Journal articles: 'Pab1'

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Ardelean, Radu, Adriana Popa, Ecaterina Stela Drăgan, Corneliu-Mircea Davidescu, and Maria Ignat. "New Polymeric Adsorbents Functionalized with Aminobenzoic Groups for the Removal of Residual Antibiotics." Molecules 27, no. 9 (2022): 2894. http://dx.doi.org/10.3390/molecules27092894.

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In this paper, we present the synthesis of new polymeric adsorbents derived from macroporous chloromethylated styrene–divinylbenzene (DVB) copolymers with different cross-linking degrees functionalized with the following aminobenzoic groups: styrene—6.7% DVB (PAB1), styrene—10% DVB (PAB2), and styrene—15% DVB (PAB3). The new polymeric products, PAB1, PAB2, and PAB3, were characterized by FTIR spectroscopy, thermogravimetric analysis, and EDX, SEM, and BET analysis, respectively. The evolution of the functionalization reaction was followed by FTIR spectroscopy, which revealed a decrease in the intensity of the γCH2Cl band at 1260 cm−1, and, simultaneously, the appearance of C=O carboxylic bands from 1685–1695 cm−1 and at 1748 cm−1. The thermal stability increased with the increase in the cross-linking degree. The data obtained from the EDX analysis of the novel cross-linked copolymers confirmed the functionalization with aminobenzoic groups through the presence and content of nitrogen, as follows: PAB1: N% = 0.47; PAB2: N% = 0.85; and PAB3: N% = 1.30. The adsorption performances of the novel polymeric adsorbents, PAB1, PAB2, and PAB3, were tested in the adsorption of three antibiotics, tetracycline, sulfamethoxazole, and amoxicillin, from aqueous solutions, by using extensive kinetic, equilibrium, and thermodynamic studies. The best adsorption capacity was demonstrated by the tetracycline. Amoxicillin adsorption was also attempted, but it did not show positive results.

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Amirkhosravi, Ali, Todd V. Meyer, Liza Robles-Carrillo та ін. "β2-Glycoprotein 1 Antibodies Directly Activate the Platelet IgG Receptor, FcγRIIa, and Cause Thrombosis in FCGR2A Transgenic but Not in Wild Type Mice". Blood 120, № 21 (2012): 106. http://dx.doi.org/10.1182/blood.v120.21.106.106.

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Abstract Abstract 106 Antibodies targeting β2-glycoprotein 1 (β2-GP1; β2-Abs) are of primary importance in antiphospholipid syndrome (APS), a thrombotic autoimmune disorder. The predominance of the IgG antibody isotype in APS is conspicuously associated with increased risk of thrombosis, raising the question whether the platelet IgG receptor, FcγRIIa, may play a role in thrombosis in APS, as is the case in heparin-induced thrombocytopenia (HIT). The hypothesis that platelet FcγRIIa may contribute to thrombosis in APS has received little attention, with research emphasis instead placed on several proposed alternative mechanisms of action. We have shown that, like HIT antibodies, antibodies targeting VEGF or CD154 are also potently thrombotic in mice transgenic for human FcγRIIa but have no activity in mice lacking FcγRIIa (i.e., wild type mice). We therefore asked whether antiphospholipid antibodies can activate platelets and cause thrombosis via FcγRIIa. To this end, we tested mouse monoclonal (mAb) and goat polyclonal anti-human β2-Abs alone or complexed to human β2-glycoprotein 1 (i.e., to form immune complexes, or ICs) by the serotonin release assay (SRA) and platelet aggregation methods using washed human platelets. We found that two of three commercially available polyclonal anti-β2-Abs (pAb1 and pAb3), both alone or in IC form, induced platelet granule release and aggregation, and that this activity was abolished by anti-FcγRIIa mAb, IV.3. pAb2 and mAb were inactive. Activity analysis (SRA) of preformed ICs using constant pAb1 concentration with varied β2-GP1 stoichiometries revealed a zone-of-equivalence pattern, with maximal activity near balanced stoichiometry (1:1). Because pAb2 did not activate platelets, we sought to determine its capacity to form higher order ICs (which are known to be required for FcγRIIa activation) by size exclusion chromatography (SEC). All antibodies tested in isolation were shown by HPLC-SEC to be free of aggregates or degradation products. Antibody-antigen complex size analysis revealed that, as expected, mAb+β2-GP1 in 1:1 stoichiometry failed to form higher order ICs (i.e., complexes having ≥2 IgGs/complex). pAb2 (inactive) did form higher order ICs at 1:1 and 4:1 (IgG:Ag) stoichiometries, but less extensively than pAb1 (active), which efficiently formed higher order ICs at both 1:1 and 4:1 stoichiometries. pAb1 alone (i.e., not in IC form) caused aggregation, while pAb2 did not. Furthermore, preincubation of washed platelets with pAb2 prevented pAb1-induced aggregation, suggesting that pAb1 activity is β2-GP1-specific. A single intravenous injection of anti-β2-GP1 ICs (20 μg β2-GP1 plus 120 μg pAb1, a 1:2 molar stoichiometry) induced severe thrombocytopenia (>90%) and caused thrombotic shock in FcγRIIa-transgenic mice but not in wild type mice. Symptoms of shock occurred within 10 minutes. Pervasive occlusive thrombi were observed in the lungs of all FcγRIIa-transgenic but not in any wild type mice (H&E microscopy). Injection of pAb2 ICs produced none of these effects in transgenic or wild type mice. Finally, injection of pAb1 or pAb2 alone (neither of which bind mouse β2-GP1) had no effects in transgenic mice. In summary, these findings confirm previous in vitro studies that β2-Abs can directly activate platelets in a manner wholly dependent on the platelet IgG receptor, FcγRIIa. Additionally, we have shown for the first time in vivo that β2-Abs can also cause FcγRIIa-dependent thrombosis. This mechanism may contribute to thrombosis in APS, suggesting that further studies on the importance of FcγRIIa in APS are warranted. Disclosures: No relevant conflicts of interest to declare.

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Mangus, David A., Nadia Amrani, and Allan Jacobson. "Pbp1p, a Factor Interacting withSaccharomyces cerevisiae Poly(A)-Binding Protein, Regulates Polyadenylation." Molecular and Cellular Biology 18, no. 12 (1998): 7383–96. http://dx.doi.org/10.1128/mcb.18.12.7383.

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ABSTRACT The poly(A) tail of an mRNA is believed to influence the initiation of translation, and the rate at which the poly(A) tail is removed is thought to determine how fast an mRNA is degraded. One key factor associated with this 3′-end structure is the poly(A)-binding protein (Pab1p) encoded by the PAB1 gene inSaccharomyces cerevisiae. In an effort to learn more about the functional role of this protein, we used a two-hybrid screen to determine the factor(s) with which it interacts. We identified five genes encoding factors that specifically interact with the carboxy terminus of Pab1p. Of a total of 44 specific clones identified,PBP1 (for Pab1p-binding protein) was isolated 38 times. Of the putative interacting genes examined, PBP1 promoted the highest level of resistance to 3-aminotriazole (>100 mM) in constructs in which HIS3 was used as a reporter. We determined that a fraction of Pbp1p cosediments with polysomes in sucrose gradients and that its distribution is very similar to that of Pab1p. Disruption ofPBP1 showed that it is not essential for viability but can suppress the lethality associated with a PAB1 deletion. The suppression of pab1Δ by pbp1Δ appears to be different from that mediated by other pab1 suppressors, since disruption of PBP1 does not alter translation rates, affect accumulation of ribosomal subunits, change mRNA poly(A) tail lengths, or result in a defect in mRNA decay. Rather, Pbp1p appears to function in the nucleus to promote proper polyadenylation. In the absence of Pbp1p, 3′ termini of pre-mRNAs are properly cleaved but lack full-length poly(A) tails. These effects suggest that Pbp1p may act to repress the ability of Pab1p to negatively regulate polyadenylation.

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Dufresne, Philippe J., Eliane Ubalijoro, Marc G. Fortin, and Jean-François Laliberté. "Arabidopsis thaliana class II poly(A)-binding proteins are required for efficient multiplication of turnip mosaic virus." Journal of General Virology 89, no. 9 (2008): 2339–48. http://dx.doi.org/10.1099/vir.0.2008/002139-0.

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The poly(A)-binding protein (PABP) is an important translation initiation factor that binds to the polyadenylated 3′ end of mRNA. We have previously shown that PABP2 interacts with the RNA-dependent RNA polymerase (RdRp) and VPg-Pro of turnip mosaic virus (TuMV) within virus-induced vesicles. At least eight PABP isoforms are produced in Arabidopsis thaliana, three of which (PABP2, PABP4 and PABP8) are highly and broadly expressed and probably constitute the bulk of PABP required for cellular functions. Upon TuMV infection, an increase in protein and mRNA expression from PAB2, PAB4 and PAB8 genes was recorded. In vitro binding assays revealed that RdRp and the viral genome-linked protein (VPg-Pro) interact preferentially with PABP2 but are also capable of interaction with one or both of the other class II PABPs (i.e. PABP4 and PABP8). To assess whether PABP is required for potyvirus replication, A. thaliana single and double pab knockouts were isolated and inoculated with TuMV. All lines showed susceptibility to TuMV. However, when precise monitoring of viral RNA accumulation was performed, it was found to be reduced by 2.2- and 3.5-fold in pab2 pab4 and pab2 pab8 mutants, respectively, when compared with wild-type plants. PABP levels were most significantly reduced in the membrane-associated fraction in both of these mutants. TuMV mRNA levels thus correlated with cellular PABP concentrations in these A. thaliana knockout lines. These data provide further support for a role of PABP in potyvirus replication.

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Yao, Gang, Yueh-Chin Chiang, Chongxu Zhang, Darren J. Lee, Thomas M. Laue, and Clyde L. Denis. "PAB1 Self-Association Precludes Its Binding to Poly(A), Thereby Accelerating CCR4 Deadenylation In Vivo." Molecular and Cellular Biology 27, no. 17 (2007): 6243–53. http://dx.doi.org/10.1128/mcb.00734-07.

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ABSTRACT The mRNA deadenylation process, catalyzed by the CCR4 deadenylase, is known to be the major factor controlling mRNA decay rates in Saccharomyces cerevisiae. We have identified the proline-rich region and RRM1 domains of poly(A) binding protein (PAB1) as necessary for CCR4 deadenylation. Deletion of either of these regions but not other regions of PAB1 significantly reduced PAB1-PAB1 protein interactions, suggesting that PAB1 oligomerization is a required step for deadenylation. Moreover, defects in these two regions inhibited the formation of a novel, circular monomeric PAB1 species that forms in the absence of poly(A). Removal of the PAB1 RRM3 domain, which promoted PAB1 oligomerization and circularization, correspondingly accelerated CCR4 deadenylation. Circular PAB1 was unable to bind poly(A), and PAB1 multimers were severely deficient or unable to bind poly(A), implicating the PAB1 RNA binding surface as critical in making contacts that allow PAB1 self-association. These results support the model that the control of CCR4 deadenylation in vivo occurs in part through the removal of PAB1 from the poly(A) tail following its self-association into multimers and/or a circular species. Known alterations in the P domains of different PAB proteins and factors and conditions that affect PAB1 self-association would, therefore, be expected to be critical to controlling mRNA turnover in the cell.

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Amrani, N., M. Minet, M. Le Gouar, F. Lacroute, and F. Wyers. "Yeast Pab1 interacts with Rna15 and participates in the control of the poly(A) tail length in vitro." Molecular and Cellular Biology 17, no. 7 (1997): 3694–701. http://dx.doi.org/10.1128/mcb.17.7.3694.

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In Saccharomyces cerevisiae, the single poly(A) binding protein, Pab1, is the major ribonucleoprotein associated with the poly(A) tails of mRNAs in both the nucleus and the cytoplasm. We found that Pab1 interacts with Rna15 in two-hybrid assays and in coimmunoprecipitation experiments. Overexpression of PAB1 partially but specifically suppressed the rna15-2 mutation in vivo. RNA15 codes for a component of the cleavage and polyadenylation factor CF I, one of the four factors needed for pre-mRNA 3'-end processing. We show that Pab1 and CF I copurify in anion-exchange chromatography. These data suggest that Pab1 is physically associated with CF I. Extracts from a thermosensitive pab1 mutant and from a wild-type strain immunoneutralized for Pab1 showed normal cleavage activity but a large increase in poly(A) tail length. A normal tail length was restored by adding recombinant Pab1 to the mutant extract. The longer poly(A) tails were not due to an inhibition of exonuclease activities. Pab1 has previously been implicated in the regulation of translation initiation and in cytoplasmic mRNA stability. Our data indicate that Pab1 is also a part of the 3'-end RNA-processing complex and thus participates in the control of the poly(A) tail lengths during the polyadenylation reaction.

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Konopka, Catherine A., Melissa N. Locke, Pamela S. Gallagher, et al. "A yeast model for polyalanine-expansion aggregation and toxicity." Molecular Biology of the Cell 22, no. 12 (2011): 1971–84. http://dx.doi.org/10.1091/mbc.e11-01-0037.

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Nine human disorders result from the toxic accumulation and aggregation of proteins with expansions in their endogenous polyalanine (polyA) tracts. Given the prevalence of polyA tracts in eukaryotic proteomes, we wanted to understand the generality of polyA-expansion cytotoxicity by using yeast as a model organism. In our initial case, we expanded the polyA tract within the native yeast poly(Adenine)-binding protein Pab1 from 8A to 13A, 15A, 17A, and 20A. These expansions resulted in increasing formation of Pab1 inclusions, insolubility, and cytotoxicity that correlated with the length of the polyA expansion. Pab1 binds mRNA as part of its normal function, and disrupting RNA binding or altering cytoplasmic mRNA levels suppressed the cytotoxicity of 17A-expanded Pab1, indicating a requisite role for mRNA in Pab1 polyA-expansion toxicity. Surprisingly, neither manipulation suppressed the cytotoxicity of 20A-expanded Pab1. Thus longer expansions may have a different mechanism for toxicity. We think that this difference underscores the potential need to examine the cytotoxic mechanisms of both long and short expansions in models of expansion disorders.

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Anderson, J. T., M. R. Paddy, and M. S. Swanson. "PUB1 is a major nuclear and cytoplasmic polyadenylated RNA-binding protein in Saccharomyces cerevisiae." Molecular and Cellular Biology 13, no. 10 (1993): 6102–13. http://dx.doi.org/10.1128/mcb.13.10.6102-6113.1993.

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Proteins that directly associate with nuclear polyadenylated RNAs, or heterogeneous nuclear RNA-binding proteins (hnRNPs), and those that associate with cytoplasmic mRNAs, or mRNA-binding proteins (mRNPs), play important roles in regulating gene expression at the posttranscriptional level. Previous work with a variety of eukaryotic cells has demonstrated that hnRNPs are localized predominantly within the nucleus whereas mRNPs are cytoplasmic. While studying proteins associated with polyadenylated RNAs in Saccharomyces cerevisiae, we discovered an abundant polyuridylate-binding protein, PUB1, which appears to be both an hnRNP and an mRNP. PUB1 and PAB1, the polyadenylate tail-binding protein, are the two major proteins cross-linked by UV light to polyadenylated RNAs in vivo. The deduced primary structure of PUB1 indicates that it is a member of the ribonucleoprotein consensus sequence family of RNA-binding proteins and is structurally related to the human hnRNP M proteins. Even though the PUB1 protein is a major cellular polyadenylated RNA-binding protein, it is nonessential for cell growth. Indirect cellular immunofluorescence combined with digital image processing allowed a detailed comparison of the intracellular distributions of PUB1 and PAB1. While PAB1 is predominantly, and relatively uniformly, distributed within the cytoplasm, PUB1 is localized in a nonuniform pattern throughout both the nucleus and the cytoplasm. The cytoplasmic distribution of PUB1 is considerably more discontinuous than that of PAB1. Furthermore, sucrose gradient sedimentation analysis demonstrates that PAB1 cofractionates with polyribosomes whereas PUB1 does not. These results suggest that PUB1 is both an hnRNP and an mRNP and that it may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm.

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Anderson, J. T., M. R. Paddy, and M. S. Swanson. "PUB1 is a major nuclear and cytoplasmic polyadenylated RNA-binding protein in Saccharomyces cerevisiae." Molecular and Cellular Biology 13, no. 10 (1993): 6102–13. http://dx.doi.org/10.1128/mcb.13.10.6102.

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Proteins that directly associate with nuclear polyadenylated RNAs, or heterogeneous nuclear RNA-binding proteins (hnRNPs), and those that associate with cytoplasmic mRNAs, or mRNA-binding proteins (mRNPs), play important roles in regulating gene expression at the posttranscriptional level. Previous work with a variety of eukaryotic cells has demonstrated that hnRNPs are localized predominantly within the nucleus whereas mRNPs are cytoplasmic. While studying proteins associated with polyadenylated RNAs in Saccharomyces cerevisiae, we discovered an abundant polyuridylate-binding protein, PUB1, which appears to be both an hnRNP and an mRNP. PUB1 and PAB1, the polyadenylate tail-binding protein, are the two major proteins cross-linked by UV light to polyadenylated RNAs in vivo. The deduced primary structure of PUB1 indicates that it is a member of the ribonucleoprotein consensus sequence family of RNA-binding proteins and is structurally related to the human hnRNP M proteins. Even though the PUB1 protein is a major cellular polyadenylated RNA-binding protein, it is nonessential for cell growth. Indirect cellular immunofluorescence combined with digital image processing allowed a detailed comparison of the intracellular distributions of PUB1 and PAB1. While PAB1 is predominantly, and relatively uniformly, distributed within the cytoplasm, PUB1 is localized in a nonuniform pattern throughout both the nucleus and the cytoplasm. The cytoplasmic distribution of PUB1 is considerably more discontinuous than that of PAB1. Furthermore, sucrose gradient sedimentation analysis demonstrates that PAB1 cofractionates with polyribosomes whereas PUB1 does not. These results suggest that PUB1 is both an hnRNP and an mRNP and that it may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm.

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Cosson, Bertrand, Anne Couturier, Svetlana Chabelskaya, et al. "Poly(A)-Binding Protein Acts in Translation Termination via Eukaryotic Release Factor 3 Interaction and Does Not Influence [PSI+] Propagation." Molecular and Cellular Biology 22, no. 10 (2002): 3301–15. http://dx.doi.org/10.1128/mcb.22.10.3301-3315.2002.

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ABSTRACT Recent studies of translational control suggest that translation termination may not be simply the end of synthesizing a protein but rather be involved in modulating both the translation efficiency and stability of a given transcript. Using recombinant eukaryotic release factor 3 (eRF3) and cellular extracts, we have shown for Saccharomyces cerevisiae that yeast eRF3 and Pab1p can interact. This interaction, mediated by the N+M domain of eRF3 and amino acids 473 to 577 of Pab1p, was demonstrated to be direct by the two-hybrid approach. We confirmed that a genetic interaction exists between eRF3 and Pab1p and showed that Pab1p overexpression enhances the efficiency of termination in SUP35 (eRF3) mutant and [PSI +] cells. This effect requires the interaction of Pab1p with eRF3. These data further strengthen the possibility that Pab1p has a role in coupling translation termination events with initiation of translation. Several lines of evidence indicate that Pab1p does not influence [PSI +] propagation. First, “[PSI +]-no-more” mutations do not affect eRF3-Pab1p two-hybrid interaction. Second, overexpression of PAB1 does not cure the [PSI +] phenotype or solubilize detectable amounts of eRF3. Third, prion-curing properties of overexpressed HSP104p, which is required for formation and maintenance of [PSI +], were not modified by excess Pab1p.

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Kobayashi, Tetsuo, Yuji Funakoshi, Shin-ichi Hoshino, and Toshiaki Katada. "The GTP-binding Release Factor eRF3 as a Key Mediator Coupling Translation Termination to mRNA Decay." Journal of Biological Chemistry 279, no. 44 (2004): 45693–700. http://dx.doi.org/10.1074/jbc.m405163200.

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GTP is essential for eukaryotic translation termination, where the release factor 3 (eRF3) complexed with eRF1 is involved as the guanine nucleotide-binding protein. In addition, eRF3 regulates the termination-coupled events, eRF3 interacts with poly(A)-binding protein (Pab1) and the surveillance factor Upf1 to mediate normal and nonsense-mediated mRNA decay. However, the roles of GTP binding to eRF3 in these processes remain largely unknown. Here, we showed in yeast that GTP is essentially required for the association of eRF3 with eRF1, but not with Pab1 and Upf1. A mutation in the GTP-binding motifs of eRF3 impairs the eRF1-binding ability without altering the Pab1- or Upf1-binding activity. Interestingly, the mutation causes not only a defect in translation termination but also delay of normal and nonsense-mediated mRNA decay, suggesting that GTP/eRF3-dependent termination exerts its influence on the subsequent mRNA degradation. The termination reaction itself is not sufficient, but eRF3 is essential for triggering mRNA decay. Thus, eRF3 is a key mediator that transduces termination signal to mRNA decay.

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Wyers, Françoise, Michèle Minet, Marie Elisabeth Dufour, Le Thuy Anh Vo, and François Lacroute. "Deletion of the PAT1 Gene Affects Translation Initiation and Suppresses a PAB1 Gene Deletion in Yeast." Molecular and Cellular Biology 20, no. 10 (2000): 3538–49. http://dx.doi.org/10.1128/mcb.20.10.3538-3549.2000.

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ABSTRACT The yeast poly(A) binding protein Pab1p mediates the interactions between the 5′ cap structure and the 3′ poly(A) tail of mRNA, whose structures synergistically activate translation in vivo and in vitro. We found that deletion of the PAT1 (YCR077c) gene suppresses a PAB1 gene deletion and that Pat1p is required for the normal initiation of translation. A fraction of Pat1p cosediments with free 40S ribosomal subunits on sucrose gradients. ThePAT1 gene is not essential for viability, although disruption of the gene severely impairs translation initiation in vivo, resulting in the accumulation of 80S ribosomes and in a large decrease in the amounts of heavier polysomes. Pat1p contributes to the efficiency of translation in a yeast cell-free system. However, the synergy between the cap structure and the poly(A) tail is maintained in vitro in the absence of Pat1p. Analysis of translation initiation intermediates on gradients indicates that Pat1p acts at a step before or during the recruitment of the 40S ribosomal subunit by the mRNA, a step which may be independent of that involving Pab1p. We conclude that Pat1p is a new factor involved in protein synthesis and that Pat1p might be required for promoting the formation or the stabilization of the preinitiation translation complexes.

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Zhong, Guo-wei, Ping Jiang, Wei-ran Qiao, Yuan-wei Zhang, Wen-fan Wei, and Ling Lu. "Protein Phosphatase 2A (PP2A) Regulatory Subunits ParA and PabA Orchestrate Septation and Conidiation and Are Essential for PP2A Activity in Aspergillus nidulans." Eukaryotic Cell 13, no. 12 (2014): 1494–506. http://dx.doi.org/10.1128/ec.00201-14.

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ABSTRACTProtein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. Different activities of PP2A and subcellular localization are determined by its regulatory subunits. Here we identified and characterized the functions of two protein phosphatase regulatory subunit homologs, ParA and PabA, inAspergillus nidulans. Our results demonstrate that ParA localizes to the septum site and that deletion ofparAcauses hyperseptation, while overexpression ofparAabolishes septum formation; this suggests that ParA may function as a negative regulator of septation. In comparison, PabA displays a clear colocalization pattern with 4′,6-diamidino-2-phenylindole (DAPI)-stained nuclei, and deletion ofpabAinduces a remarkable delayed-septation phenotype. BothparAandpabAare required for hyphal growth, conidiation, and self-fertilization, likely to maintain normal levels of PP2A activity. Most interestingly,parAdeletion is capable of suppressing septation defects inpabAmutants, suggesting that ParA counteracts PabA during the septation process. In contrast, double mutants ofparAandpabAled to synthetic defects in colony growth, indicating that ParA functions synthetically with PabA during hyphal growth. Moreover, unlike the case for PP2A-Par1 and PP2A-Pab1 in yeast (which are negative regulators that inactivate the septation initiation network [SIN]), loss of ParA or PabA fails to suppress defects of temperature-sensitive mutants of the SEPH kinase of the SIN. Thus, our findings support the previously unrealized evidence that the B-family subunits of PP2A have comprehensive functions as partners of heterotrimeric enzyme complexes of PP2A, both spatially and temporally, inA. nidulans.

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Brown, Justin T., Xianmei Yang, and Arlen W. Johnson. "Inhibition of mRNA Turnover in Yeast by an xrn1 Mutation Enhances the Requirement for eIF4E Binding to eIF4G and for Proper Capping of Transcripts by Ceg1p." Genetics 155, no. 1 (2000): 31–42. http://dx.doi.org/10.1093/genetics/155.1.31.

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Abstract Null mutants of XRN1, encoding the major cytoplasmic exoribonuclease in yeast, are viable but accumulate decapped, deadenylated transcripts. A screen for mutations synthetic lethal with xrn1Δ identified a mutation in CDC33, encoding eIF4E. This mutation (glutamate to glycine at position 72) affected a highly conserved residue involved in interaction with eIF4G. Synthetic lethality between xrn1 and cdc33 was not relieved by high-copy expression of eIF4G or by disruption of the yeast eIF4E binding protein Caf20p. High-copy expression of a mutant eIF4G defective for eIF4E binding resulted in a dominant negative phenotype in an xrn1 mutant, indicating the importance of this interaction in an xrn1 mutant. Another allele of CDC33, cdc33-1, along with mutations in CEG1, encoding the nuclear guanylyltransferase, were also synthetic lethal with xrn1Δ, whereas mutations in PRT1, encoding a subunit of eIF3, were not. Mutations in CDC33, CEG1, PRT1, PAB1, and TIF4631, encoding eIF4G1, have been shown to lead to destabilization of mRNAs. Although such destabilization in cdc33, ceg1, and pab1 mutants can be partially suppressed by an xrn1 mutation, we observed synthetic lethality between xrn1 and either cdc33 or ceg1 and no suppression of the inviability of a pab1 null mutation by xrn1Δ. Thus, the inhibition of mRNA turnover by blocking Xrn1p function does not suppress the lethality of defects upstream in the turnover pathway but it does enhance the requirement for 7mG caps and for proper formation of the eIF4E/eIF4G cap recognition complex.

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Wegkamp, Arno, Wietske van Oorschot, Willem M. de Vos, and Eddy J. Smid. "Characterization of the Role of para-Aminobenzoic Acid Biosynthesis in Folate Production by Lactococcus lactis." Applied and Environmental Microbiology 73, no. 8 (2007): 2673–81. http://dx.doi.org/10.1128/aem.02174-06.

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ABSTRACT The pab genes for para-aminobenzoic acid (pABA) biosynthesis in Lactococcus lactis were identified and characterized. In L. lactis NZ9000, only two of the three genes needed for pABA production were initially found. No gene coding for 4-amino-4-deoxychorismate lyase (pabC) was initially annotated, but detailed analysis revealed that pabC was fused with the 3′ end of the gene coding for chorismate synthetase component II (pabB). Therefore, we hypothesize that all three enzyme activities needed for pABA production are present in L. lactis, allowing for the production of pABA. Indeed, the overexpression of the pABA gene cluster in L. lactis resulted in elevated pABA pools, demonstrating that the genes are involved in the biosynthesis of pABA. Moreover, a pABA knockout (KO) strain lacking pabA and pabB C was constructed and shown to be unable to produce folate when cultivated in the absence of pABA. This KO strain was unable to grow in chemically defined medium lacking glycine, serine, nucleobases/nucleosides, and pABA. The addition of the purine guanine, adenine, xanthine, or inosine restored growth but not the production of folate. This suggests that, in the presence of purines, folate is not essential for the growth of L. lactis. It also shows that folate is not strictly required for the pyrimidine biosynthesis pathway. L. lactis strain NZ7024, overexpressing both the folate and pABA gene clusters, was found to produce 2.7 mg of folate/liter per optical density unit at 600 nm when the strain was grown on chemically defined medium without pABA. This is in sharp contrast to L. lactis strains overexpressing only one of the two gene clusters. Therefore, we conclude that elevated folate levels can be obtained only by the overexpression of folate combined with the overexpression of the pABA biosynthesis gene cluster, suggesting the need for a balanced carbon flux through the folate and pABA biosynthesis pathway in the wild-type strain.

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Dunn, E. F. "Yeast poly(A)-binding protein, Pab1, and PAN, a poly(A) nuclease complex recruited by Pab1, connect mRNA biogenesis to export." Genes & Development 19, no. 1 (2005): 90–103. http://dx.doi.org/10.1101/gad.1267005.

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Kahan, Darren N., Ruofan Chen, Joshua Riback, Christopher Katanski, Allan Drummond, and Tobin R. Sosnick. "Molecular Factors Underlying Stress-Triggered Phase-Separation of Pab1." Biophysical Journal 116, no. 3 (2019): 350a. http://dx.doi.org/10.1016/j.bpj.2018.11.1903.

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WANG, HONG, LIJUN WANG, QINQIN HU, RONGHUI WANG, YANBIN LI, and MICHAEL KIDD. "Rapid and Sensitive Detection of Campylobacter jejuni in Poultry Products Using a Nanoparticle-Based Piezoelectric Immunosensor Integrated with Magnetic Immunoseparation." Journal of Food Protection 81, no. 8 (2018): 1321–30. http://dx.doi.org/10.4315/0362-028x.jfp-17-381.

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ABSTRACT Campylobacter jejuni is one of the leading causes of foodborne human gastrointestinal diseases. Poultry and poultry products have been identified as the major transmission routes to humans for this pathogenic bacterium. The objective of this research was to develop a rapid and sensitive immunosensor for detection of C. jejuni in poultry products on the basis of a quartz crystal microbalance (QCM) using magnetic nanobeads (MNBs) for separation of target pathogen and gold nanoparticles for amplification of the measurement. A QCM sensor in a flow cell was prepared by immobilizing the mouse anti–C. jejuni monoclonal antibody (mAb1) on the sensor surface to specifically capture C. jejuni. Rabbit anti–C. jejuni polyclonal antibody (pAb1) was conjugated with MNBs to capture and separate C. jejuni from food matrices. MNB–pAb1–C. jejuni complexes were injected into the flow cell to bind with the mAb1 immobilized on the QCM sensor surface. Goat anti-rabbit immunoglobulin G polyclonal antibody conjugated with gold nanoparticles was injected into the flow cell to bind with pAb1 on MNBs. Finally, resonant frequency was measured with a QCM analyzer, and the change in resonant frequency was correlated to the cell number of C. jejuni. The specificity of this immunosensor was confirmed with different strains of Campylobacter, Salmonella, and other foodborne pathogens commonly colonized in the broiler gastrointestinal tract. Samples of broiler carcass wash and ground turkey were spiked with C. jejuni at different concentrations for use in tests. Results showed that the QCM immunosensor could rapidly detect C. jejuni in poultry products, with a detection limit of 20 to 30 CFU/mL without preenrichment, and a total detection time of less than 30 min. Characteristics of C. jejuni captured by the antibody immobilized on the surface of the QCM sensor were visualized by using atomic force microscopy. This highly adaptive and flexible method could provide the poultry industry a more rapid, sensitive, and effective method for detection of major foodborne pathogens in poultry products.

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James, Timothy Y., Robert P. Boulianne, Alan P. F. Bottoli, José D. Granado, Markus Aebi, and Ursula Kües. "The pab1 gene of Coprinus cinereus encodes a bifunctional protein for para-aminobenzoic acid (PABA) synthesis: implications for the evolution of fused PABA synthases." Journal of Basic Microbiology 42, no. 2 (2002): 91. http://dx.doi.org/10.1002/1521-4028(200205)42:2<91::aid-jobm91>3.0.co;2-8.

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Pintard, Lionel, Dieter Kressler, and Bruno Lapeyre. "Spb1p Is a Yeast Nucleolar Protein Associated with Nop1p and Nop58p That Is Able To BindS-Adenosyl-l-Methionine In Vitro." Molecular and Cellular Biology 20, no. 4 (2000): 1370–81. http://dx.doi.org/10.1128/mcb.20.4.1370-1381.2000.

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ABSTRACT We present here the characterization of SPB1, an essential yeast gene that is required for ribosome synthesis. A cold-sensitive allele for that gene (referred to here asspb1-1) had been previously isolated as a suppressor of a mutation affecting the poly(A)-binding protein gene (PAB1) and a thermosensitive allele (referred to here asspb1-2) was isolated in a search for essential genes required for gene silencing in Saccharomyces cerevisiae. The two mutants are able to suppress the deletion of PAB1, and they both present a strong reduction in their 60S ribosomal subunit content. In an spb1-2 strain grown at the restrictive temperature, processing of the 27S pre-rRNA into mature 25S rRNA and 5.8S is completely abolished and production of mature 18S is reduced, while the abnormal 23S species is accumulated. Spb1p is a 96.5-kDa protein that is localized to the nucleolus. Coimmunoprecipitation experiments show that Spb1p is associated in vivo with the nucleolar proteins Nop1p and Nop5/58p. Protein sequence analysis reveals that Spb1p possesses a putative S-adenosyl-l-methionine (AdoMet)-binding domain, which is common to the AdoMet-dependent methyltransferases. We show here that Spb1p is able to bind [3H]AdoMet in vitro, suggesting that it is a novel methylase, whose possible substrates will be discussed.

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Le, Hanh, Su-Chih Chang, Robert L. Tanguay, and Daniel R. Gallie. "The Wheat Poly (A)-Binding Protein Functionally Complements Pab1 in Yeast." European Journal of Biochemistry 243, no. 1-2 (1997): 350–57. http://dx.doi.org/10.1111/j.1432-1033.1997.0350a.x.

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Padariya, Monikaben, and Umesh Kalathiya. "The Binding Specificity of PAB1 with Poly(A) mRNA, Regulated by Its Structural Folding." Biomedicines 10, no. 11 (2022): 2981. http://dx.doi.org/10.3390/biomedicines10112981.

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The poly(A)-binding protein cytoplasmic 1 (PAB1 or PABPC1) protein is associated with the long poly(A) mRNA tails, inducing stability. Herein, we investigated the dynamics of the PABPC1 protein, along with tracing its mRNA binding specificity. During molecular dynamics simulations (MDS), the R176-Y408 amino acids (RRM3–4 domains; RNA recognition motifs) initiated a folded structure that resulted in the formation of different conformations. The RRM4 domain formed high-frequency intramolecular interactions, despite such induced flexibility. Residues D45, Y54, Y56, N58, Q88, and N100 formed long-lasting interactions, and specifically, aromatic residues (Y14, Y54, Y56, W86, and Y140) gained a unique binding pattern with the poly(A) mRNA. In addition, the poly(A) mRNA motif assembled a PABPC1-specific conformation, by inducing movement of the center three nucleotides to face towards RRM1–2 domains. The majority of the high-frequency cancer mutations in PAB1 reside within the RRM4 domain and amino acids engaging in high-frequency interactions with poly(A) mRNA were found to be preserved in different cancer types. Except for the G123C variant, other studied cancer-derived mutants hindered the stability of the protein. Molecular details from this study will provide a detailed understanding of the PABPC1 structure, which can be used to modulate the activity of this gene, resulting in production of mutant peptide or neoantigens in cancer.

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Zhang, Yirong, Linquan Bai, and Zixin Deng. "Functional characterization of the first two actinomycete 4-amino-4-deoxychorismate lyase genes." Microbiology 155, no. 7 (2009): 2450–59. http://dx.doi.org/10.1099/mic.0.026336-0.

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In some antibiotic producers, p-aminobenzoic acid (PABA) or its immediate precursor, 4-amino-4-deoxychorismate (ADC), is involved in primary metabolism and antibiotic biosynthesis. In Streptomyces sp. FR-008, a gene pabC-1 putatively encoding a fold-type IV pyridoxal 5′-phosphate (PLP)-dependent enzyme was found within the antibiotic FR-008/candicidin biosynthetic gene cluster, whose inactivation significantly reduced the productivity of antibiotic FR-008 to about 20 % of the wild-type level. Its specific role in PABA formation was further demonstrated by the successful complementation of an Escherichia coli pabC mutant. Moreover, a free-standing gene pabC-2, probably encoding another fold-type IV PLP-dependent enzyme, was cloned from the same strain. Inactivation of pabC-2 reduced antibiotic FR-008 yield to about 57 % of the wild-type level in the mutant, and the complementation of the E. coli pabC mutant established its involvement in PABA biosynthesis. Furthermore, a pabC-1/pabC-2 double mutant only retained about 4 % of the wild-type antibiotic FR-008 productivity, clearly indicating that pabC-2 also contributed to biosynthesis of this antibiotic. Surprisingly, apparently retarded growth of the double mutant was observed on minimal medium, which suggested that both pabC-1 and pabC-2 are involved in PABA biosynthesis for primary metabolism. Finally, both PabC-1 and PabC-2 were shown to be functional ADC lyases by in vitro enzymic lysis with the release of pyruvate. pabC-1 and pabC-2 appear to represent the first two functional ADC lyase genes identified in actinomycetes. The involvement of these two ADC lyase genes in both cell growth and antibiotic FR-008 biosynthesis sets an example for the interplay between primary and secondary metabolisms in bacteria.

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Zhang, Chongxu, Xin Wang, Shiwha Park, et al. "Only a subset of the PAB1-mRNP proteome is present in mRNA translation complexes." Protein Science 23, no. 8 (2014): 1036–49. http://dx.doi.org/10.1002/pro.2490.

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Cui, Ningning, Haihui Tong, Yan Li, et al. "Role of Prealbumin in Predicting the Prognosis of Severely and Critically Ill COVID-19 Patients." American Journal of Tropical Medicine and Hygiene 105, no. 3 (2021): 718–26. http://dx.doi.org/10.4269/ajtmh.21-0234.

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ABSTRACT. Most critically ill patients experience malnutrition, resulting in a poor prognosis. This study aimed to evaluate the association of prealbumin (PAB) with the prognosis for severely and critically ill coronavirus disease 2019 (COVID-19) patients and explore factors related to this association. Patients with laboratory-confirmed COVID-19 from West Campus of Union Hospital in Wuhan from January 29, 2020 to March 31, 2020 were enrolled in this study. Patients were classified into the PAB1 (150–400 mg/L; N = 183) and PAB2 (< 150 mg/L; N = 225) groups. Data collection was performed using the hospital’s electronic medical records system. The predictive value of PAB was evaluated by measuring the area under the receiver-operating characteristic (AUROC) curve. Patients were defined as severely or critically ill based on the Guidance for COVID-19 (7th edition) by the National Health Commission of China. During this analysis, 316 patients had severe cases and 65 had critical cases. A reduced PAB level was associated with a higher risk of mortality and a longer hospital stay. The AUROC curve for the prognosis based on the PAB level was 0.93, with sensitivity of 97.2% and specificity of 77.6%. For severe cases, a lower level of PAB was associated with a higher risk of malnutrition, higher NK cell counts, and lower B lymphocyte counts; these factors were not significant in critical cases. C-reactive protein and nutritional status mediated the association between PAB and prognosis. This retrospective analysis suggests that the PAB level on admission is an indicator of the prognosis for COVID-19.

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Boeck, Ronald, Bruno Lapeyre, Christine E. Brown, and Alan B. Sachs. "Capped mRNA Degradation Intermediates Accumulate in the Yeast spb8-2 Mutant." Molecular and Cellular Biology 18, no. 9 (1998): 5062–72. http://dx.doi.org/10.1128/mcb.18.9.5062.

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ABSTRACT mRNA in the yeast Saccharomyces cerevisiae is primarily degraded through a pathway that is stimulated by removal of the mRNA cap structure. Here we report that a mutation in the SPB8(YJL124c) gene, initially identified as a suppressor mutation of a poly(A)-binding protein (PAB1) gene deletion, stabilizes the mRNA cap structure. Specifically, we find that thespb8-2 mutation results in the accumulation of capped, poly(A)-deficient mRNAs. The presence of this mutation also allows for the detection of mRNA species trimmed from the 3′ end. These data show that this Sm-like protein family member is involved in the process of mRNA decapping, and they provide an example of 3′-5′ mRNA degradation intermediates in yeast.

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Lahoz, Aurelia, María Alcaide-Gavilán, Rafael R. Daga, and Juan Jimenez. "Antagonistic Roles of PP2A-Pab1 and Etd1 in the Control of Cytokinesis in Fission Yeast." Genetics 186, no. 4 (2010): 1261–70. http://dx.doi.org/10.1534/genetics.110.121368.

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28

Brandariz-Núñez, Alberto, Fuxing Zeng, Quan Ngoc Lam, and Hong Jin. "Sbp1 modulates the translation of Pab1 mRNA in a poly(A)- and RGG-dependent manner." RNA 24, no. 1 (2017): 43–55. http://dx.doi.org/10.1261/rna.062547.117.

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Meaux, Stacie, Ambro van Hoof, and Kristian E. Baker. "Nonsense-Mediated mRNA Decay in Yeast Does Not Require PAB1 or a Poly(A) Tail." Molecular Cell 29, no. 1 (2008): 134–40. http://dx.doi.org/10.1016/j.molcel.2007.10.031.

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Wyers, Françoise, Michèle Minet, Marie Elisabeth Dufour, Le Thuy Anh Vo, and François Lacroute. "Deletion of the PAT1 Gene Affects Translation Initiation and Suppresses a PAB1 Gene Deletion in Yeast." Molecular and Cellular Biology 20, no. 10 (2000): 3538–49. http://dx.doi.org/10.1128/.20.10.3538-3549.2000.

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31

Moqtaderi, Zarmik, Joseph V. Geisberg, and Kevin Struhl. "Extensive Structural Differences of Closely Related 3′ mRNA Isoforms: Links to Pab1 Binding and mRNA Stability." Molecular Cell 72, no. 5 (2018): 849–61. http://dx.doi.org/10.1016/j.molcel.2018.08.044.

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Brambilla, Marco, Francesca Martani, Stefano Bertacchi, Ilaria Vitangeli, and Paola Branduardi. "The Saccharomyces cerevisiae poly (A) binding protein (Pab1): Master regulator of mRNA metabolism and cell physiology." Yeast 36, no. 1 (2018): 23–34. http://dx.doi.org/10.1002/yea.3347.

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Chen, Ruofan, Julia Shangguan, Darren N. Kahan, Joshua A. Riback, D. A. Drummond, and Tobin R. Sosnick. "Molecular basis of stress-triggered phase separation of Pab1 mediated by folded domains rather than disordered regions." Biophysical Journal 121, no. 3 (2022): 146a. http://dx.doi.org/10.1016/j.bpj.2021.11.1988.

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34

Swisher, Kylie D., and Roy Parker. "Localization to, and Effects of Pbp1, Pbp4, Lsm12, Dhh1, and Pab1 on Stress Granules in Saccharomyces cerevisiae." PLoS ONE 5, no. 4 (2010): e10006. http://dx.doi.org/10.1371/journal.pone.0010006.

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BRUNE, C. "Yeast poly(A)-binding protein Pab1 shuttles between the nucleus and the cytoplasm and functions in mRNA export." RNA 11, no. 4 (2005): 517–31. http://dx.doi.org/10.1261/rna.7291205.

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Horton, Lynn E., Philip James, Elizabeth A. Craig, and Jack O. Hensold. "The Yeast hsp70 Homologue Ssa Is Required for Translation and Interacts with Sis1 and Pab1 on Translating Ribosomes." Journal of Biological Chemistry 276, no. 17 (2001): 14426–33. http://dx.doi.org/10.1074/jbc.m100266200.

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37

Valentini, Sandro R., Jason M. Casolari, Carla C. Oliveira, Pamela A. Silver, and Anne E. McBride. "Genetic Interactions of Yeast Eukaryotic Translation Initiation Factor 5A (eIF5A) Reveal Connections to Poly(A)-Binding Protein and Protein Kinase C Signaling." Genetics 160, no. 2 (2002): 393–405. http://dx.doi.org/10.1093/genetics/160.2.393.

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Abstract The highly conserved eukaryotic translation initiation factor eIF5A has been proposed to have various roles in the cell, from translation to mRNA decay to nuclear protein export. To further our understanding of this essential protein, three temperature-sensitive alleles of the yeast TIF51A gene have been characterized. Two mutant eIF5A proteins contain mutations in a proline residue at the junction between the two eIF5A domains and the third, strongest allele encodes a protein with a single mutation in each domain, both of which are required for the growth defect. The stronger tif51A alleles cause defects in degradation of short-lived mRNAs, supporting a role for this protein in mRNA decay. A multicopy suppressor screen revealed six genes, the overexpression of which allows growth of a tif51A-1 strain at high temperature; these genes include PAB1, PKC1, and PKC1 regulators WSC1, WSC2, and WSC3. Further results suggest that eIF5A may also be involved in ribosomal synthesis and the WSC/PKC1 signaling pathway for cell wall integrity or related processes.

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Gaillard, Hélène, and Andrés Aguilera. "A Novel Class of mRNA-containing Cytoplasmic Granules Are Produced in Response to UV-Irradiation." Molecular Biology of the Cell 19, no. 11 (2008): 4980–92. http://dx.doi.org/10.1091/mbc.e08-02-0193.

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Nucleic acids are substrates for different types of damage, but little is known about the fate of damaged RNAs. We addressed the existence of an RNA-damage response in yeast. The decay kinetics of GAL1p-driven mRNAs revealed a dose-dependent mRNA stabilization upon UV-irradiation that was not observed after heat or saline shocks, or during nitrogen starvation. UV-induced mRNA stabilization did not depend on DNA repair, damage checkpoint or mRNA degradation machineries. Notably, fluorescent in situ hybridization revealed that after UV-irradiation, polyadenylated mRNA accumulated in cytoplasmic foci that increased in size with time. In situ colocalization showed that these foci are not processing-bodies, eIF4E-, eIF4G-, and Pab1-containing bodies, stress granules, autophagy vesicles, or part of the secretory or endocytic pathways. These results point to the existence of a specific eukaryotic RNA-damage response, which leads to new polyadenylated mRNA-containing granules (UV-induced mRNA granules; UVGs). We propose that potentially damaged mRNAs, which may be deleterious to the cell, are temporarily stored in UVG granules to safeguard cell viability.

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Tadauchi, Tomofumi, Toshifumi Inada, Kunihiro Matsumoto, and Kenji Irie. "Posttranscriptional Regulation of HO Expression by the Mkt1-Pbp1 Complex." Molecular and Cellular Biology 24, no. 9 (2004): 3670–81. http://dx.doi.org/10.1128/mcb.24.9.3670-3681.2004.

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ABSTRACT Cells of budding yeast give rise to mother and daughter cells, which differ in that only mother cells express the HO endonuclease gene and are thereby able to switch mating types. In this study, we identified the MKT1 gene as a positive regulator of HO expression. The MKT1 gene encodes a protein with two domains, XPG-N and XPG-I, which are conserved among a family of nucleases, including human XPG endonuclease. Loss of MKT1 had little effect on HO mRNA levels but resulted in decreased protein levels. This decrease was dependent on the 3′ untranslated region of the HO transcript. We screened for proteins that associate with Mkt1 and isolated Pbp1, a protein that is known to associate with Pab1, a poly(A)-binding protein. Loss of PBP1 resembles an mkt1Δ deletion, causing decreased expression of HO at the posttranscriptional level. Mkt1 and Pbp1 cosedimented with polysomes in sucrose gradients, with Mkt1 distribution in the polysomes dependent on Pbp1, but not vice versa. These observations suggest that a complex of Mkt1 and Pbp1 regulates the translation of HO mRNA.

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Assis, Ludmila A., Moezio V. C. Santos Filho, Joao R. da Cruz Silva, et al. "Identification of novel proteins and mRNAs differentially bound to the Leishmania Poly(A) Binding Proteins reveals a direct association between PABP1, the RNA-binding protein RBP23 and mRNAs encoding ribosomal proteins." PLOS Neglected Tropical Diseases 15, no. 10 (2021): e0009899. http://dx.doi.org/10.1371/journal.pntd.0009899.

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Poly(A) Binding Proteins (PABPs) are major eukaryotic RNA-binding proteins (RBPs) with multiple roles associated with mRNA stability and translation and characterized mainly from multicellular organisms and yeasts. A variable number of PABP homologues are seen in different organisms however the biological reasons for multiple PABPs are generally not well understood. In the unicellular Leishmania, dependent on post-transcriptional mechanisms for the control of its gene expression, three distinct PABPs are found, with yet undefined functional distinctions. Here, using RNA-immunoprecipitation sequencing analysis we show that the Leishmania PABP1 preferentially associates with mRNAs encoding ribosomal proteins, while PABP2 and PABP3 bind to an overlapping set of mRNAs distinct to those enriched in PABP1. Immunoprecipitation studies combined to mass-spectrometry analysis identified RBPs differentially associated with PABP1 or PABP2, including RBP23 and DRBD2, respectively, that were investigated further. Both RBP23 and DRBD2 bind directly to the three PABPs in vitro, but reciprocal experiments confirmed preferential co-immunoprecipitation of PABP1, as well as the EIF4E4/EIF4G3 based translation initiation complex, with RBP23. Other RBP23 binding partners also imply a direct role in translation. DRBD2, in contrast, co-immunoprecipitated with PABP2, PABP3 and with RBPs unrelated to translation. Over 90% of the RBP23-bound mRNAs code for ribosomal proteins, mainly absent from the transcripts co-precipitated with DRBD2. These experiments suggest a novel and specific route for translation of the ribosomal protein mRNAs, mediated by RBP23, PABP1 and the associated EIF4E4/EIF4G3 complex. They also highlight the unique roles that different PABP homologues may have in eukaryotic cells associated with mRNA translation.

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Peltz, S. W., J. L. Donahue, and A. Jacobson. "A mutation in the tRNA nucleotidyltransferase gene promotes stabilization of mRNAs in Saccharomyces cerevisiae." Molecular and Cellular Biology 12, no. 12 (1992): 5778–84. http://dx.doi.org/10.1128/mcb.12.12.5778-5784.1992.

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To identify trans-acting factors involved in mRNA decay in the yeast Saccharomyces cerevisiae, we have begun to characterize conditional lethal mutants that affect mRNA steady-state levels. A screen of a collection of temperature-sensitive mutants identified ts352, a mutant that accumulated moderately stable and unstable mRNAs after a shift from 23 to 37 degrees C (M. Aebi, G. Kirchner, J.-Y. Chen, U. Vijayraghavan, A. Jacobson, N.C. Martin, and J. Abelson, J. Biol. Chem. 265:16216-16220, 1990). ts352 has a defect in the CCA1 gene, which codes for tRNA nucleotidyltransferase, the enzyme that adds 3' CCA termini to tRNAs (Aebi et al., J. Biol. Chem., 1990). In a shift to the nonpermissive temperature, ts352 (cca1-1) cells rapidly cease protein synthesis, reduce the rates of degradation of the CDC4, TCM1, and PAB1 mRNAs three- to fivefold, and increase the relative number of ribosomes associated with mRNAs and the overall size of polysomes. These results were analogous to those observed for cycloheximide-treated cells and are generally consistent with models that invoke a role for translational elongation in the process of mRNA turnover.

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Peltz, S. W., J. L. Donahue, and A. Jacobson. "A mutation in the tRNA nucleotidyltransferase gene promotes stabilization of mRNAs in Saccharomyces cerevisiae." Molecular and Cellular Biology 12, no. 12 (1992): 5778–84. http://dx.doi.org/10.1128/mcb.12.12.5778.

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To identify trans-acting factors involved in mRNA decay in the yeast Saccharomyces cerevisiae, we have begun to characterize conditional lethal mutants that affect mRNA steady-state levels. A screen of a collection of temperature-sensitive mutants identified ts352, a mutant that accumulated moderately stable and unstable mRNAs after a shift from 23 to 37 degrees C (M. Aebi, G. Kirchner, J.-Y. Chen, U. Vijayraghavan, A. Jacobson, N.C. Martin, and J. Abelson, J. Biol. Chem. 265:16216-16220, 1990). ts352 has a defect in the CCA1 gene, which codes for tRNA nucleotidyltransferase, the enzyme that adds 3' CCA termini to tRNAs (Aebi et al., J. Biol. Chem., 1990). In a shift to the nonpermissive temperature, ts352 (cca1-1) cells rapidly cease protein synthesis, reduce the rates of degradation of the CDC4, TCM1, and PAB1 mRNAs three- to fivefold, and increase the relative number of ribosomes associated with mRNAs and the overall size of polysomes. These results were analogous to those observed for cycloheximide-treated cells and are generally consistent with models that invoke a role for translational elongation in the process of mRNA turnover.

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Marin, Ambroise, Emmanuel Denimal, Lucie Bertheau, Stéphane Guyot, Ludovic Journaux, and Paul Molin. "Automatic Counting of Intra-Cellular Ribonucleo-Protein Aggregates in Saccharomyces cerevisiae Using a Textural Approach." Microscopy and Microanalysis 25, no. 1 (2019): 164–79. http://dx.doi.org/10.1017/s1431927619000084.

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AbstractIn the context of microbiology, recent studies show the importance of ribonucleo-protein aggregates (RNPs) for the understanding of mechanisms involved in cell responses to specific environmental conditions. The assembly and disassembly of aggregates is a dynamic process, the characterization of the stage of their evolution can be performed by the evaluation of their number. The aim of this study is to propose a method to automatically determine the count of RNPs. We show that the determination of a precise count is an issue by itself and hence, we propose three textural approaches: a classical point of view using Haralick features, a frequency point of view with generalized Fourier descriptors, and a structural point of view with Zernike moment descriptors (ZMD). These parameters are then used as inputs for a supervised classification in order to determine the most relevant. An experiment using a specific Saccharomyces cerevisiae strain presenting a fusion between a protein found in RNPs (PAB1) and the green fluorescent protein was performed to benchmark this approach. The fluorescence was observed with two-photon fluorescence microscopy. Results show that the textural approach, by mixing ZMD with Haralick features, allows for the characterization of the number of RNPs.

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Kops, Anne de Bruyn, Jordan E. Burke, and Christine Guthrie. "Brr6 plays a role in gene recruitment and transcriptional regulation at the nuclear envelope." Molecular Biology of the Cell 29, no. 21 (2018): 2578–90. http://dx.doi.org/10.1091/mbc.e18-04-0258.

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Correlation between transcriptional regulation and positioning of genes at the nuclear envelope is well established in eukaryotes, but the mechanisms involved are not well understood. We show that brr6-1, a mutant of the essential yeast envelope transmembrane protein Brr6p, impairs normal positioning and expression of the PAB1 and FUR4- GAL1,10,7 loci. Similarly, expression of a dominant negative nucleoplasmic Brr6 fragment in wild-type cells reproduced many of the brr6-1 effects. Histone chromatin immunoprecipitation (ChIP) experiments showed decreased acetylation at the key histone H4K16 residue in the FUR4-GAL1,10,7 region in brr6-1. Importantly, blocking deacetylation significantly suppressed selected brr6-1 phenotypes. ChIPseq with FLAG-tagged Brr6 fragments showed enrichment at FUR4 and several other genes that showed striking changes in brr6-1 RNAseq data. These associations depended on a Brr6 putative zinc finger domain. Importantly, artificially tethering the GAL1 locus to the envelope suppressed the brr6-1 effects on GAL1 and FUR4 expression and increased H4K16 acetylation between GAL1 and FUR4 in the mutant. Together these results argue that Brr6 interacts with chromatin, helping to maintain normal chromatin architecture and transcriptional regulation of certain loci at the nuclear envelope.

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Turtola, Matti, M. Cemre Manav, Ananthanarayanan Kumar, et al. "Three-layered control of mRNA poly(A) tail synthesis in Saccharomyces cerevisiae." Genes & Development 35, no. 17-18 (2021): 1290–303. http://dx.doi.org/10.1101/gad.348634.121.

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Biogenesis of most eukaryotic mRNAs involves the addition of an untemplated polyadenosine (pA) tail by the cleavage and polyadenylation machinery. The pA tail, and its exact length, impacts mRNA stability, nuclear export, and translation. To define how polyadenylation is controlled in S. cerevisiae, we have used an in vivo assay capable of assessing nuclear pA tail synthesis, analyzed tail length distributions by direct RNA sequencing, and reconstituted polyadenylation reactions with purified components. This revealed three control mechanisms for pA tail length. First, we found that the pA binding protein (PABP) Nab2p is the primary regulator of pA tail length. Second, when Nab2p is limiting, the nuclear pool of Pab1p, the second major PABP in yeast, controls the process. Third, when both PABPs are absent, the cleavage and polyadenylation factor (CPF) limits pA tail synthesis. Thus, Pab1p and CPF provide fail-safe mechanisms to a primary Nab2p-dependent pathway, thereby preventing uncontrolled polyadenylation and allowing mRNA export and translation.

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Kitamura, Satoshi, Yutaka Oono, and Issay Narumi. "Arabidopsis pab1, a mutant with reduced anthocyanins in immature seeds from banyuls, harbors a mutation in the MATE transporter FFT." Plant Molecular Biology 90, no. 1-2 (2015): 7–18. http://dx.doi.org/10.1007/s11103-015-0389-8.

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Lee, Darren, Takbum Ohn, Yueh-Chin Chiang, et al. "PUF3 Acceleration of Deadenylation in Vivo Can Operate Independently of CCR4 Activity, Possibly Involving Effects on the PAB1–mRNP Structure." Journal of Molecular Biology 399, no. 4 (2010): 562–75. http://dx.doi.org/10.1016/j.jmb.2010.04.034.

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Álvarez, Enrique, Alfredo Castelló, Luis Menéndez-Arias, and Luis Carrasco. "HIV protease cleaves poly(A)-binding protein." Biochemical Journal 396, no. 2 (2006): 219–26. http://dx.doi.org/10.1042/bj20060108.

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The PABP [poly(A)-binding protein] is able to interact with the 3′ poly(A) tail of eukaryotic mRNA, promoting its translation. Cleavage of PABP by viral proteases encoded by several picornaviruses and caliciviruses plays a role in the abrogation of cellular protein synthesis. We report that infection of MT-2 cells with HIV-1 leads to efficient proteolysis of PABP. Analysis of PABP integrity was carried out in BHK-21 (baby-hamster kidney) and COS-7 cells upon individual expression of the protease from several members of the Retroviridae family, e.g. MoMLV (Moloney murine leukaemia virus), MMTV (mouse mammary tumour virus), HTLV-I (human T-cell leukaemia virus type I), SIV (simian immunodeficiency virus), HIV-1 and HIV-2. Moreover, protease activity against PABP was tested in a HeLa-cell-free system. Only MMTV, HIV-1 and HIV-2 proteases were able to cleave PABP in the absence of other viral proteins. Purified HIV-1 and HIV-2 proteases cleave PABP1 directly at positions 237 and 477, separating the two first RNA-recognition motifs from the C-terminal domain of PABP. An additional cleavage site located at position 410 was detected for HIV-2 protease. These findings indicate that some retroviruses may share with picornaviruses and caliciviruses the capacity to proteolyse PABP.

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Brook, Matthew, Lora McCracken, James P. Reddington, Zhi-Liang Lu, Nicholas A. Morrice, and Nicola K. Gray. "The multifunctional poly(A)-binding protein (PABP) 1 is subject to extensive dynamic post-translational modification, which molecular modelling suggests plays an important role in co-ordinating its activities." Biochemical Journal 441, no. 3 (2012): 803–16. http://dx.doi.org/10.1042/bj20111474.

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PABP1 [poly(A)-binding protein 1] is a central regulator of mRNA translation and stability and is required for miRNA (microRNA)-mediated regulation and nonsense-mediated decay. Numerous protein, as well as RNA, interactions underlie its multi-functional nature; however, it is unclear how its different activities are co-ordinated, since many partners interact via overlapping binding sites. In the present study, we show that human PABP1 is subject to elaborate post-translational modification, identifying 14 modifications located throughout the functional domains, all but one of which are conserved in mouse. Intriguingly, PABP1 contains glutamate and aspartate methylations, modifications of unknown function in eukaryotes, as well as lysine and arginine methylations, and lysine acetylations. The latter dramatically alter the pI of PABP1, an effect also observed during the cell cycle, suggesting that different biological processes/stimuli can regulate its modification status, although PABP1 also probably exists in differentially modified subpopulations within cells. Two lysine residues were differentially acetylated or methylated, revealing that PABP1 may be the first example of a cytoplasmic protein utilizing a ‘methylation/acetylation switch’. Modelling using available structures implicates these modifications in regulating interactions with individual PAM2 (PABP-interacting motif 2)-containing proteins, suggesting a direct link between PABP1 modification status and the formation of distinct mRNP (messenger ribonucleoprotein) complexes that regulate mRNA fate in the cytoplasm.

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Salaun, C., A. I. MacDonald, O. Larralde, et al. "Poly(A)-Binding Protein 1 Partially Relocalizes to the Nucleus during Herpes Simplex Virus Type 1 Infection in an ICP27-Independent Manner and Does Not Inhibit Virus Replication." Journal of Virology 84, no. 17 (2010): 8539–48. http://dx.doi.org/10.1128/jvi.00668-10.

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ABSTRACT Infection of cells by herpes simplex virus type 1 (HSV-1) triggers host cell shutoff whereby mRNAs are degraded and cellular protein synthesis is diminished. However, virus protein translation continues because the translational apparatus in HSV-infected cells is maintained in an active state. Surprisingly, poly(A)-binding protein 1 (PABP1), a predominantly cytoplasmic protein that is required for efficient translation initiation, is partially relocated to the nucleus during HSV-1 infection. This relocalization occurred in a time-dependent manner with respect to virus infection. Since HSV-1 infection causes cell stress, we examined other cell stress inducers and found that oxidative stress similarly relocated PABP1. An examination of stress-induced kinases revealed similarities in HSV-1 infection and oxidative stress activation of JNK and p38 mitogen-activated protein (MAP) kinases. Importantly, PABP relocalization in infection was found to be independent of the viral protein ICP27. The depletion of PABP1 by small interfering RNA (siRNA) knockdown had no significant effect on viral replication or the expression of selected virus late proteins, suggesting that reduced levels of cytoplasmic PABP1 are tolerated during infection.

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Journal articles on the topic 'Pab1'

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