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1.
Biochimie ; 203: 93-105, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36184002

ABSTRACT

The objective of the present review is to provide an insight into modifications of microbial cell walls and membrane constituents by using the aminoacyl-tRNA as amino acid donor. In bacteria, phospholipids are modified by Multiple peptide resistance Factor enzymes and peptidoglycan precursors by so called fem ligases. Although these modifications were thought to be restricted to procaryotes, we discovered enzymes that modify ergosterol (the main component of fungal membrane) with glycine and aspartate. The focus of this review is to present the molecular mechanisms underlying all these processes together with the structure of the enzymes and their substrates. This article also reviews how substrates are recognized and modified and how the products are subsequently exported in various organisms. Finally, the physiological outcome and the discoveries of each family of enzymes is also discussed.


Subject(s)
Amino Acids , Amino Acyl-tRNA Synthetases , Amino Acids/metabolism , RNA, Transfer/metabolism , Cell Wall/metabolism , RNA, Transfer, Amino Acyl/metabolism , Peptidoglycan/metabolism , Amino Acyl-tRNA Synthetases/chemistry
2.
J Med Genet ; 59(12): 1227-1233, 2022 12.
Article in English | MEDLINE | ID: mdl-36041817

ABSTRACT

BACKGROUND: Aminoacyl-tRNA synthetases (ARS) are key enzymes catalysing the first reactions in protein synthesis, with increasingly recognised pleiotropic roles in tumourgenesis, angiogenesis, immune response and lifespan. Germline mutations in several ARS genes have been associated with both recessive and dominant neurological diseases. Recently, patients affected with microcephaly, intellectual disability and ataxia harbouring biallelic variants in the seryl-tRNA synthetase encoded by seryl-tRNA synthetase 1 (SARS1) were reported. METHODS: We used exome sequencing to identify the causal variant in a patient affected by complex spastic paraplegia with ataxia, intellectual disability, developmental delay and seizures, but without microcephaly. Complementation and serylation assays using patient's fibroblasts and an Saccharomyces cerevisiae model were performed to examine this variant's pathogenicity. RESULTS: A de novo splice site deletion in SARS1 was identified in our patient, resulting in a 5-amino acid in-frame insertion near its active site. Complementation assays in S. cerevisiae and serylation assays in both yeast strains and patient fibroblasts proved a loss-of-function, dominant negative effect. Fibroblasts showed an abnormal cell shape, arrested division and increased beta-galactosidase staining along with a senescence-associated secretory phenotype (raised interleukin-6, p21, p16 and p53 levels). CONCLUSION: We refine the phenotypic spectrum and modes of inheritance of a newly described, ultrarare neurodevelopmental disorder, while unveiling the role of SARS1 as a regulator of cell growth, division and senescence.


Subject(s)
Amino Acyl-tRNA Synthetases , Intellectual Disability , Microcephaly , Serine-tRNA Ligase , Humans , Amino Acyl-tRNA Synthetases/genetics , Ataxia , Cellular Senescence/genetics , Intellectual Disability/genetics , Ligases , Microcephaly/genetics , Paraplegia/genetics , Saccharomyces cerevisiae/genetics , Serine-tRNA Ligase/chemistry , Serine-tRNA Ligase/metabolism
3.
Methods Mol Biol ; 2497: 255-267, 2022.
Article in English | MEDLINE | ID: mdl-35771447

ABSTRACT

Proving with certainty that a GFP-tagged protein is imported inside mitochondria by visualizing its fluorescence emission with an epifluorescence microscope is currently impossible using regular GFP-tagging. This is particularly true for proteins dual localized in the cytosol and mitochondria, which have been estimated to represent up to one third of the established mitoproteomes. These proteins are usually composed of a surpassingly abundant pool of the cytosolic isoform compared to the mitochondrial isoform. As a consequence, when tagged with a regular GFP, the fluorescence emission of the cytosolic isoform will inevitably eclipse that of the mitochondrial one and prevent the detection of the mitochondrial echoform. To overcome this technical limit, we engineered a yeast strain expressing a new type of GFP called Bi-Genomic Mitochondrial-Split-GFP (BiG Mito-Split-GFP). In this strain, one moiety of the GFP is encoded by the mitochondrial DNA while the second moiety of the GFP can be tagged to any nuclear-encoded protein (suspected to be dual localized or bona fide mitochondrial). By doing so, only mitochondrial proteins or echoforms of dual localized proteins, regardless of their organismal origin, trigger GFP reconstitution that can be visualized by regular fluorescence microscopy. The strength of the BiG Mito-Split-GFP system is that proof of the mitochondrial localization of a given protein rests on a simple and effortless microscopy observation.


Subject(s)
Mitochondria , Saccharomyces cerevisiae , Genomics , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Microscopy, Fluorescence , Mitochondria/genetics , Mitochondria/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism
4.
J Biol Chem ; 298(3): 101657, 2022 03.
Article in English | MEDLINE | ID: mdl-35131263

ABSTRACT

A wide range of bacteria possess virulence factors such as aminoacyl-tRNA transferases (ATTs) that are capable of rerouting aminoacyl-transfer RNAs away from protein synthesis to conjugate amino acids onto glycerolipids. We recently showed that, although these pathways were thought to be restricted to bacteria, higher fungi also possess ergosteryl-3ß-O-L-aspartate synthases (ErdSs), which transfer the L-Asp moiety of aspartyl-tRNAAsp onto the 3ß-OH group of ergosterol (Erg), yielding ergosteryl-3ß-O-L-aspartate (Erg-Asp). Here, we report the discovery, in fungi, of a second type of fungal sterol-specific ATTs, namely, ergosteryl-3ß-O-glycine (Erg-Gly) synthase (ErgS). ErgS consists of a freestanding DUF2156 domain encoded by a gene distinct from and paralogous to that of ErdS. We show that the enzyme only uses Gly-tRNAGly produced by an independent glycyl-tRNA synthetase (GlyRS) to transfer glycine onto the 3ß-OH of Erg, producing Erg-Gly. Phylogenomics analysis also show that the Erg-Gly synthesis pathway exists only in Ascomycota, including species of biotechnological interest, and more importantly, in human pathogens, such as Aspergillus fumigatus. The discovery of a second type of Erg-aa not only expands the repertoire of this particular class of fungal lipids but suggests that Erg-aa synthases might constitute a genuine subfamily of lipid-modifying ATTs.


Subject(s)
Ascomycota , Ergosterol , Glycine , Amino Acids , Ascomycota/genetics , Ascomycota/metabolism , Aspartic Acid , Glycine/biosynthesis , Glycine/genetics , Glycine/metabolism , Humans , RNA, Fungal/genetics , RNA, Fungal/metabolism , RNA, Transfer, Amino Acyl/genetics , RNA, Transfer, Amino Acyl/metabolism
5.
Biol Open ; 10(3)2021 03 22.
Article in English | MEDLINE | ID: mdl-33753324

ABSTRACT

COPI (coatomer complex I) coated vesicles are involved in Golgi-to-ER and intra-Golgi trafficking pathways, and mediate retrieval of ER resident proteins. Functions and components of the COPI-mediated trafficking pathways, beyond the canonical set of Sec/Arf proteins, are constantly increasing in number and complexity. In mammalian cells, GORAB, SCYL1 and SCYL3 proteins regulate Golgi morphology and protein glycosylation in concert with the COPI machinery. Here, we show that Cex1, homologous to the mammalian SCYL proteins, is a component of the yeast COPI machinery, by interacting with Sec27, Sec28 and Sec33 (Ret1/Cop1) proteins of the COPI coat. Cex1 was initially reported to mediate channeling of aminoacylated tRNA outside of the nucleus. Our data show that Cex1 localizes at membrane compartments, on structures positive for the Sec33 α-COP subunit. Moreover, the Wbp1 protein required for N-glycosylation and interacting via its di-lysine motif with the Sec27 ß'-COP subunit is mis-targeted in cex1Δ deletion mutant cells. Our data point to the possibility of developing Cex1 yeast-based models to study neurodegenerative disorders linked to pathogenic mutations of its human homologue SCYL1.


Subject(s)
Coat Protein Complex I/metabolism , Fungal Proteins/metabolism , Nucleocytoplasmic Transport Proteins/metabolism , RNA-Binding Proteins/metabolism , Chromatography, Liquid , Coat Protein Complex I/genetics , Endoplasmic Reticulum/metabolism , Fungal Proteins/genetics , Gene Deletion , Golgi Apparatus/metabolism , Intracellular Space , Mass Spectrometry , Mutation , Nucleocytoplasmic Transport Proteins/genetics , Protein Binding , Protein Transport , Proteomics/methods , RNA-Binding Proteins/genetics
6.
Elife ; 92020 07 13.
Article in English | MEDLINE | ID: mdl-32657755

ABSTRACT

A single nuclear gene can be translated into a dual localized protein that distributes between the cytosol and mitochondria. Accumulating evidences show that mitoproteomes contain lots of these dual localized proteins termed echoforms. Unraveling the existence of mitochondrial echoforms using current GFP (Green Fluorescent Protein) fusion microscopy approaches is extremely difficult because the GFP signal of the cytosolic echoform will almost inevitably mask that of the mitochondrial echoform. We therefore engineered a yeast strain expressing a new type of Split-GFP that we termed Bi-Genomic Mitochondrial-Split-GFP (BiG Mito-Split-GFP). Because one moiety of the GFP is translated from the mitochondrial machinery while the other is fused to the nuclear-encoded protein of interest translated in the cytosol, the self-reassembly of this Bi-Genomic-encoded Split-GFP is confined to mitochondria. We could authenticate the mitochondrial importability of any protein or echoform from yeast, but also from other organisms such as the human Argonaute 2 mitochondrial echoform.


Subject(s)
Fungal Proteins/metabolism , Mitochondrial Proteins/metabolism , Saccharomyces cerevisiae/physiology , Cytosol/metabolism , Green Fluorescent Proteins/metabolism , Mitochondria/physiology , Protein Transport
7.
Proc Natl Acad Sci U S A ; 117(26): 14948-14957, 2020 06 30.
Article in English | MEDLINE | ID: mdl-32541034

ABSTRACT

Diverting aminoacyl-transfer RNAs (tRNAs) from protein synthesis is a well-known process used by a wide range of bacteria to aminoacylate membrane constituents. By tRNA-dependently adding amino acids to glycerolipids, bacteria change their cell surface properties, which intensifies antimicrobial drug resistance, pathogenicity, and virulence. No equivalent aminoacylated lipids have been uncovered in any eukaryotic species thus far, suggesting that tRNA-dependent lipid remodeling is a process restricted to prokaryotes. We report here the discovery of ergosteryl-3ß-O-l-aspartate (Erg-Asp), a conjugated sterol that is produced by the tRNA-dependent addition of aspartate to the 3ß-OH group of ergosterol, the major sterol found in fungal membranes. In fact, Erg-Asp exists in the majority of "higher" fungi, including species of biotechnological interest, and, more importantly, in human pathogens like Aspergillus fumigatus We show that a bifunctional enzyme, ergosteryl-3ß-O-l-aspartate synthase (ErdS), is responsible for Erg-Asp synthesis. ErdS corresponds to a unique fusion of an aspartyl-tRNA synthetase-that produces aspartyl-tRNAAsp (Asp-tRNAAsp)-and of a Domain of Unknown Function 2156, which actually transfers aspartate from Asp-tRNAAsp onto ergosterol. We also uncovered that removal of the Asp modifier from Erg-Asp is catalyzed by a second enzyme, ErdH, that is a genuine Erg-Asp hydrolase participating in the turnover of the conjugated sterol in vivo. Phylogenomics highlights that the entire Erg-Asp synthesis/degradation pathway is conserved across "higher" fungi. Given the central roles of sterols and conjugated sterols in fungi, we propose that this tRNA-dependent ergosterol modification and homeostasis system might have broader implications in membrane remodeling, trafficking, antimicrobial resistance, or pathogenicity.


Subject(s)
Aspartic Acid/metabolism , Aspergillus fumigatus/metabolism , RNA, Fungal/metabolism , RNA, Transfer, Amino Acyl/metabolism , Sterols/metabolism , Aminoacylation , Aspartic Acid/chemistry , Aspergillus fumigatus/chemistry , Aspergillus fumigatus/genetics , RNA, Fungal/chemistry , RNA, Fungal/genetics , RNA, Transfer, Amino Acyl/chemistry , RNA, Transfer, Amino Acyl/genetics , Sterols/chemistry
8.
Enzymes ; 48: 117-147, 2020.
Article in English | MEDLINE | ID: mdl-33837702

ABSTRACT

The aminoacylation reaction is one of most extensively studied cellular processes. The so-called "canonical" reaction is carried out by direct charging of an amino acid (aa) onto its corresponding transfer RNA (tRNA) by the cognate aminoacyl-tRNA synthetase (aaRS), and the canonical usage of the aminoacylated tRNA (aa-tRNA) is to translate a messenger RNA codon in a translating ribosome. However, four out of the 22 genetically-encoded aa are made "noncanonically" through a two-step or indirect route that usually compensate for a missing aaRS. Additionally, from the 22 proteinogenic aa, 13 are noncanonically used, by serving as substrates for the tRNA- or aa-tRNA-dependent synthesis of other cellular components. These nontranslational processes range from lipid aminoacylation, and heme, aa, antibiotic and peptidoglycan synthesis to protein degradation. This chapter focuses on these noncanonical usages of aa-tRNAs and the ways of generating them, and also highlights the strategies that cells have evolved to balance the use of aa-tRNAs between protein synthesis and synthesis of other cellular components.


Subject(s)
Amino Acyl-tRNA Synthetases , Transfer RNA Aminoacylation , Amino Acids , Amino Acyl-tRNA Synthetases/genetics , Amino Acyl-tRNA Synthetases/metabolism , Aminoacylation , RNA, Transfer/genetics , RNA, Transfer/metabolism
9.
Biochim Biophys Acta Gene Regul Mech ; 1861(4): 387-400, 2018 Apr.
Article in English | MEDLINE | ID: mdl-29155070

ABSTRACT

Prokaryotic and eukaryotic cytosolic aminoacyl-tRNA synthetases (aaRSs) are essentially known for their conventional function of generating the full set of aminoacyl-tRNA species that are needed to incorporate each organism's repertoire of genetically-encoded amino acids during ribosomal translation of messenger RNAs. However, bacterial and eukaryotic cytosolic aaRSs have been shown to exhibit other essential nonconventional functions. Here we review all the subcellular compartments that prokaryotic and eukaryotic cytosolic aaRSs can reach to exert either a conventional or nontranslational role. We describe the physiological and stress conditions, the mechanisms and the signaling pathways that trigger their relocation and the new functions associated with these relocating cytosolic aaRS. Finally, given that these relocating pools of cytosolic aaRSs participate to a wide range of cellular pathways beyond translation, but equally important for cellular homeostasis, we mention some of the pathologies and diseases associated with the dis-regulation or malfunctioning of these nontranslational functions.


Subject(s)
Amino Acids/metabolism , Amino Acyl-tRNA Synthetases/physiology , Cytosol/enzymology , RNA, Transfer/metabolism , Transfer RNA Aminoacylation/physiology , Amino Acyl-tRNA Synthetases/genetics , Animals , Bacterial Proteins/genetics , Bacterial Proteins/physiology , Biological Transport , Cytokines/biosynthesis , Eukaryotic Cells/enzymology , HIV/physiology , Host-Pathogen Interactions , Humans , Membrane Proteins/physiology , Mitochondria/metabolism , Mitochondrial Proteins/physiology , Neoplasm Proteins/physiology , Neovascularization, Physiologic/physiology , Phagocytosis/physiology , Prokaryotic Cells/enzymology , Protein Isoforms/physiology , Rous sarcoma virus/physiology , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/physiology , Species Specificity , Vertebrates/genetics , Vertebrates/metabolism
10.
Methods ; 113: 91-104, 2017 01 15.
Article in English | MEDLINE | ID: mdl-27725303

ABSTRACT

By definition, cytosolic aminoacyl-tRNA synthetases (aaRSs) should be restricted to the cytosol of eukaryotic cells where they supply translating ribosomes with their aminoacyl-tRNA substrates. However, it has been shown that other translationally-active compartments like mitochondria and plastids can simultaneously contain the cytosolic aaRS and its corresponding organellar ortholog suggesting that both forms do not share the same organellar function. In addition, a fair number of cytosolic aaRSs have also been found in the nucleus of cells from several species. Hence, these supposedly cytosolic-restricted enzymes have instead the potential to be multi-localized. As expected, in all examples that were studied so far, when the cytosolic aaRS is imported inside an organelle that already contains its bona fide corresponding organellar-restricted aaRSs, the cytosolic form was proven to exert a nonconventional and essential function. Some of these essential functions include regulating homeostasis and protecting against various stresses. It thus becomes critical to assess meticulously the subcellular localization of each of these cytosolic aaRSs to unravel their additional roles. With this objective in mind, we provide here a review on what is currently known about cytosolic aaRSs multi-compartmentalization and we describe all commonly used protocols and procedures for identifying the compartments in which cytosolic aaRSs relocalize in yeast and human cells.


Subject(s)
Amino Acyl-tRNA Synthetases/metabolism , Cell Nucleus/enzymology , Cytosol/enzymology , Mitochondria/enzymology , Ribosomes/enzymology , Saccharomyces cerevisiae/enzymology , Amino Acyl-tRNA Synthetases/classification , Amino Acyl-tRNA Synthetases/genetics , Antibodies/chemistry , Blotting, Western/methods , Cell Compartmentation , Cell Fractionation/methods , Cell Line , Cell Nucleus/ultrastructure , Cytosol/ultrastructure , Fluorescent Antibody Technique/methods , Gene Expression , Humans , Mitochondria/ultrastructure , Protein Transport , Ribosomes/ultrastructure , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/ultrastructure
11.
Mol Cell ; 56(6): 763-76, 2014 Dec 18.
Article in English | MEDLINE | ID: mdl-25453761

ABSTRACT

In eukaryotic cells, oxidative phosphorylation involves multisubunit complexes of mixed genetic origin. Assembling these complexes requires an organelle-independent synchronizing system for the proper expression of nuclear and mitochondrial genes. Here we show that proper expression of the F1FO ATP synthase (complex V) depends on a cytosolic complex (AME) made of two aminoacyl-tRNA synthetases (cERS and cMRS) attached to an anchor protein, Arc1p. When yeast cells adapt to respiration the Snf1/4 glucose-sensing pathway inhibits ARC1 expression triggering simultaneous release of cERS and cMRS. Free cMRS and cERS relocate to the nucleus and mitochondria, respectively, to synchronize nuclear transcription and mitochondrial translation of ATP synthase genes. Strains releasing asynchronously the two aminoacyl-tRNA synthetases display aberrant expression of nuclear and mitochondrial genes encoding subunits of complex V resulting in severe defects of the oxidative phosphorylation mechanism. This work shows that the AME complex coordinates expression of enzymes that require intergenomic control.


Subject(s)
Proton-Translocating ATPases/genetics , Saccharomyces cerevisiae/genetics , Cell Nucleus/genetics , Gene Expression , Gene Expression Regulation, Fungal , Mitochondria/genetics , Multienzyme Complexes , Protein Multimerization , Proton-Translocating ATPases/metabolism , RNA-Binding Proteins/physiology , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae Proteins/physiology
12.
FEBS Lett ; 588(23): 4268-78, 2014 Nov 28.
Article in English | MEDLINE | ID: mdl-25315413

ABSTRACT

Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous and ancient enzymes, mostly known for their essential role in generating aminoacylated tRNAs. During the last two decades, many aaRSs have been found to perform additional and equally crucial tasks outside translation. In metazoans, aaRSs have been shown to assemble, together with non-enzymatic assembly proteins called aaRSs-interacting multifunctional proteins (AIMPs), into so-called multi-synthetase complexes (MSCs). Metazoan MSCs are dynamic particles able to specifically release some of their constituents in response to a given stimulus. Upon their release from MSCs, aaRSs can reach other subcellular compartments, where they often participate to cellular processes that do not exploit their primary function of synthesizing aminoacyl-tRNAs. The dynamics of MSCs and the expansion of the aaRSs functional repertoire are features that are so far thought to be restricted to higher and multicellular eukaryotes. However, much can be learnt about how MSCs are assembled and function from apparently 'simple' organisms. Here we provide an overview on the diversity of these MSCs, their composition, mode of assembly and the functions that their constituents, namely aaRSs and AIMPs, exert in unicellular organisms.


Subject(s)
Amino Acyl-tRNA Synthetases/chemistry , Amino Acyl-tRNA Synthetases/metabolism , Evolution, Molecular , Protein Structure, Quaternary , Animals , Humans , Protein Structure, Tertiary , Species Specificity
13.
Nucleic Acids Res ; 42(9): 6052-63, 2014 May.
Article in English | MEDLINE | ID: mdl-24692665

ABSTRACT

Yeast mitochondrial Gln-mtRNAGln is synthesized by the transamidation of mischarged Glu-mtRNAGln by a non-canonical heterotrimeric tRNA-dependent amidotransferase (AdT). The GatA and GatB subunits of the yeast AdT (GatFAB) are well conserved among bacteria and eukaryota, but the GatF subunit is a fungi-specific ortholog of the GatC subunit found in all other known heterotrimeric AdTs (GatCAB). Here we report the crystal structure of yeast mitochondrial GatFAB at 2.0 Å resolution. The C-terminal region of GatF encircles the GatA-GatB interface in the same manner as GatC, but the N-terminal extension domain (NTD) of GatF forms several additional hydrophobic and hydrophilic interactions with GatA. NTD-deletion mutants displayed growth defects, but retained the ability to respire. Truncation of the NTD in purified mutants reduced glutaminase and transamidase activities when glutamine was used as the ammonia donor, but increased transamidase activity relative to the full-length enzyme when the donor was ammonium chloride. Our structure-based functional analyses suggest the NTD is a trans-acting scaffolding peptide for the GatA glutaminase active site. The positive surface charge and novel fold of the GatF-GatA interface, shown in this first crystal structure of an organellar AdT, stand in contrast with the more conventional, negatively charged bacterial AdTs described previously.


Subject(s)
Amino Acyl-tRNA Synthetases/chemistry , Mitochondrial Proteins/chemistry , Nitrogenous Group Transferases/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae/enzymology , Transaminases/chemistry , Catalytic Domain , Crystallography, X-Ray , Mitochondria/enzymology , Models, Molecular , Protein Binding , Protein Multimerization , Protein Structure, Quaternary , Protein Structure, Secondary , Protein Subunits/chemistry , RNA, Transfer/chemistry
14.
Nucleic Acids Res ; 41(6): 3901-14, 2013 Apr 01.
Article in English | MEDLINE | ID: mdl-23396276

ABSTRACT

In all eukaryotes, transcribed precursor tRNAs are maturated by processing and modification processes in nucleus and are transported to the cytoplasm. The cytoplasmic export protein (Cex1p) captures mature tRNAs from the nuclear export receptor (Los1p) on the cytoplasmic side of the nuclear pore complex, and it delivers them to eukaryotic elongation factor 1α. This conserved Cex1p function is essential for the quality control of mature tRNAs to ensure accurate translation. However, the structural basis of how Cex1p recognizes tRNAs and shuttles them to the translational apparatus remains unclear. Here, we solved the 2.2 Å resolution crystal structure of Saccharomyces cerevisiae Cex1p with C-terminal 197 disordered residues truncated. Cex1p adopts an elongated architecture, consisting of N-terminal kinase-like and a C-terminal α-helical HEAT repeat domains. Structure-based biochemical analyses suggested that Cex1p binds tRNAs on its inner side, using the positively charged HEAT repeat surface and the C-terminal disordered region. The N-terminal kinase-like domain acts as a scaffold to interact with the Ran-exportin (Los1p·Gsp1p) machinery. These results provide the structural basis of Los1p·Gsp1p·Cex1p·tRNA complex formation, thus clarifying the dynamic mechanism of tRNA shuttling from exportin to the translational apparatus.


Subject(s)
Models, Molecular , Nucleocytoplasmic Transport Proteins/chemistry , RNA, Transfer/metabolism , RNA-Binding Proteins/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Active Transport, Cell Nucleus , Cell Nucleus/metabolism , Crystallography, X-Ray , Cytoplasm/metabolism , Monomeric GTP-Binding Proteins/metabolism , Nuclear Pore Complex Proteins/metabolism , Nuclear Proteins/metabolism , Nucleocytoplasmic Transport Proteins/metabolism , Protein Binding , Protein Multimerization , Protein Structure, Tertiary , RNA-Binding Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism
15.
FEBS Lett ; 584(2): 427-33, 2010 Jan 21.
Article in English | MEDLINE | ID: mdl-19914242

ABSTRACT

Accurate synthesis of aminoacyl-tRNAs (aa-tRNA) by aminoacyl-tRNA synthetases (aaRS) is an absolute requirement for errorless decoding of the genetic code and is studied since more than four decades. In all three kingdoms of life aaRSs are capable of assembling into multi-enzymatic complexes that are held together by auxiliary non-enzymatic factors, but the role of such macromolecular assemblies is still poorly understood. In the yeast Saccharomyces cerevisiae, Arc1p holds cytosolic methionyl-tRNA synthetase ((c)MRS) and glutamyl-tRNA synthetase ((c)ERS) together and plays an important role in fine tuning several cellular processes like aminoacylation, translation and carbon source adaptation.


Subject(s)
Coenzymes/metabolism , Glutamate-tRNA Ligase/metabolism , RNA, Transfer, Amino Acyl/metabolism , RNA, Transfer/metabolism , RNA-Binding Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Cytosol/metabolism , Transfer RNA Aminoacylation
16.
Genes Dev ; 23(9): 1119-30, 2009 May 01.
Article in English | MEDLINE | ID: mdl-19417106

ABSTRACT

It is impossible to predict which pathway, direct glutaminylation of tRNA(Gln) or tRNA-dependent transamidation of glutamyl-tRNA(Gln), generates mitochondrial glutaminyl-tRNA(Gln) for protein synthesis in a given species. The report that yeast mitochondria import both cytosolic glutaminyl-tRNA synthetase and tRNA(Gln) has challenged the widespread use of the transamidation pathway in organelles. Here we demonstrate that yeast mitochondrial glutaminyl-tRNA(Gln) is in fact generated by a transamidation pathway involving a novel type of trimeric tRNA-dependent amidotransferase (AdT). More surprising is the fact that cytosolic glutamyl-tRNA synthetase ((c)ERS) is imported into mitochondria, where it constitutes the mitochondrial nondiscriminating ERS that generates the mitochondrial mischarged glutamyl-tRNA(Gln) substrate for the AdT. We show that dual localization of (c)ERS is controlled by binding to Arc1p, a tRNA nuclear export cofactor that behaves as a cytosolic anchoring platform for (c)ERS. Expression of Arc1p is down-regulated when yeast cells are switched from fermentation to respiratory metabolism, thus allowing increased import of (c)ERS to satisfy a higher demand of mitochondrial glutaminyl-tRNA(Gln) for mitochondrial protein synthesis. This novel strategy that enables a single protein to be localized in both the cytosol and mitochondria provides a new paradigm for regulation of the dynamic subcellular distribution of proteins between membrane-separated compartments.


Subject(s)
Glutamate-tRNA Ligase/metabolism , Mitochondria/enzymology , RNA, Transfer, Amino Acyl/metabolism , RNA-Binding Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae/metabolism , Transferases/metabolism , Cytoplasm/enzymology , Gene Expression Regulation, Fungal , Glutamic Acid/metabolism , Protein Binding , Protein Transport
17.
J Mol Biol ; 352(2): 355-69, 2005 Sep 16.
Article in English | MEDLINE | ID: mdl-16095611

ABSTRACT

Previous work suggested that the release of the nucleolar Tif6 from nascent 60 S subunits occurs in the cytoplasm and requires the cytoplasmic EF-2-like GTPase, Efl1. To check whether this release involves an rRNA structural rearrangement mediated by Efl1, we analyzed the rRNA conformation of the GTPase center of 80 S ribosomes in three contexts: wild-type, Deltaefl1 and a dominant suppressor R1 of Deltaefl1. This analysis was restricted to domain II and VI of 25 S rRNA. The rRNA analysis of R1 ribosomes allows us to distinguish the effects due to depletion of Efl1 from the resulting nucleolar deficit of Tif6. Efl1 inhibits the EF-2 GTPase activity, suggesting that the two proteins share a similar ribosome-binding site. The 80 S ribosomes from either type failed to show any difference of conformation in the two rRNA domains analyzed. However, the same analysis performed on the pool of free 60 S subunits reveals several rRNA conformational differences between wild-type and Deltaefl1 subunits, whereas that from the suppressor strain is similar to wild-type. This suggests that the nucleolar deficit of Tif6 during assembly of the 60 S preribosomes is responsible for the changes in rRNA conformation observed in Deltaefl1 60 S subunits. We also purified 60 S preribosomes from the three genetic contexts by TAP-tagging Tif6. The protein content of 60 S preribosomes associated with Tif6p in a Deltaefl1 strain are obtained at a lower yield but have, surprisingly, a protein composition that is a priori similar to that of wild-type and the suppressor strain.


Subject(s)
Carrier Proteins/metabolism , GTP Phosphohydrolases/metabolism , Intermediate Filament Proteins/metabolism , Phosphoproteins/metabolism , RNA, Fungal/metabolism , RNA, Ribosomal/metabolism , Ribosomal Proteins/metabolism , Ribosomes/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Binding Sites , Carrier Proteins/genetics , Intermediate Filament Proteins/genetics , Mutation , Nucleic Acid Conformation , Phosphoproteins/genetics , RNA, Fungal/genetics , RNA, Ribosomal/chemistry , RNA, Ribosomal/genetics , Ribosomal Proteins/genetics , Ribosomes/genetics , Saccharomyces cerevisiae Proteins/genetics , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
18.
Biochemistry ; 44(4): 1344-52, 2005 Feb 01.
Article in English | MEDLINE | ID: mdl-15667228

ABSTRACT

Yeast methionyl-tRNA synthetase (MetRS) and glutamyl-tRNA synthetase (GluRS) possess N-terminal extensions that bind the cofactor Arc1p in trans. The strength of GluRS-Arc1p interaction is high enough to allow copurification of the two macromolecules in a 1:1 ratio, in contrast to MetRS. Deletion analysis from the C-terminal end of the GluRS appendix combined with previous N-terminal deletions of GluRS allows restriction of the Arc1p binding site to the 110-170 amino acid region of GluRS. This region has been shown to correspond to a novel protein-protein interaction domain present in both GluRS and Arc1p but not in MetRS [Galani, K., Grosshans, H., Deinert, K., Hurt, E. C., and Simos, G. (2001) EMBO J. 20, 6889-6898]. The GluRS apoenzyme fails to show significant kinetics of tRNA aminoacylation and charges unfractionated yeast tRNA at a level 10-fold reduced compared to Arc1p-bound GluRS. The K(m) values for tRNA(Glu) measured in the ATP-PP(i) exchange were similar for the two forms of GluRS, whereas k(cat) is increased 2-fold in the presence of Arc1p. Band-shift analysis revealed a 100-fold increase in tRNA binding affinity when Arc1p is bound to GluRS. This increase requires the RNA binding properties of the full-length Arc1p since Arc1p N domain leaves the K(d) of GluRS for tRNA unchanged. Transcripts of yeast tRNA(Glu) were poor substrates for measuring tRNA aminoacylation and could not be used to clarify whether Arc1p has a specific effect on the tRNA charging reaction.


Subject(s)
Glutamate-tRNA Ligase/metabolism , RNA-Binding Proteins/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Adenosine Triphosphate/chemistry , Adenosine Triphosphate/metabolism , Amino Acid Sequence , Aminoacylation , Base Sequence , Diphosphates/chemistry , Diphosphates/metabolism , Enzyme Activation , Gene Expression Regulation, Fungal , Glutamate-tRNA Ligase/isolation & purification , Kinetics , Molecular Sequence Data , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Protein Binding , Protein Structure, Tertiary , RNA, Fungal/genetics , RNA, Fungal/metabolism , RNA, Transfer, Glu/genetics , RNA, Transfer, Glu/metabolism , RNA-Binding Proteins/isolation & purification , RNA-Binding Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/isolation & purification , Saccharomyces cerevisiae Proteins/metabolism , Transcription, Genetic
19.
Gene ; 313: 17-42, 2003 Aug 14.
Article in English | MEDLINE | ID: mdl-12957375

ABSTRACT

Ribosome synthesis is a highly complex and coordinated process that occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells. Based on the protein composition of several ribosomal subunit precursors recently characterized in yeast, a total of more than 170 factors are predicted to participate in ribosome biogenesis and the list is still growing. So far the majority of ribosomal factors have been implicated in RNA maturation (nucleotide modification and processing). Recent advances gave insight into the process of ribosome export and assembly. Proteomic approaches have provided the first indications for a ribosome assembly pathway in eukaryotes and confirmed the dynamic character of the whole process.


Subject(s)
Eukaryotic Cells/metabolism , Ribosomes/metabolism , Animals , Cell Nucleolus/genetics , Cell Nucleolus/metabolism , RNA, Ribosomal/genetics , RNA, Ribosomal/metabolism , Ribosomal Proteins/genetics , Ribosomal Proteins/metabolism , Ribosomes/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism
20.
FEMS Yeast Res ; 3(1): 35-43, 2003 Mar.
Article in English | MEDLINE | ID: mdl-12702244

ABSTRACT

An extensive homology search based on the sequence of the yeast protein Brx1p (biogenesis of ribosomes in Xenopus, YOL077c) revealed that it is a member of a superfamily of proteins sharing remarkable sequence similarities. Previous work on Brx1p showed that this protein is involved in the process of ribosome biogenesis [Kaser et al., Biol. Chem. 382 (2001) 1637-1647]. Brx1p is the founding member of one of the five existing eukaryotic subfamilies which are all present in yeast. Four of them are represented by one essential gene each and one family is represented by two closely related genes which can functionally replace each other but are essential together for survival. We created conditional alleles of four of the five genes which allowed us to study the effect of depletion of the respective proteins on the ribosome profiles of the strains. In this study we show that not only Brx1p but also three additional superfamily members, namely YHR088w (Rpf1p), YKR081c (Rpf2p) and the homologous proteins Ssf1p (YHR066w)/Ssf2p (YDR312w) are all involved in the multistep process of the assembly of the large ribosomal subunit. This agrees well with the fact that these three proteins, like Brx1p, are located in the nucleolus. Moreover, all four proteins closely interact functionally, because all four mutants are suppressed by the same multicopy suppressor gene.


Subject(s)
Cell Nucleolus/metabolism , RNA-Binding Proteins/physiology , Ribosomal Proteins/biosynthesis , Ribosomes/physiology , Saccharomyces cerevisiae Proteins/physiology , Saccharomyces cerevisiae/physiology , Genes, Suppressor , Organelle Biogenesis , Peptide Initiation Factors/metabolism , RNA-Binding Proteins/metabolism , Ribosomal Proteins/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism
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