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Yeast Mitochondrial Biogenesis: A Role for the PUF RNA-Binding Protein Puf3p in mRNA Localization  [PDF]
Yann Saint-Georges, Mathilde Garcia, Thierry Delaveau, Laurent Jourdren, Stephane Le Crom, Sophie Lemoine, Veronique Tanty, Frederic Devaux, Claude Jacq
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002293
Abstract: The asymmetric localization of mRNA plays an important role in coordinating posttranscriptional events in eukaryotic cells. We investigated the peripheral mitochondrial localization of nuclear-encoded mRNAs (MLR) in various conditions in which the mRNA binding protein context and the translation efficiency were altered. We identified Puf3p, a Pumilio family RNA-binding protein, as the first trans-acting factor controlling the MLR phenomenon. This allowed the characterization of two classes of genes whose mRNAs are translated to the vicinity of mitochondria. Class I mRNAs (256 genes) have a Puf3p binding motif in their 3'UTR region and many of them have their MLR properties deeply affected by PUF3 deletion. Conversely, mutations in the Puf3p binding motif alter the mitochondrial localization of BCS1 mRNA. Class II mRNAs (224 genes) have no Puf3p binding site and their asymmetric localization is not affected by the absence of PUF3. In agreement with a co-translational import process, we observed that the presence of puromycin loosens the interactions between most of the MLR-mRNAs and mitochondria. Unexpectedly, cycloheximide, supposed to solidify translational complexes, turned out to destabilize a class of mRNA-mitochondria interactions. Classes I and II mRNAs, which are therefore transported to the mitochondria through different pathways, correlated with different functional modules. Indeed, Class I genes code principally for the assembly factors of respiratory chain complexes and the mitochondrial translation machinery (ribosomes and translation regulators). Class II genes encode proteins of the respiratory chain or proteins involved in metabolic pathways. Thus, MLR, which is intimately linked to translation control, and the activity of mRNA-binding proteins like Puf3p, may provide the conditions for a fine spatiotemporal control of mitochondrial protein import and mitochondrial protein complex assembly. This work therefore provides new openings for the global study of mitochondria biogenesis.
The P-Loop Domain of Yeast Clp1 Mediates Interactions Between CF IA and CPF Factors in Pre-mRNA 3′ End Formation  [PDF]
Sandra Holbein, Simonetta Scola, Bernhard Loll, Beatriz Solange Dichtl, Wolfgang Hübner, Anton Meinhart, Bernhard Dichtl
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0029139
Abstract: Cleavage factor IA (CF IA), cleavage and polyadenylation factor (CPF), constitute major protein complexes required for pre-mRNA 3′ end formation in yeast. The Clp1 protein associates with Pcf11, Rna15 and Rna14 in CF IA but its functional role remained unclear. Clp1 carries an evolutionarily conserved P-loop motif that was previously shown to bind ATP. Interestingly, human and archaean Clp1 homologues, but not the yeast protein, carry 5′ RNA kinase activity. We show that depletion of Clp1 in yeast promoted defective 3′ end formation and RNA polymerase II termination; however, cells expressing Clp1 with mutant P-loops displayed only minor defects in gene expression. Similarly, purified and reconstituted mutant CF IA factors that interfered with ATP binding complemented CF IA depleted extracts in coupled in vitro transcription/3′ end processing reactions. We found that Clp1 was required to assemble recombinant CF IA and that certain P-loop mutants failed to interact with the CF IA subunit Pcf11. In contrast, mutations in Clp1 enhanced binding to the 3′ endonuclease Ysh1 that is a component of CPF. Our results support a structural role for the Clp1 P-loop motif. ATP binding by Clp1 likely contributes to CF IA formation and cross-factor interactions during the dynamic process of 3′ end formation.
mRNA Localization Mechanisms in Trypanosoma cruzi  [PDF]
Lysangela R. Alves, Eloise P. Guerra-Slompo, Arthur V. de Oliveira, Juliane S. Malgarin, Samuel Goldenberg, Bruno Dallagiovanna
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0081375
Abstract: Asymmetric mRNA localization is a sophisticated tool for regulating and optimizing protein synthesis and maintaining cell polarity. Molecular mechanisms involved in the regulated localization of transcripts are widespread in higher eukaryotes and fungi, but not in protozoa. Trypanosomes are ancient eukaryotes that branched off early in eukaryote evolution. We hypothesized that these organisms would have basic mechanisms of mRNA localization. FISH assays with probes against transcripts coding for proteins with restricted distributions showed a discrete localization of the mRNAs in the cytoplasm. Moreover, cruzipain mRNA was found inside reservosomes suggesting new unexpected functions for this vacuolar organelle. Individual mRNAs were also mobilized to RNA granules in response to nutritional stress. The cytoplasmic distribution of these transcripts changed with cell differentiation, suggesting that localization mechanisms might be involved in the regulation of stage-specific protein expression. Transfection assays with reporter genes showed that, as in higher eukaryotes, 3′UTRs were responsible for guiding mRNAs to their final location. Our results strongly suggest that Trypanosoma cruzi have a core, basic mechanism of mRNA localization. This kind of controlled mRNA transport is ancient, dating back to early eukaryote evolution.
Articles selected by Faculty of 1000: transcriptional regulation in parasitic helminths; interspecies expression-profile comparison; rice microRNAs; mRNA localization to the yeast bud tip; compartmental localisation of E. coli proteins
Genome Biology , 2005, DOI: 10.1186/gb-2005-6-7-332
Abstract: For the Faculty of 1000 evaluation of this article please see: http://genomebiology.com/reports/F1000/gb-2005-6-7-332.asp#Wippersteg webciteMulti-species microarrays reveal the effect of sequence divergence on gene expression profiles. Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. Genome Res 2005, 15:674-680.For the Faculty of 1000 evaluation of this article please see: http://genomebiology.com/reports/F1000/gb-2005-6-7-332.asp#Gilad webciteCloning and characterization of microRNAs from rice. Sunkar R, Girke T, Jain PK, Zhu JK. Plant Cell 2005, 17:1397-1411.For the Faculty of 1000 evaluation of this article please see: http://genomebiology.com/reports/F1000/gb-2005-6-7-332.asp#Sunkar webciteIdentification of a conserved RNA motif essential for she2p recognition and mRNA localization to the yeast bud. Olivier C, Poirier G, Gendron P, Boisgontier A, Major F, Chartrand P. Mol Cell Biol 2005, 25:4752-4766.For the Faculty of 1000 evaluation of this article please see: http://genomebiology.com/reports/F1000/gb-2005-6-7-332.asp#Olivier webciteLocalization, annotation & comparison of the Escherichia coli K-12 proteome under two states of growth. Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ. Mol Cell Proteomics 2005, May 18.For the Faculty of 1000 evaluation of this article please see: http://genomebiology.com/reports/F1000/gb-2005-6-7-332.asp#Lopez-Campistrous webcite
The Furin Cytoplasmic Domain is Localized to the trans-Golgi Network of Yeast  [cached]
Alison J Farrell,Katherine A Keltner,Kathyrn L Bruce,Jessica L Snell
International Journal of Biology , 2011, DOI: 10.5539/ijb.v3n3p3
Abstract: Kex2p and furin are well-characterized, structurally similar, membrane-bound proteases localized to the trans-Golgi network (TGN) of yeast and animal cells. While their N-terminal and lumenal catalytic domains are highly homologous, they do not share common sorting signals in their C-terminal cytoplasmic tails. To study furin’s localization in yeast, we created a chimera with the N-terminal regions of Kex2p and the C-terminal regions of human furin. Our mating, biochemical, and immunofluorescent studies of the KFp chimeras in yeast have demonstrated sorting consistent with furin’s trafficking patterns in human cells. Next, to see if furin sorting signals are recognized by yeast sorting machinery, key signals were mutated. For two chimeras (KF5p/6p) mating activity was abolished indicating that the Kex2p enzyme is no longer resident to the yeast TGN. This is surprising since this furin sorting signal in animal cells binds a sorting protein (PACS-1) not known to exist in yeast
A novel link between Sus1 and the cytoplasmic mRNA decay machinery suggests a broad role in mRNA metabolism
Bernardo Cuenca-Bono, Varinia García-Molinero, Pau Pascual-García, Encar García-Oliver, Ana Llopis, Susana Rodríguez-Navarro
BMC Cell Biology , 2010, DOI: 10.1186/1471-2121-11-19
Abstract: In this study, we have investigated whether the yeast Sus1 protein is linked to factors involved in mRNA degradation pathways. We provide evidence for genetic interactions between SUS1 and genes coding for components of P-bodies such as PAT1, LSM1, LSM6 and DHH1. We demonstrate that SUS1 deletion is synthetic lethal with 5'→3' decay machinery components LSM1 and PAT1 and has a strong genetic interaction with LSM6 and DHH1. Interestingly, Sus1 overexpression led to an accumulation of Sus1 in cytoplasmic granules, which can co-localise with components of P-bodies and stress granules. In addition, we have identified novel physical interactions between Sus1 and factors associated to P-bodies/stress granules. Finally, absence of LSM1 and PAT1 slightly promotes the Sus1-TREX2 association.In this study, we found genetic and biochemical association between Sus1 and components responsible for cytoplasmic mRNA metabolism. Moreover, Sus1 accumulates in discrete cytoplasmic granules, which partially co-localise with P-bodies and stress granules under specific conditions. These interactions suggest a role for Sus1 in gene expression during cytoplasmic mRNA metabolism in addition to its nuclear function.During gene expression, the coordinated action of several multiprotein complexes couple transcription, mRNA biogenesis and export, to guarantee the proper maturation of transcripts before their translation in the cytoplasm [1]. mRNA levels are highly regulated by transcription rate adjustments and mRNA decay, to produce the appropriate number of transcripts competent for translation [2]. In yeast, two major cytoplasmic mRNA degradation pathways control transcript turnover: the cytoplasmic exosome and the 5'→3' mRNA decay. Moreover, 5'→3' mRNA decay and translation are interconnected processes providing an exquisite equilibrium between degradation, storage and translation that correlates with the type and localisation of the mRNP in the cell (reviewed in [3]). Work over the last fe
Dynein Regulates Epithelial Polarity and the Apical Localization of stardust A mRNA  [PDF]
Sally Horne-Badovinac,David Bilder
PLOS Genetics , 2008, DOI: 10.1371/journal.pgen.0040008
Abstract: Intense investigation has identified an elaborate protein network controlling epithelial polarity. Although precise subcellular targeting of apical and basolateral determinants is required for epithelial architecture, little is known about how the individual determinant proteins become localized within the cell. Through a genetic screen for epithelial defects in the Drosophila follicle cells, we have found that the cytoplasmic Dynein motor is an essential regulator of apico–basal polarity. Our data suggest that Dynein acts through the cytoplasmic scaffolding protein Stardust (Sdt) to localize the transmembrane protein Crumbs, in part through the apical targeting of specific sdt mRNA isoforms. We have mapped the sdt mRNA localization signal to an alternatively spliced coding exon. Intriguingly, the presence or absence of this exon corresponds to a developmental switch in sdt mRNA localization in which apical transcripts are only found during early stages of epithelial development, while unlocalized transcripts predominate in mature epithelia. This work represents the first demonstration that Dynein is required for epithelial polarity and suggests that mRNA localization may have a functional role in the regulation of apico–basal organization. Moreover, we introduce a unique mechanism in which alternative splicing of a coding exon is used to control mRNA localization during development.
DEAD Box Protein DDX1 Regulates Cytoplasmic Localization of KSRP  [PDF]
Chu-Fang Chou, Wei-Jye Lin, Chen-Chung Lin, Christian A. Luber, Roseline Godbout, Matthias Mann, Ching-Yi Chen
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0073752
Abstract: mRNA decay mediated by the AU-rich elements (AREs) is one of the most studied post-transcriptional mechanisms and is modulated by ARE-binding proteins (ARE-BPs). To understand the regulation of K homology splicing regulatory protein (KSRP), a decay-promoting ARE-BP, we purified KSRP protein complexes and identified an RNA helicase, DDX1. We showed that down-regulation of DDX1 expression elevated cytoplasmic levels of KSRP and facilitated ARE-mediated mRNA decay. Association of KSRP with 14-3-3 proteins, that are predominately located in the cytoplasm, increased upon reduction of DDX1. We also demonstrated that KSRP associated with DDX1 or 14-3-3, but not both. These observations indicate that subcellular localization of KSRP is regulated by competing interactions with DDX1 or 14-3-3.
G-quadruplexes and mRNA localization  [PDF]
Valentina Agoni
Quantitative Biology , 2013,
Abstract: G-quadruplexes represent a novelty for molecular biology. Their role inside the cell remains mysterious. We investigate a possible correlation with mRNA localization. In particular, we hypothesize that Gquadruplexes influence fluid dynamics.
mRNA Decay Proteins Are Targeted to poly(A)+ RNA and dsRNA-Containing Cytoplasmic Foci That Resemble P-Bodies in Entamoeba histolytica  [PDF]
Itzel López-Rosas, Esther Orozco, Laurence A. Marchat, Guillermina García-Rivera, Nancy Guillen, Christian Weber, Eduardo Carrillo-Tapia, Olga Hernández de la Cruz, Carlos Pérez-Plasencia, César López-Camarillo
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045966
Abstract: In higher eukaryotes, mRNA degradation and RNA-based gene silencing occur in cytoplasmic foci referred to as processing bodies (P-bodies). In protozoan parasites, the presence of P-bodies and their putative role in mRNA decay have yet to be comprehensively addressed. Identification of P-bodies might provide information on how mRNA degradation machineries evolved in lower eukaryotes. Here, we used immunofluorescence and confocal microscopy assays to investigate the cellular localization of mRNA degradation proteins in the human intestinal parasite Entamoeba histolytica and found evidence of the existence of P-bodies. Two mRNA decay factors, namely the EhXRN2 exoribonuclease and the EhDCP2 decapping enzyme, were localized in cytoplasmic foci in a pattern resembling P-body organization. Given that amoebic foci appear to be smaller and less rounded than those described in higher eukaryotes, we have named them “P-body-like structures”. These foci contain additional mRNA degradation factors, including the EhCAF1 deadenylase and the EhAGO2-2 protein involved in RNA interference. Biochemical analysis revealed that EhCAF1 co-immunoprecipitated with EhXRN2 but not with EhDCP2 or EhAGO2-2, thus linking deadenylation to 5′-to-3′ mRNA decay. The number of EhCAF1-containing foci significantly decreased after inhibition of transcription and translation with actinomycin D and cycloheximide, respectively. Furthermore, results of RNA-FISH assays showed that (i) EhCAF1 colocalized with poly(A)+ RNA and (ii) during silencing of the Ehpc4 gene by RNA interference, EhAGO2-2 colocalized with small interfering RNAs in cytoplasmic foci. Our observation of decapping, deadenylation and RNA interference proteins within P-body-like foci suggests that these structures have been conserved after originating in the early evolution of eukaryotic lineages. To the best of our knowledge, this is the first study to report on the localization of mRNA decay proteins within P-body-like structures in E. histolytica. Our findings should open up opportunities for deciphering the mechanisms of mRNA degradation and RNA-based gene silencing in this deep-branching eukaryote.
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