniel J. Leary ◽  
Sui Huang
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Binding ◽  
Binding Protein ◽  
Dependent Manner ◽  
Polypyrimidine Tract ◽  
Nucleocytoplasmic Shuttling ◽  
Polypyrimidine Tract Binding ◽  
Polypyrimidine Tract Binding Protein ◽  
Rna Export

Polypyrimidine tract binding protein, PTB/hnRNP I, is involved in pre-mRNA processing in the nucleus and RNA localization and translation in the cytoplasm. In this report, we demonstrate that PTB shuttles between the nucleus and cytoplasm in an energy-dependent manner. Deletion mutagenesis demonstrated that a minimum of the N terminus and RNA recognition motifs (RRMs) 1 and 2 are necessary for nucleocytoplasmic shuttling. Deletion of RRM3 and 4, domains that are primarily responsible for RNA binding, accelerated the nucleocytoplasmic shuttling of PTB. Inhibition of transcription directed by either RNA polymerase II alone or all RNA polymerases yielded similar results. In contrast, selective inhibition of RNA polymerase I did not influence the shuttling kinetics of PTB. Furthermore, the intranuclear mobility of GFP-PTB, as measured by fluorescence recovery after photobleaching analyses, increased significantly in transcriptionally inactive cells compared with transcriptionally active cells. These observations demonstrate that nuclear RNA transcription and export are not necessary for the shuttling of PTB. In addition, binding to nascent RNAs transcribed by RNA polymerase II and/or III retards both the nuclear export and nucleoplasmic movement of PTB. The uncoupling of PTB shuttling and RNA export suggests that the nucleocytoplasmic shuttling of PTB may also play a regulatory role for its functions in the nucleus and cytoplasm.

Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein

2008 ◽  
Vol 36 (4) ◽  
pp. 641-647 ◽  
Author(s):  
Kirsty Sawicka ◽  
Martin Bushell ◽  
Keith A. Spriggs ◽  
Anne E. Willis
Keyword(s):  
Translation Initiation ◽  
Cellular Localization ◽  
Rna Binding ◽  
Binding Protein ◽  
Control Cell ◽  
Rna Binding Protein ◽  
Alternative Form ◽  
Polypyrimidine Tract ◽  
Polypyrimidine Tract Binding ◽  
Polypyrimidine Tract Binding Protein

PTB (polypyrimidine-tract-binding protein) is a ubiquitous RNA-binding protein. It was originally identified as a protein with a role in splicing but it is now known to function in a large number of diverse cellular processes including polyadenylation, mRNA stability and translation initiation. Specificity of PTB function is achieved by a combination of changes in the cellular localization of this protein (its ability to shuttle from the nucleus to the cytoplasm is tightly controlled) and its interaction with additional proteins. These differences in location and trans-acting factor requirements account for the fact that PTB acts both as a suppressor of splicing and an activator of translation. In the latter case, the role of PTB in translation has been studied extensively and it appears that this protein is required for an alternative form of translation initiation that is mediated by a large RNA structural element termed an IRES (internal ribosome entry site) that allows the synthesis of picornaviral proteins and cellular proteins that function to control cell growth and cell death. In the present review, we discuss how PTB regulates these disparate processes.

scholarly journals Efficient Incorporation of Multiple Selenocysteines Involves an Inefficient Decoding Step Serving as a Potential Translational Checkpoint and RibosomeBottleneck

2006 ◽  
Vol 26 (24) ◽  
pp. 9177-9184 ◽  
Author(s):  
Zoia Stoytcheva ◽  
Rosa M. Tujebajeva ◽  
John W. Harney ◽  
Marla J. Berry
Keyword(s):  
Untranslated Region ◽  
Stop Codon ◽  
Secondary Structures ◽  
Selenoprotein P ◽  
Secis Element ◽  
Nonsense Mediated Decay ◽  
Slowing Down ◽  
Uga Codon ◽  
Sense Codon ◽  
Selenoprotein Mrnas

ABSTRACT Selenocysteine is incorporated into proteins via “recoding” of UGA from a stop codon to a sense codon, a process that requires specific secondary structures in the 3′ untranslated region, termed selenocysteine incorporation sequence (SECIS) elements, and the protein factors that they recruit. Whereas most selenoprotein mRNAs contain a single UGA codon and a single SECIS element, selenoprotein P genes encode multiple UGAs and two SECIS elements. We have identified evolutionary adaptations in selenoprotein P genes that contribute to the efficiency of incorporating multiple selenocysteine residues in this protein. The first is a conserved, inefficiently decoded UGA codon in the N-terminal region, which appears to serve both as a checkpoint for the presence of factors required for selenocysteine incorporation and as a“ bottleneck,” slowing down the progress of elongating ribosomes. The second adaptation involves the presence of introns downstream of this inefficiently decoded UGA which confer the potential for nonsense-mediated decay when factors required for selenocysteine incorporation are limiting. Third, the two SECIS elements in selenoprotein P mRNA function with differing efficiencies, affecting both the rate and the efficiency of decoding different UGAs. The implications for how these factors contribute to the decoding of multiple selenocysteine residues are discussed.

scholarly journals Solution and crystal structures of a C-terminal fragment of the neuronal isoform of the polypyrimidine tract binding protein (nPTB)

2014 ◽  
Author(s):  
Amar Joshi ◽  
Vicent Esteve ◽  
Adrian N Buckroyd ◽  
Markus Blatter ◽  
Frédéric HT Allain ◽  
...  
Keyword(s):  
Amino Acid ◽  
Rna Splicing ◽  
Messenger Rna ◽  
Solution Structure ◽  
Rna Binding ◽  
Binding Protein ◽  
Amino Acid Side Chain ◽  
Polypyrimidine Tract ◽  
Polypyrimidine Tract Binding ◽  
Polypyrimidine Tract Binding Protein

The eukaryotic polypyrimidine tract binding protein (PTB) serves primarily as a regulator of alternative splicing of messenger RNA, but is also co-opted to other roles such as RNA localisation and translation initiation from internal ribosome entry sites. The neuronal paralogue of PTB (nPTB) protein is 75% identical in amino acid sequence with PTB. Although the two proteins have broadly similar RNA binding specificities and effects on RNA splicing, differential expression of PTB and nPTB can lead to the generation of alternatively spliced mRNAs. RNA binding by PTB and nPTB is mediated by four RNA recognition motifs (RRMs). We present here the crystal and solution structures of the C-terminal domain of nPTB (nPTB34) which contains RRMs 3 and 4. As expected the structures are similar to each other and to the solution structure of the equivalent fragment from PTB (PTB34). The result confirms that, as found for PTB, RRMs 3 and 4 of nPTB interact with one another to form a stable unit that presents the RNA-binding surfaces of the component RRMs on opposing sides. The major differences between PTB34 and nPTB34 arise from amino acid side chain substitutions on the exposed β-sheet surfaces and adjoining loops of each RRM, which are likely to modulate interactions with RNA.

scholarly journals Protein Factor Requirements of the Apaf-1 Internal Ribosome Entry Segment: Roles of Polypyrimidine Tract Binding Protein and upstream of N-ras

2001 ◽  
Vol 21 (10) ◽  
pp. 3364-3374 ◽  
Author(s):  
Sally A. Mitchell ◽  
Emma C. Brown ◽  
Mark J. Coldwell ◽  
Richard J. Jackson ◽  
Anne E. Willis
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Cell Types ◽  
Polypyrimidine Tract ◽  
Internal Ribosome Entry ◽  
Polypyrimidine Tract Binding ◽  
Polypyrimidine Tract Binding Protein ◽  
Different Cell Types

ABSTRACT It has been reported previously that the 5′ untranslated region of the mRNA encoding Apaf-1 (apoptotic protease-activating factor 1) has an internal ribosome entry site (IRES), whose activity varies widely among different cell types. Here it is shown that the Apaf-1 IRES is active in rabbit reticulocyte lysates, provided that the system is supplemented with polypyrimidine tract binding protein (PTB) and upstream of N-ras (unr), two cellular RNA binding proteins previously identified to be required for rhinovirus IRES activity. In UV cross-linking assays and electrophoretic mobility shift assays with individual recombinant proteins, the Apaf-1 IRES binds unr but not PTB; however, PTB binding occurs if unr is present. Over a range of different cell types there is a broad correlation between the activity of the Apaf-1 IRES and their content of PTB and unr. In cell lines deficient in these proteins, overexpression of PTB and unr stimulated Apaf-1 IRES function. This is the first example where an IRES in a cellular mRNA has been shown to be functionally dependent, both in vitro and in vivo, on specific cellular RNA binding proteins. Given the critical role of Apaf-1 in apoptosis, these results have important implications for the control of the apoptotic cascade.

scholarly journals Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins

2016 ◽  
Vol 44 (4) ◽  
pp. 1058-1065 ◽  
Author(s):  
Miguel B. Coelho ◽  
David B. Ascher ◽  
Clare Gooding ◽  
Emma Lang ◽  
Hannah Maude ◽  
...  
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Dorsal Surface ◽  
Peptide Ligand ◽  
Rna Recognition Motif ◽  
Polypyrimidine Tract ◽  
Polypyrimidine Tract Binding ◽  
Binding Domains ◽  
Polypyrimidine Tract Binding Protein ◽  
Nuclear Ribonucleoprotein

Polypyrimidine tract binding protein (PTBP1) is a heterogeneous nuclear ribonucleoprotein (hnRNP) that plays roles in most stages of the life-cycle of pre-mRNA and mRNAs in the nucleus and cytoplasm. PTBP1 has four RNA binding domains of the RNA recognition motif (RRM) family, each of which can bind to pyrimidine motifs. In addition, RRM2 can interact via its dorsal surface with proteins containing short peptide ligands known as PTB RRM2 interacting (PRI) motifs, originally found in the protein Raver1. Here we review our recent progress in understanding the interactions of PTB with RNA and with various proteins containing PRI ligands.

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