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1.
PLoS One ; 18(11): e0293228, 2023.
Article in English | MEDLINE | ID: mdl-38011112

ABSTRACT

Translation initiation is a complex and highly regulated process that represents an important mechanism, controlling gene expression. eIF2A was proposed as an alternative initiation factor, however, its role and biological targets remain to be discovered. To further gain insight into the function of eIF2A in Saccharomyces cerevisiae, we identified mRNAs associated with the eIF2A complex and showed that 24% of the most enriched mRNAs encode proteins related to cell wall biogenesis and maintenance. In agreement with this result, we showed that an eIF2A deletion sensitized cells to cell wall damage induced by calcofluor white. eIF2A overexpression led to a growth defect, correlated with decreased synthesis of several cell wall proteins. In contrast, no changes were observed in the transcriptome, suggesting that eIF2A controls the expression of cell wall-related proteins at a translational level. The biochemical characterization of the eIF2A complex revealed that it strongly interacts with the RNA binding protein, Ssd1, which is a negative translational regulator, controlling the expression of cell wall-related genes. Interestingly, eIF2A and Ssd1 bind several common mRNA targets and we found that the binding of eIF2A to some targets was mediated by Ssd1. Surprisingly, we further showed that eIF2A is physically and functionally associated with the exonuclease Xrn1 and other mRNA degradation factors, suggesting an additional level of regulation. Altogether, our results highlight new aspects of this complex and redundant fine-tuned regulation of proteins expression related to the cell wall, a structure required to maintain cell shape and rigidity, providing protection against harmful environmental stress.


Subject(s)
Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , RNA, Messenger/metabolism , Cell Wall/genetics , Cell Wall/metabolism , Gene Expression , Gene Expression Regulation, Fungal
2.
MicroPubl Biol ; 20232023.
Article in English | MEDLINE | ID: mdl-37746059

ABSTRACT

mRNA degradation is one of the main steps of gene expression, and a key player is the 5'-3' exonuclease Xrn1. In Saccharomyces cerevisiae , it was previously shown, by a microscopy approach, that Xrn1 is located to different cellular compartments, depending on physiological state. During exponential growth, Xrn1 is distributed in the cytoplasm, while it co-localizes with eisosomes after the post-diauxic shift (PDS). Here, we biochemically characterize the Xrn1-associated complexes in different cellular states. We demonstrate that, after PDS, Xrn1 but not the decapping nor Lsm1-7/Pat1 complexes associates with eisosomal proteins, strengthening the model that sequestration of Xrn1 in eisosomes preserves mRNAs from degradation during PDS.

3.
Methods Mol Biol ; 2477: 225-236, 2022.
Article in English | MEDLINE | ID: mdl-35524120

ABSTRACT

Multiple protein complexes are fundamental parts of living systems. Identification of the components of these complexes and characterization of the molecular mechanisms that allow their formation, function, and regulation can be done by affinity purification of proteins and associated factors followed by mass spectrometry of peptides. Speed and specificity for the isolation of complexes from whole cell extracts improved over time, together with the reliable identification and quantification of proteins by mass spectrometry. Relative quantification of proteins in such samples can now be done to characterize even relatively nonabundant complexes. We describe here our experience with proteins fused with the Z domain, derived from staphylococcal protein A, and IgG affinity purification for the analysis of protein complexes involved in RNA metabolism in the budding yeast Saccharomyces cerevisiae. We illustrate the use of enrichment calculations for proteins in purified samples as a way to robust identification of protein partners. While the protocols presented here are specific for yeast, their principles can be applied to the study of protein complexes in any other organism.


Subject(s)
Proteins , Saccharomyces cerevisiae , Chromatography, Affinity/methods , Mass Spectrometry/methods , Peptides/chemistry , Proteins/metabolism , Saccharomyces cerevisiae/genetics
4.
EMBO J ; 40(1): e105179, 2021 01 04.
Article in English | MEDLINE | ID: mdl-33289941

ABSTRACT

In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. These comprise/include the large eIF3 complex, eIF3j (Hcr1 in yeast) and the ATP-binding cassette protein ABCE1 (Rli1 in yeast). The ATPase is mainly active as a recycling factor, but it can remain bound to the dissociated 40S subunit until formation of the next 43S pre-initiation complexes. However, its functional role and native architectural context remains largely enigmatic. Here, we present an architectural inventory of native yeast and human ABCE1-containing pre-initiation complexes by cryo-EM. We found that ABCE1 was mostly associated with early 43S, but also with later 48S phases of initiation. It adopted a novel hybrid conformation of its nucleotide-binding domains, while interacting with the N-terminus of eIF3j. Further, eIF3j occupied the mRNA entry channel via its ultimate C-terminus providing a structural explanation for its antagonistic role with respect to mRNA binding. Overall, the native human samples provide a near-complete molecular picture of the architecture and sophisticated interaction network of the 43S-bound eIF3 complex and the eIF2 ternary complex containing the initiator tRNA.


Subject(s)
ATP-Binding Cassette Transporters/metabolism , Ribosome Subunits, Small, Eukaryotic/metabolism , Cell Line , DNA-Binding Proteins/metabolism , Eukaryotic Initiation Factor-2/metabolism , HEK293 Cells , Humans , Protein Binding/physiology , Protein Biosynthesis/physiology , RNA, Messenger/metabolism , RNA, Transfer/metabolism , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism
5.
Nucleic Acids Res ; 48(10): 5670-5683, 2020 06 04.
Article in English | MEDLINE | ID: mdl-32329775

ABSTRACT

Human CWC27 is an uncharacterized splicing factor and mutations in its gene are linked to retinal degeneration and other developmental defects. We identify the splicing factor CWC22 as the major CWC27 partner. Both CWC27 and CWC22 are present in published Bact spliceosome structures, but no interacting domains are visible. Here, the structure of a CWC27/CWC22 heterodimer bound to the exon junction complex (EJC) core component eIF4A3 is solved at 3Å-resolution. According to spliceosomal structures, the EJC is recruited in the C complex, once CWC27 has left. Our 3D structure of the eIF4A3/CWC22/CWC27 complex is compatible with the Bact spliceosome structure but not with that of the C complex, where a CWC27 loop would clash with the EJC core subunit Y14. A CWC27/CWC22 building block might thus form an intermediate landing platform for eIF4A3 onto the Bact complex prior to its conversion into C complex. Knock-down of either CWC27 or CWC22 in immortalized retinal pigment epithelial cells affects numerous common genes, indicating that these proteins cooperate, targeting the same pathways. As the most up-regulated genes encode factors involved in inflammation, our findings suggest a possible link to the retinal degeneration associated with CWC27 deficiencies.


Subject(s)
Cyclophilins/chemistry , Eukaryotic Initiation Factor-4A/chemistry , RNA-Binding Proteins/chemistry , Spliceosomes/chemistry , Cell Line , Cyclophilins/genetics , Cyclophilins/metabolism , Eukaryotic Initiation Factor-4A/metabolism , Exons , Gene Knockdown Techniques , HeLa Cells , Humans , Inflammation/genetics , Models, Molecular , Protein Domains , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Retinal Pigment Epithelium/metabolism , Spliceosomes/metabolism
6.
EMBO J ; 38(14): e100640, 2019 07 15.
Article in English | MEDLINE | ID: mdl-31304628

ABSTRACT

The Ski2-Ski3-Ski8 (SKI) complex assists the RNA exosome during the 3' to 5' degradation of cytoplasmic transcripts. Previous reports showed that the SKI complex is involved in the 3' to 5' degradation of mRNAs, including 3' untranslated regions (UTRs) and devoid of ribosomes. Paradoxically, we recently showed that the SKI complex directly interacts with ribosomes during the co-translational mRNA decay and that this interaction is necessary for its RNA degradation promoting activity. Here, we characterised a new SKI-associated factor, Ska1, that associates with a subpopulation of the SKI complex. We showed that Ska1 is specifically involved in the degradation of long 3'UTR-containing mRNAs, poorly translated mRNAs as well as other RNA regions not associated with ribosomes, such as cytoplasmic lncRNAs. We further show that the overexpression of SKA1 antagonises the SKI-ribosome association. We propose that the Ska1-SKI complex assists the cytoplasmic exosome in the absence of direct association of the SKI complex with ribosomes.


Subject(s)
Exosome Multienzyme Ribonuclease Complex/metabolism , Ribosomes/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/genetics , 3' Untranslated Regions , 5' Untranslated Regions , Cytoplasm/genetics , RNA Stability , RNA, Fungal/chemistry , RNA, Long Noncoding/chemistry , RNA, Messenger/chemistry , Saccharomyces cerevisiae/metabolism
8.
EMBO J ; 37(21)2018 11 02.
Article in English | MEDLINE | ID: mdl-30275269

ABSTRACT

Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway involved in many cellular pathways and crucial for telomere maintenance and embryo development. Core NMD factors Upf1, Upf2 and Upf3 are conserved from yeast to mammals, but a universal NMD model is lacking. We used affinity purification coupled with mass spectrometry and an improved data analysis protocol to characterize the composition and dynamics of yeast NMD complexes in yeast (112 experiments). Unexpectedly, we identified two distinct complexes associated with Upf1: Upf1-23 (Upf1, Upf2, Upf3) and Upf1-decappingUpf1-decapping contained the mRNA decapping enzyme, together with Nmd4 and Ebs1, two proteins that globally affected NMD and were critical for RNA degradation mediated by the Upf1 C-terminal helicase region. The fact that Nmd4 association with RNA was partially dependent on Upf1-23 components and the similarity between Nmd4/Ebs1 and mammalian Smg5-7 proteins suggest that NMD operates through conserved, successive Upf1-23 and Upf1-decapping complexes. This model can be extended to accommodate steps that are missing in yeast, to serve for further mechanistic studies of NMD in eukaryotes.


Subject(s)
Models, Biological , Multiprotein Complexes/metabolism , Nonsense Mediated mRNA Decay , RNA Helicases/metabolism , RNA, Fungal/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Multiprotein Complexes/genetics , RNA Helicases/genetics , RNA, Fungal/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics
9.
Mol Biol Cell ; 28(9): 1165-1176, 2017 May 01.
Article in English | MEDLINE | ID: mdl-28298488

ABSTRACT

Protein quality control mechanisms eliminate defective polypeptides to ensure proteostasis and to avoid the toxicity of protein aggregates. In eukaryotes, the ribosome-bound quality control (RQC) complex detects aberrant nascent peptides that remain stalled in 60S ribosomal particles due to a dysfunction in translation termination. The RQC complex polyubiquitylates aberrant polypeptides and recruits a Cdc48 hexamer to extract them from 60S particles in order to escort them to the proteasome for degradation. Whereas the steps from stalled 60S recognition to aberrant peptide polyubiquitylation by the RQC complex have been described, the mechanism leading to proteasomal degradation of these defective translation products remains unknown. We show here that the RQC complex also exists as a ribosome-unbound complex during the escort of aberrant peptides to the proteasome. In addition, we identify a new partner of this light version of the RQC complex, the E3 ubiquitin ligase Tom1. Tom1 interacts with aberrant nascent peptides and is essential to limit their accumulation and aggregation in the absence of Rqc1; however, its E3 ubiquitin ligase activity is not required. Taken together, these results reveal new roles for Tom1 in protein quality control, aggregate prevention, and, therefore, proteostasis maintenance.


Subject(s)
Ribosomes/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/physiology , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/physiology , Cell Cycle Proteins/metabolism , Peptide Chain Termination, Translational/physiology , Peptides/metabolism , Proteasome Endopeptidase Complex/metabolism , Proteasome Endopeptidase Complex/physiology , Protein Biosynthesis , Proteolysis , RNA-Binding Proteins/metabolism , Ribosome Subunits, Large, Eukaryotic/metabolism , Ribosomes/physiology , Saccharomyces cerevisiae/metabolism , Ubiquitination
10.
Science ; 354(6318): 1431-1433, 2016 12 16.
Article in English | MEDLINE | ID: mdl-27980209

ABSTRACT

Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski complex directly associates with 80S ribosomes presenting a short mRNA 3' overhang. We determined the structure of an endogenous ribosome-Ski complex using cryo-electron microscopy (EM) with a local resolution of the Ski complex ranging from 4 angstroms (Å) in the core to about 10 Å for intrinsically flexible regions. Ribosome binding displaces the autoinhibitory domain of the Ski2 helicase, positioning it in an open conformation near the ribosomal mRNA entry tunnel. We observe that the mRNA 3' overhang is threaded directly from the small ribosomal subunit to the helicase channel of Ski2, primed for ongoing exosome-mediated 3'-5' degradation.


Subject(s)
DNA Helicases/ultrastructure , Exosome Multienzyme Ribonuclease Complex/ultrastructure , Nuclear Proteins/ultrastructure , RNA Stability , Ribosome Subunits, Large, Eukaryotic/ultrastructure , Saccharomyces cerevisiae Proteins/ultrastructure , Saccharomyces cerevisiae/enzymology , Cryoelectron Microscopy , Protein Conformation , RNA, Fungal/metabolism , RNA, Messenger/metabolism , RNA, Ribosomal/metabolism , Ribosome Subunits, Large, Eukaryotic/enzymology
11.
Nat Commun ; 7: 13582, 2016 12 05.
Article in English | MEDLINE | ID: mdl-27917880

ABSTRACT

The nucleotidyl cyclase toxin ExoY is one of the virulence factors injected by the Pseudomonas aeruginosa type III secretion system into host cells. Inside cells, it is activated by an unknown eukaryotic cofactor to synthesize various cyclic nucleotide monophosphates. ExoY-like adenylate cyclases are also found in Multifunctional-Autoprocessing Repeats-in-ToXin (MARTX) toxins produced by various Gram-negative pathogens. Here we demonstrate that filamentous actin (F-actin) is the hitherto unknown cofactor of ExoY. Association with F-actin stimulates ExoY activity more than 10,000 fold in vitro and results in stabilization of actin filaments. ExoY is recruited to actin filaments in transfected cells and alters F-actin turnover. Actin also activates an ExoY-like adenylate cyclase MARTX effector domain from Vibrio nigripulchritudo. Finally, using a yeast genetic screen, we identify actin mutants that no longer activate ExoY. Our results thus reveal a new sub-group within the class II adenylyl cyclase family, namely actin-activated nucleotidyl cyclase (AA-NC) toxins.


Subject(s)
Actins/metabolism , Bacterial Proteins/metabolism , Bacterial Toxins/metabolism , Glucosyltransferases/metabolism , Pseudomonas aeruginosa/metabolism , Actins/genetics , Bacterial Proteins/genetics , Bacterial Toxins/genetics , Glucosyltransferases/genetics , Mutation , Protein Binding , Pseudomonas aeruginosa/genetics , Pseudomonas aeruginosa/pathogenicity , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Type III Secretion Systems/genetics , Type III Secretion Systems/metabolism , Virulence/genetics
12.
Microb Drug Resist ; 22(6): 477-86, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27447281

ABSTRACT

The human gastric pathogen, Helicobacter pylori, is becoming increasingly resistant to most available antibiotics. Peptidoglycan (PG) metabolism is essential to eubacteria, hence, an excellent target for the development of new therapeutic strategies. However, our knowledge on PG metabolism in H. pylori remains poor. We have further characterized an isogenic mutant of the amiA gene encoding a N-acetylmuramoyl-l-alanyl amidase. The amiA mutant displayed long chains of unseparated cells, an impaired motility despite the presence of intact flagella and a tolerance to amoxicillin. Interestingly, the amiA mutant was impaired in colonizing the mouse stomach suggesting that AmiA is a valid target in H. pylori for the development of new antibiotics. Using reverse phase high-pressure liquid chromatography, we analyzed the PG muropeptide composition and glycan chain length distribution of strain 26695 and its amiA mutant. The analysis showed that H. pylori lacked muropeptides with a degree of cross-linking higher than dimeric muropeptides. The amiA mutant was also characterized by a decrease of muropeptides carrying 1,6-anhydro-N-acetylmuramic acid residues, which represent the ends of the glycan chains. This correlated with an increase of very long glycan strands in the amiA mutant. It is suggested that these longer glycan strands are trademarks of the division site. Taken together, we show that the low redundancy on genes involved in PG maturation supports H. pylori as an actractive alternative model to study PG metabolism and cell shape regulation.


Subject(s)
Amidohydrolases/metabolism , Bacterial Proteins/metabolism , Helicobacter Infections/pathology , Helicobacter pylori/enzymology , Peptidoglycan/metabolism , Amidohydrolases/genetics , Amoxicillin/pharmacology , Animals , Anti-Bacterial Agents/pharmacology , Bacterial Proteins/genetics , Cell Division , Gene Expression , Helicobacter Infections/drug therapy , Helicobacter Infections/microbiology , Helicobacter pylori/drug effects , Helicobacter pylori/genetics , Helicobacter pylori/pathogenicity , Mice , Mice, Inbred C57BL , Muramic Acids/chemistry , Muramic Acids/metabolism , Mutation , Peptidoglycan/chemistry , Stomach/drug effects , Stomach/microbiology , Stomach/pathology , Virulence
13.
J Biol Chem ; 291(23): 12245-53, 2016 Jun 03.
Article in English | MEDLINE | ID: mdl-27129255

ABSTRACT

Protein homeostasis is maintained by quality control mechanisms that detect and eliminate deficient translation products. Cytosolic defective proteins can arise from translation of aberrant mRNAs lacking a termination codon (NonStop) or containing a sequence that blocks translation elongation (No-Go), which results in translational arrest. Stalled ribosomes are dissociated, aberrant mRNAs are degraded by the cytoplasmic exosome, and the nascent peptides remaining in stalled 60S exit tunnels are detected by the ribosome-bound quality control complex (RQC) composed of Ltn1, Rqc1, Rqc2, and Cdc48. Whereas Ltn1 polyubiquitylates these nascent peptides, Rqc2 directs the addition of C-terminal alanine-threonine tails (CAT-tails), and a Cdc48 hexamer is recruited to extract the nascent peptides, which are addressed to the proteasome for degradation. Although the functions of most RQC components have been described, the role of Rqc1 in this quality control process remains undetermined. In this article we show that the absence of Rqc1 or Ltn1 results in the aggregation of aberrant proteins, a phenomenon that requires CAT-tail addition to the nascent peptides by Rqc2. Our results suggest that aberrant CAT-tailed protein aggregation results from a defect in Cdc48 recruitment to stalled 60S particles, a process that requires both Rqc1 and Ltn1. These protein aggregates contain Ltn1-dependent polyubiquitin chains and are degraded by the proteasome. Finally, aggregate characterization by proteomics revealed that they contain specific chaperones including Sis1, Sgt2, Ssa1/2, and Hsp82, suggesting that these protein aggregates may be addressed to aggresome-like structures when the RQC complex fails to deliver aberrant nascent peptides to the proteasome for degradation.


Subject(s)
Adenosine Triphosphatases/metabolism , Cell Cycle Proteins/metabolism , Ribosome Subunits, Large, Eukaryotic/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , Adenosine Triphosphatases/chemistry , Adenosine Triphosphatases/genetics , Alanine/chemistry , Alanine/genetics , Alanine/metabolism , Blotting, Western , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/genetics , Microscopy, Fluorescence , Mutation , Proteasome Endopeptidase Complex/metabolism , Protein Aggregates , Protein Biosynthesis/genetics , Proteolysis , Proteomics/methods , RNA-Binding Proteins/chemistry , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Ribosome Subunits, Large, Eukaryotic/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Threonine/chemistry , Threonine/genetics , Threonine/metabolism , Ubiquitin-Protein Ligases/chemistry , Ubiquitin-Protein Ligases/genetics , Ubiquitination , Valosin Containing Protein
14.
Mol Cell Proteomics ; 13(7): 1769-86, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24741115

ABSTRACT

Cilia and flagella are complex organelles made of hundreds of proteins of highly variable structures and functions. Here we report the purification of intact flagella from the procyclic stage of Trypanosoma brucei using mechanical shearing. Structural preservation was confirmed by transmission electron microscopy that showed that flagella still contained typical elements such as the membrane, the axoneme, the paraflagellar rod, and the intraflagellar transport particles. It also revealed that flagella severed below the basal body, and were not contaminated by other cytoskeletal structures such as the flagellar pocket collar or the adhesion zone filament. Mass spectrometry analysis identified a total of 751 proteins with high confidence, including 88% of known flagellar components. Comparison with the cell debris fraction revealed that more than half of the flagellum markers were enriched in flagella and this enrichment criterion was taken into account to identify 212 proteins not previously reported to be associated to flagella. Nine of these were experimentally validated including a 14-3-3 protein not yet reported to be associated to flagella and eight novel proteins termed FLAM (FLAgellar Member). Remarkably, they localized to five different subdomains of the flagellum. For example, FLAM6 is restricted to the proximal half of the axoneme, no matter its length. In contrast, FLAM8 is progressively accumulating at the distal tip of growing flagella and half of it still needs to be added after cell division. A combination of RNA interference and Fluorescence Recovery After Photobleaching approaches demonstrated very different dynamics from one protein to the other, but also according to the stage of construction and the age of the flagellum. Structural proteins are added to the distal tip of the elongating flagellum and exhibit slow turnover whereas membrane proteins such as the arginine kinase show rapid turnover without a detectible polarity.


Subject(s)
Flagella/metabolism , Membrane Proteins/analysis , Protozoan Proteins/analysis , Trypanosoma brucei brucei/metabolism , 14-3-3 Proteins/genetics , 14-3-3 Proteins/metabolism , Fluorescence Recovery After Photobleaching , Gene Expression Profiling , Membrane Proteins/genetics , Membrane Proteins/metabolism , Microscopy, Electron, Transmission , Proteomics , Protozoan Proteins/genetics , Protozoan Proteins/metabolism , RNA Interference , RNA, Small Interfering
15.
Protein J ; 33(1): 61-74, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24384926

ABSTRACT

Three-step chromatography and proteomic analysis have been used to purify and characterize a new basic phospholipase A2 named CC2-PLA2 from the venom of Cerastes cerastes. This phospholipase A2 has been isolated to an extent of about 50-folds and its molecular weight was estimated at 13,534 Da. For CC2-PLA2 identification and LC-MALDI-MS/MS analysis, the protein was reduced, alkylated and double hydrolyzed by lysine-C endopeptidase and trypsin. Tryptic fragments of LC-MS/MS analyzed CC2-PLA2 showed sequence similarities with other snake venom PLA2. This presents only 51 % (61/120 amino acid residues) sequence homology with the first PLA2 (gi |129506|) previously purified from the same venom. The isolated CC2-PLA2 displayed anti-aggregative effect on platelets and induced an inflammatory response characterized by leukocytosis in the peripheral blood. This inflammatory response is accompanied by a release of inflammatory mediators such as IL-6, eosinophil peroxidase and complement system. Obtained results indicate that CC2-PLA2 induced a release of high level of pro-inflammatory (IL-6) cytokine and no effect on the level of anti-inflammatory cytokine (IL-10) in blood sera. Furthermore, eosinophil peroxidase activity and hemolytic complement effect increased in peripheral blood. Mononuclear and neutrophil cells were found predominant in the induced leucocytosis following CC2-PLA2 administration into animals.


Subject(s)
DNA-Binding Proteins/chemistry , Endosomal Sorting Complexes Required for Transport/chemistry , Phospholipases A2/chemistry , Platelet Activating Factor/chemistry , Transcription Factors/chemistry , Viper Venoms/chemistry , Animals , DNA-Binding Proteins/metabolism , Endosomal Sorting Complexes Required for Transport/metabolism , Interleukin-10/chemistry , Interleukin-10/metabolism , Phospholipases A2/metabolism , Platelet Activating Factor/metabolism , Proteomics , Tandem Mass Spectrometry , Transcription Factors/metabolism , Viperidae/metabolism
16.
J Proteomics ; 96: 29-43, 2014 Jan 16.
Article in English | MEDLINE | ID: mdl-24189444

ABSTRACT

In Europe, Ixodes ricinus is the main vector of Lyme borreliosis. Their salivary glands play a critical role in the biological success of ticks. To better understand the cross-talk between Borrelia burgdorferi and tick salivary glands, we analyzed protein expression in the salivary glands of I. ricinus adult ticks that were infected by various strains of the B. burgdorferi sl complex. iTRAQ allowed the identification of more than 120 proteins, providing the first proteomic data pertaining to I. ricinus salivary glands. Among these proteins, only 12 were modulated in the presence of various Borrelia strains. Most of them are up-regulated and are involved in cell defense and protein synthesis and processing. Down-regulated proteins are mostly implicated in the cytoskeleton. The DIGE analysis allowed us to identify 35 proteins and showed the down-regulation of 4 proteins. All 15 proteins were not modulated by all strains. Overall, these observations showed that the presence of Borrelia in tick salivary glands is a factor of stress for the protein machinery, and also that some Borrelia strains produce a dysregulation of cytoskeletal proteins. Interestingly, a protein from Borrelia, OspA, was found in infected salivary glands. The consequence of its presence in salivary glands is discussed. BIOLOGICAL SIGNIFICANCE: Lyme borreliosis is still the most prevalent arthropod-borne disease in the temperate regions of the northern hemisphere. The geographical distribution of Lyme borreliosis is expanding, especially towards higher altitudes and latitudes. Human pathogenic spirochetes causing Lyme borreliosis belong to the B. burgdorferi sensu lato complex. They are extracellular pathogens transmitted to humans through the bite of Ixodes spp. ticks. The bioactive molecules present in tick saliva not only promote tick feeding, but also create an advantageous microenvironment at the tick bite site for survival and replication of Borrelia bacteria. Investigation of the tick-host-pathogen interface would provide new strategies to control tick-borne infections. We chose to analyze the interaction of several strains of the B. burgdorferi sensu lato complex with I. ricinus salivary glands. We also investigated the presence of bacterial proteins in salivary glands. For these purposes, we undertook a proteomic study implying the complementary approaches of iTRAQ and DIGE. Our study allowed identifying several salivary markers of infection that were shown to vary according to the strain. Moreover, OspA, a bacterial protein was shown to be expressed in salivary glands and may be implied in the pathogenicity of some Borrelia strains.


Subject(s)
Arachnid Vectors/metabolism , Arthropod Proteins/biosynthesis , Borrelia burgdorferi Group , Gene Expression Regulation , Ixodes/metabolism , Salivary Glands/metabolism , Salivary Proteins and Peptides/biosynthesis , Animals , Arachnid Vectors/microbiology , Female , Humans , Ixodes/microbiology , Lyme Disease/metabolism , Lyme Disease/transmission , Mice , Salivary Glands/microbiology
17.
Nucleic Acids Res ; 41(20): 9461-70, 2013 Nov.
Article in English | MEDLINE | ID: mdl-23945946

ABSTRACT

Ribosome biogenesis requires >300 assembly factors in Saccharomyces cerevisiae. Ribosome assembly factors Imp3, Mrt4, Rlp7 and Rlp24 have sequence similarity to ribosomal proteins S9, P0, L7 and L24, suggesting that these pre-ribosomal factors could be placeholders that prevent premature assembly of the corresponding ribosomal proteins to nascent ribosomes. However, we found L7 to be a highly specific component of Rlp7-associated complexes, revealing that the two proteins can bind simultaneously to pre-ribosomal particles. Cross-linking and cDNA analysis experiments showed that Rlp7 binds to the ITS2 region of 27S pre-rRNAs, at two sites, in helix III and in a region adjacent to the pre-rRNA processing sites C1 and E. However, L7 binds to mature 25S and 5S rRNAs and cross-linked predominantly to helix ES7(L)b within 25S rRNA. Thus, despite their predicted structural similarity, our data show that Rlp7 and L7 clearly bind at different positions on the same pre-60S particles. Our results also suggest that Rlp7 facilitates the formation of the hairpin structure of ITS2 during 60S ribosomal subunit maturation.


Subject(s)
RNA, Ribosomal/metabolism , Ribosomal Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Base Sequence , Binding Sites , Molecular Sequence Data , RNA Precursors/chemistry , RNA Precursors/metabolism , RNA, Ribosomal/chemistry , RNA, Ribosomal, 5S/chemistry , RNA, Ribosomal, 5S/metabolism , Ribosome Subunits, Large, Eukaryotic/chemistry
18.
Proc Natl Acad Sci U S A ; 110(13): 5046-51, 2013 Mar 26.
Article in English | MEDLINE | ID: mdl-23479637

ABSTRACT

Ribosome stalling on eukaryotic mRNAs triggers cotranslational RNA and protein degradation through conserved mechanisms. For example, mRNAs lacking a stop codon are degraded by the exosome in association with its cofactor, the SKI complex, whereas the corresponding aberrant nascent polypeptides are ubiquitinated by the E3 ligases Ltn1 and Not4 and become proteasome substrates. How translation arrest is linked with polypeptide degradation is still unclear. Genetic screens with SKI and LTN1 mutants allowed us to identify translation-associated element 2 (Tae2) and ribosome quality control 1 (Rqc1), two factors that we found associated, together with Ltn1 and the AAA-ATPase Cdc48, to 60S ribosomal subunits. Translation-associated element 2 (Tae2), Rqc1, and Cdc48 were all required for degradation of polypeptides synthesized from Non-Stop mRNAs (Non-Stop protein decay; NSPD). Both Ltn1 and Rqc1 were essential for the recruitment of Cdc48 to 60S particles. Polysome gradient analyses of mutant strains revealed unique intermediates of this pathway, showing that the polyubiquitination of Non-Stop peptides is a progressive process. We propose that ubiquitination of the nascent peptide starts on the 80S and continues on the 60S, on which Cdc48 is recruited to escort the substrate for proteasomal degradation.


Subject(s)
Adenosine Triphosphatases/metabolism , Cell Cycle Proteins/metabolism , Protein Biosynthesis/physiology , Proteolysis , Ribosome Subunits, Large, Eukaryotic/metabolism , Saccharomyces cerevisiae/metabolism , Ubiquitination/physiology , Adenosine Triphosphatases/genetics , Cell Cycle Proteins/genetics , Proteasome Endopeptidase Complex/genetics , Proteasome Endopeptidase Complex/metabolism , RNA-Binding Proteins , Repressor Proteins , Ribosome Subunits, Large, Eukaryotic/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Valosin Containing Protein
19.
Nucleic Acids Res ; 41(1): 288-301, 2013 Jan 07.
Article in English | MEDLINE | ID: mdl-23093592

ABSTRACT

Protein complexes directing messenger RNA (mRNA) degradation are present in all kingdoms of life. In Escherichia coli, mRNA degradation is performed by an RNA degradosome organized by the major ribonuclease RNase E. In bacteria lacking RNase E, the existence of a functional RNA degradosome is still an open question. Here, we report that in the bacterial pathogen Helicobacter pylori, RNA degradation is directed by a minimal RNA degradosome consisting of Hp-RNase J and the only DExD-box RNA helicase of H. pylori, RhpA. We show that the protein complex promotes faster degradation of double-stranded RNA in vitro in comparison with Hp-RNase J alone. The ATPase activity of RhpA is stimulated in the presence of Hp-RNase J, demonstrating that the catalytic capacity of both partners is enhanced upon interaction. Remarkably, both proteins are associated with translating ribosomes and not with individual 30S and 50S subunits. Moreover, Hp-RNase J is not recruited to ribosomes to perform rRNA maturation. Together, our findings imply that in H. pylori, the mRNA-degrading machinery is associated with the translation apparatus, a situation till now thought to be restricted to eukaryotes and archaea.


Subject(s)
Endoribonucleases/metabolism , Helicobacter pylori/enzymology , Multienzyme Complexes/metabolism , Polyribonucleotide Nucleotidyltransferase/metabolism , RNA Helicases/metabolism , RNA, Messenger/metabolism , Ribosomes/enzymology , Adenosine Triphosphatases/metabolism , Bacillus subtilis/enzymology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Endoribonucleases/genetics , Endoribonucleases/isolation & purification , Helicobacter pylori/genetics , Helicobacter pylori/growth & development , Membrane Transport Proteins/genetics , Membrane Transport Proteins/metabolism , Mutation , Protein Biosynthesis , RNA Helicases/isolation & purification , RNA, Double-Stranded/metabolism , RNA, Ribosomal/metabolism
20.
Parasit Vectors ; 5: 264, 2012 Nov 15.
Article in English | MEDLINE | ID: mdl-23153178

ABSTRACT

BACKGROUND: Arthropod-borne viral infections cause several emerging and resurging infectious diseases. Among the diseases caused by arboviruses, chikungunya is responsible for a high level of severe human disease worldwide. The salivary glands of mosquitoes are the last barrier before pathogen transmission. METHODS: We undertook a proteomic approach to characterize the key virus/vector interactions and host protein modifications that occur in the salivary glands that could be responsible for viral transmission by using quantitative two-dimensional electrophoresis. RESULTS: We defined the protein modulations in the salivary glands of Aedes aegypti that were triggered 3 and 5 days after an oral infection (3 and 5 DPI) with chikungunya virus (CHIKV). Gel profile comparisons showed that CHIKV at 3 DPI modulated the level of 13 proteins, and at 5 DPI 20 proteins. The amount of 10 putatively secreted proteins was regulated at both time points. These proteins were implicated in blood-feeding or in immunity, but many have no known function. CHIKV also modulated the quantity of proteins involved in several metabolic pathways and in cell signalling. CONCLUSION: Our study constitutes the first analysis of the protein response of Aedes aegypti salivary glands infected with CHIKV. We found that the differentially regulated proteins in response to viral infection include structural proteins and enzymes for several metabolic pathways. Some may favour virus survival, replication and transmission, suggesting a subversion of the insect cell metabolism by arboviruses. For example, proteins involved in blood-feeding such as the short D7, an adenosine deaminase and inosine-uridine preferring nucleoside hydrolase, may favour virus transmission by exerting an increased anti-inflammatory effect. This would allow the vector to bite without the bite being detected. Other proteins, like the anti-freeze protein, may support vector protection.


Subject(s)
Aedes/virology , Alphavirus Infections/transmission , Chikungunya virus/physiology , Insect Proteins/metabolism , Insect Vectors/virology , Proteomics , Aedes/metabolism , Aedes/physiology , Alphavirus Infections/virology , Animals , Chikungunya Fever , Electrophoresis, Gel, Two-Dimensional , Female , Host-Pathogen Interactions , Humans , Insect Proteins/isolation & purification , Insect Vectors/metabolism , Insect Vectors/physiology , Mass Spectrometry , RNA, Viral/analysis , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction , Salivary Glands/virology
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