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1.
Sci Rep ; 14(1): 14815, 2024 06 27.
Article in English | MEDLINE | ID: mdl-38937573

ABSTRACT

The association of postpartum cardiac reverse remodeling (RR) with urinary proteome, particularly in pregnant women with cardiovascular (CV) risk factors who show long-term increased risk of cardiovascular disease and mortality is unknown. We aim to profile the urinary proteome in pregnant women with/without CV risk factors to identify proteins associated with postpartum RR. Our study included a prospective cohort of 32 healthy and 27 obese and/or hypertensive and/or diabetic pregnant women who underwent transthoracic echocardiography, pulse-wave-velocity, and urine collection at the 3rd trimester and 6 months postpartum. Shotgun HPLC-MS/MS profiled proteins. Generalized linear mixed-effects models were used to identify associations between urinary proteins and left ventricle mass (LVM), a surrogate of RR. An increase in arterial stiffness was documented from 3rd trimester to 6 months after delivery, being significantly elevated in women with CV risk factors. In addition, the presence of at least one CV risk factor was associated with worse LVM RR. We identified 6 and 11 proteins associated with high and low LVM regression, respectively. These proteins were functionally linked with insulin-like growth factor (IGF) transport and uptake regulation by IGF binding-proteins, platelet activation, signaling and aggregation and the immune system's activity. The concentration of IGF-1 in urine samples was associated with low LVM regression after delivery. Urinary proteome showed a predicting potential for identifying pregnant women with incomplete postpartum RR.


Subject(s)
Postpartum Period , Proteome , Ventricular Remodeling , Humans , Female , Pregnancy , Adult , Proteome/analysis , Postpartum Period/urine , Prospective Studies , Biomarkers/urine , Vascular Stiffness , Echocardiography , Risk Factors
2.
Methods Mol Biol ; 2808: 89-103, 2024.
Article in English | MEDLINE | ID: mdl-38743364

ABSTRACT

The study of virus-host interactions is essential to achieve a comprehensive understanding of the viral replication process. The commonly used methods are yeast two-hybrid approach and transient expression of a single tagged viral protein in host cells followed by affinity purification of interacting cellular proteins and mass spectrometry analysis (AP-MS). However, by these approaches, virus-host protein-protein interactions are detected in the absence of a real infection, not always correctly compartmentalized, and for the yeast two-hybrid approach performed in a heterologous system. Thus, some of the detected protein-protein interactions may be artificial. Here we describe a new strategy based on recombinant viruses expressing tagged viral proteins to capture both direct and indirect protein partners during the infection (AP-MS in viral context). This way, virus-host protein-protein interacting co-complexes can be purified directly from infected cells for further characterization.


Subject(s)
Host-Pathogen Interactions , Measles virus , Reverse Genetics , Viral Proteins , Measles virus/genetics , Humans , Host-Pathogen Interactions/genetics , Reverse Genetics/methods , Viral Proteins/metabolism , Viral Proteins/genetics , Two-Hybrid System Techniques , Virus Replication , Mass Spectrometry , Protein Interaction Mapping/methods , Measles/virology , Measles/metabolism , Animals , Protein Binding
3.
Nucleic Acids Res ; 52(12): 7188-7210, 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38686810

ABSTRACT

Genome-wide approaches have significantly advanced our knowledge of the repertoire of RNA-binding proteins (RBPs) that associate with cellular polyadenylated mRNAs within eukaryotic cells. Recent studies focusing on the RBP interactomes of viral mRNAs, notably SARS-Cov-2, have revealed both similarities and differences between the RBP profiles of viral and cellular mRNAs. However, the RBPome of influenza virus mRNAs remains unexplored. Herein, we identify RBPs that associate with the viral mRNA encoding the nucleoprotein (NP) of an influenza A virus. Focusing on TDP-43, we show that it binds several influenza mRNAs beyond the NP-mRNA, and that its depletion results in lower levels of viral mRNAs and proteins within infected cells, and a decreased yield of infectious viral particles. We provide evidence that the viral polymerase recruits TDP-43 onto viral mRNAs through a direct interaction with the disordered C-terminal domain of TDP-43. Notably, other RBPs found to be associated with influenza virus mRNAs also interact with the viral polymerase, which points to a role of the polymerase in orchestrating the assembly of viral messenger ribonucleoproteins.


Subject(s)
DNA-Binding Proteins , Influenza A virus , RNA, Messenger , RNA, Viral , RNA-Binding Proteins , Virus Replication , Humans , Virus Replication/genetics , RNA, Viral/metabolism , RNA, Viral/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , RNA, Messenger/metabolism , RNA, Messenger/genetics , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Influenza A virus/genetics , Influenza A virus/physiology , Influenza A virus/metabolism , Nucleocapsid Proteins/metabolism , Nucleocapsid Proteins/genetics , HEK293 Cells , Viral Core Proteins/metabolism , Viral Core Proteins/genetics , Protein Binding , Animals
4.
Nat Commun ; 14(1): 8072, 2023 Dec 06.
Article in English | MEDLINE | ID: mdl-38057323

ABSTRACT

In the gastric pathogen Helicobacter pylori, post-transcriptional regulation relies strongly on the activity of the essential ribonuclease RNase J. Here, we elucidated the crystal and cryo-EM structures of RNase J and determined that it assembles into dimers and tetramers in vitro. We found that RNase J extracted from H. pylori is acetylated on multiple lysine residues. Alanine substitution of several of these residues impacts on H. pylori morphology, and thus on RNase J function in vivo. Mutations of Lysine 649 modulates RNase J oligomerization in vitro, which in turn influences ribonuclease activity in vitro. Our structural analyses of RNase J reveal loops that gate access to the active site and rationalizes how acetylation state of K649 can influence activity. We propose acetylation as a regulatory level controlling the activity of RNase J and its potential cooperation with other enzymes of RNA metabolism in H. pylori.


Subject(s)
Helicobacter pylori , Ribonucleases , Ribonucleases/metabolism , Helicobacter pylori/genetics , Acetylation , Lysine/metabolism , Endoribonucleases/metabolism , Ribonuclease, Pancreatic/metabolism
5.
PLoS One ; 18(9): e0291736, 2023.
Article in English | MEDLINE | ID: mdl-37713445

ABSTRACT

In many Gram-negative bacteria, the stress sigma factor of RNA polymerase, σS/RpoS, remodels global gene expression to reshape the physiology of stationary phase cells and ensure their survival under non-optimal growth conditions. In the foodborne pathogen Salmonella enterica serovar Typhimurium, σS is also required for biofilm formation and virulence. We have recently shown that a ΔrpoS mutation decreases the magnesium content and expression level of the housekeeping Mg2+-transporter CorA in stationary phase Salmonella. The other two Mg2+-transporters of Salmonella are encoded by the PhoP-activated mgtA and mgtB genes and are expressed under magnesium starvation. The σS control of corA prompted us to evaluate the impact of CorA in stationary phase Salmonella cells, by using global and analytical proteomic analyses and physiological assays. The ΔcorA mutation conferred a competitive disadvantage to exit from stationary phase, and slightly impaired motility, but had no effect on total and free cellular magnesium contents. In contrast to the wild-type strain, the ΔcorA mutant produced MgtA, but not MgtB, in the presence of high extracellular magnesium concentration. Under these conditions, MgtA production in the ΔcorA mutant did not require PhoP. Consistently, a ΔmgtA, but not a ΔphoP, mutation slightly reduced the magnesium content of the ΔcorA mutant. Synthetic phenotypes were observed when the ΔphoP and ΔcorA mutations were combined, including a strong reduction in growth and motility, independently of the extracellular magnesium concentration. The abundance of several proteins involved in flagella formation, chemotaxis and secretion was lowered by the ΔcorA and ΔphoP mutations in combination, but not alone. These findings unravel the importance of PhoP-dependent functions in the absence of CorA when magnesium is sufficient. Altogether, our data pinpoint a regulatory network, where the absence of CorA is sensed by the cell and compensated by MgtA and PhoP- dependent mechanisms.


Subject(s)
Agaricales , Magnesium , Proteomics , Salmonella typhimurium/genetics , Biological Assay , Membrane Transport Proteins
6.
Microbes Infect ; 25(7): 105152, 2023.
Article in English | MEDLINE | ID: mdl-37245862

ABSTRACT

INTRODUCTION: Bordetella pertussis still circulates worldwide despite vaccination. Fimbriae are components of some acellular pertussis vaccines. Population fluctuations of B. pertussis fimbrial serotypes (FIM2 and FIM3) are observed, and fim3 alleles (fim3-1 [clade 1] and fim3-2 [clade 2]) mark a major phylogenetic subdivision of B. pertussis. OBJECTIVES: To compare microbiological characteristics and expressed protein profiles between fimbrial serotypes FIM2 and FIM3 and genomic clades. METHODS: A total of 19 isolates were selected. Absolute protein abundance of the main virulence factors, autoagglutination and biofilm formation, bacterial survival in whole blood, induced blood cell cytokine secretion, and global proteome profiles were assessed. RESULTS: Compared to FIM3, FIM2 isolates produced more fimbriae, less cellular pertussis toxin subunit 1 and more biofilm, but auto-agglutinated less. FIM2 isolates had a lower survival rate in cord blood, but induced higher levels of IL-4, IL-8 and IL-1ß secretion. Global proteome comparisons uncovered 15 differentially produced proteins between FIM2 and FIM3 isolates, involved in adhesion and metabolism of metals. FIM3 isolates of clade 2 produced more FIM3 and more biofilm compared to clade 1. CONCLUSION: FIM serotype and fim3 clades are associated with proteomic and other biological differences, which may have implications on pathogenesis and epidemiological emergence.


Subject(s)
Bordetella pertussis , Whooping Cough , Humans , Serogroup , Fimbriae Proteins/genetics , Phylogeny , Proteome/genetics , Proteomics , Virulence Factors, Bordetella/genetics , Pertussis Vaccine , Fimbriae, Bacterial/genetics , Fimbriae, Bacterial/metabolism
7.
Mol Cell Proteomics ; 21(11): 100428, 2022 11.
Article in English | MEDLINE | ID: mdl-36252736

ABSTRACT

Clostridioides difficile is the leading cause of postantibiotic diarrhea in adults. During infection, the bacterium must rapidly adapt to the host environment by using survival strategies. Protein phosphorylation is a reversible post-translational modification employed ubiquitously for signal transduction and cellular regulation. Hanks-type serine/threonine kinases (STKs) and serine/threonine phosphatases have emerged as important players in bacterial cell signaling and pathogenicity. C. difficile encodes two STKs (PrkC and CD2148) and one phosphatase. We optimized a titanium dioxide phosphopeptide enrichment approach to determine the phosphoproteome of C. difficile. We identified and quantified 2500 proteins representing 63% of the theoretical proteome. To identify STK and serine/threonine phosphatase targets, we then performed comparative large-scale phosphoproteomics of the WT strain and isogenic ΔprkC, CD2148, Δstp, and prkC CD2148 mutants. We detected 635 proteins containing phosphorylated peptides. We showed that PrkC is phosphorylated on multiple sites in vivo and autophosphorylates in vitro. We were unable to detect a phosphorylation for CD2148 in vivo, whereas this kinase was phosphorylated in vitro only in the presence of PrkC. Forty-one phosphoproteins were identified as phosphorylated under the control of CD2148, whereas 114 proteins were phosphorylated under the control of PrkC including 27 phosphoproteins more phosphorylated in the ∆stp mutant. We also observed enrichment for phosphothreonine among the phosphopeptides more phosphorylated in the Δstp mutant. Both kinases targeted pathways required for metabolism, translation, and stress response, whereas cell division and peptidoglycan metabolism were more specifically controlled by PrkC-dependent phosphorylation in agreement with the phenotypes of the ΔprkC mutant. Using a combination of approaches, we confirmed that FtsK was phosphorylated in vivo under the control of PrkC and that Spo0A was a substrate of PrkC in vitro. This study provides a detailed mapping of kinase-substrate relationships in C. difficile, paving the way for the identification of new biomarkers and therapeutic targets.


Subject(s)
Clostridioides difficile , Proteome , Proteome/metabolism , Clostridioides , Bacterial Proteins/metabolism , Protein Serine-Threonine Kinases , Phosphorylation , Phosphoproteins/metabolism , Phosphoprotein Phosphatases/metabolism , Threonine/metabolism , Serine/metabolism
8.
Cell Rep ; 40(2): 111074, 2022 07 12.
Article in English | MEDLINE | ID: mdl-35830812

ABSTRACT

Cellular senescence is an irreversible growth arrest with a dynamic secretome, termed the senescence-associated secretory phenotype (SASP). Senescence is a cell-intrinsic barrier for reprogramming, whereas the SASP facilitates cell fate conversion in non-senescent cells. However, the mechanisms by which reprogramming-induced senescence regulates cell plasticity are not well understood. Here, we investigate how the heterogeneity of paracrine senescence impacts reprogramming. We show that senescence promotes in vitro reprogramming in a stress-dependent manner. Unbiased proteomics identifies a catalog of SASP factors involved in the cell fate conversion. Amphiregulin (AREG), frequently secreted by senescent cells, promotes in vitro reprogramming by accelerating proliferation and the mesenchymal-epithelial transition via EGFR signaling. AREG treatment diminishes the negative effect of donor age on reprogramming. Finally, AREG enhances in vivo reprogramming in skeletal muscle. Hence, various SASP factors can facilitate cellular plasticity to promote reprogramming and tissue repair.


Subject(s)
Cell Plasticity , Cellular Senescence , Amphiregulin/genetics , Cellular Senescence/genetics , Phenotype , Signal Transduction
9.
iScience ; 25(5): 104233, 2022 May 20.
Article in English | MEDLINE | ID: mdl-35521527

ABSTRACT

RNA turnover is a primary source of gene expression variation, in turn promoting cellular adaptation. Mycobacteria leverage reversible mRNA stabilization to endure hostile conditions. Although RNase E is essential for RNA turnover in several species, its role in mycobacterial single-cell physiology and functional phenotypic diversification remains unexplored. Here, by integrating live-single-cell and quantitative-mass-spectrometry approaches, we show that RNase E forms dynamic foci, which are associated with cellular homeostasis and fate, and we discover a versatile molecular interactome. We show a likely interaction between RNase E and the nucleoid-associated protein HupB, which is particularly pronounced during drug treatment and infection, where phenotypic diversity increases. Disruption of RNase E expression affects HupB levels, impairing Mycobacterium tuberculosis growth homeostasis during treatment, intracellular replication, and host spread. Our work lays the foundation for targeting the RNase E and its partner HupB, aiming to undermine M. tuberculosis cellular balance, diversification capacity, and persistence.

10.
PLoS Pathog ; 18(3): e1010375, 2022 03.
Article in English | MEDLINE | ID: mdl-35294501

ABSTRACT

The protozoan parasite Leishmania donovani causes fatal human visceral leishmaniasis in absence of treatment. Genome instability has been recognized as a driver in Leishmania fitness gain in response to environmental change or chemotherapy. How genome instability generates beneficial phenotypes despite potential deleterious gene dosage effects is unknown. Here we address this important open question applying experimental evolution and integrative systems approaches on parasites adapting to in vitro culture. Phenotypic analyses of parasites from early and late stages of culture adaptation revealed an important fitness tradeoff, with selection for accelerated growth in promastigote culture (fitness gain) impairing infectivity (fitness costs). Comparative genomics, transcriptomics and proteomics analyses revealed a complex regulatory network associated with parasite fitness gain, with genome instability causing highly reproducible, gene dosage-independent and -dependent changes. Reduction of flagellar transcripts and increase in coding and non-coding RNAs implicated in ribosomal biogenesis and protein translation were not correlated to dosage changes of the corresponding genes, revealing a gene dosage-independent, post-transcriptional mechanism of regulation. In contrast, abundance of gene products implicated in post-transcriptional regulation itself correlated to corresponding gene dosage changes. Thus, RNA abundance during parasite adaptation is controled by direct and indirect gene dosage changes. We correlated differential expression of small nucleolar RNAs (snoRNAs) with changes in rRNA modification, providing first evidence that Leishmania fitness gain in culture may be controlled by post-transcriptional and epitranscriptomic regulation. Our findings propose a novel model for Leishmania fitness gain in culture, where differential regulation of mRNA stability and the generation of modified ribosomes may potentially filter deleterious from beneficial gene dosage effects and provide proteomic robustness to genetically heterogenous, adapting parasite populations. This model challenges the current, genome-centric approach to Leishmania epidemiology and identifies the Leishmania transcriptome and non-coding small RNome as potential novel sources for the discovery of biomarkers that may be associated with parasite phenotypic adaptation in clinical settings.


Subject(s)
Leishmania donovani , Leishmaniasis, Visceral , Gene Expression Regulation , Genomic Instability , Humans , Leishmania donovani/genetics , Leishmaniasis, Visceral/parasitology , Proteomics
11.
mBio ; 12(3)2021 05 18.
Article in English | MEDLINE | ID: mdl-34006648

ABSTRACT

Cell growth and division require a balance between synthesis and hydrolysis of the peptidoglycan (PG). Inhibition of PG synthesis or uncontrolled PG hydrolysis can be lethal for the cells, making it imperative to control peptidoglycan hydrolase (PGH) activity. The synthesis or activity of several key enzymes along the PG biosynthetic pathway is controlled by the Hanks-type serine/threonine kinases (STKs). In Gram-positive bacteria, inactivation of genes encoding STKs is associated with a range of phenotypes, including cell division defects and changes in cell wall metabolism, but only a few kinase substrates and associated mechanisms have been identified. We previously demonstrated that STK-PrkC plays an important role in cell division, cell wall metabolism, and resistance to antimicrobial compounds in the human enteropathogen Clostridioides difficile In this work, we characterized a PG hydrolase, CwlA, which belongs to the NlpC/P60 family of endopeptidases and hydrolyses cross-linked PG between daughter cells to allow cell separation. We identified CwlA as the first PrkC substrate in C. difficile We demonstrated that PrkC-dependent phosphorylation inhibits CwlA export, thereby controlling hydrolytic activity in the cell wall. High levels of CwlA at the cell surface led to cell elongation, whereas low levels caused cell separation defects. Thus, we provided evidence that the STK signaling pathway regulates PGH homeostasis to precisely control PG hydrolysis during cell division.IMPORTANCE Bacterial cells are encased in a PG exoskeleton that helps to maintain cell shape and confers physical protection. To allow bacterial growth and cell separation, PG needs to be continuously remodeled by hydrolytic enzymes that cleave PG at critical sites. How these enzymes are regulated remains poorly understood. We identify a new PG hydrolase involved in cell division, CwlA, in the enteropathogen C. difficile Lack or accumulation of CwlA at the bacterial surface is responsible for a division defect, while its accumulation in the absence of PrkC also increases susceptibility to antimicrobial compounds targeting the cell wall. CwlA is a substrate of the kinase PrkC in C. difficile PrkC-dependent phosphorylation controls the export of CwlA, modulating its levels and, consequently, its activity in the cell wall. This work provides a novel regulatory mechanism by STK in tightly controlling protein export.


Subject(s)
Bacterial Proteins/metabolism , Cell Division/genetics , Clostridioides difficile/metabolism , N-Acetylmuramoyl-L-alanine Amidase/genetics , N-Acetylmuramoyl-L-alanine Amidase/metabolism , Protein Serine-Threonine Kinases/metabolism , Signal Transduction , Bacterial Proteins/genetics , Cell Division/physiology , Clostridioides difficile/enzymology , Clostridioides difficile/genetics , Peptidoglycan/metabolism , Phosphorylation , Protein Serine-Threonine Kinases/genetics
12.
EMBO Rep ; 22(6): e52626, 2021 06 04.
Article in English | MEDLINE | ID: mdl-34009726

ABSTRACT

Proteomics research infrastructures and core facilities within the Core for Life alliance advocate for community policies for quality control to ensure high standards in proteomics services.


Subject(s)
Proteomics , Mass Spectrometry
13.
Nucleic Acids Res ; 49(9): 5249-5264, 2021 05 21.
Article in English | MEDLINE | ID: mdl-33893809

ABSTRACT

Ribonucleases are central players in post-transcriptional regulation, a major level of gene expression regulation in all cells. Here, we characterized the 3'-5' exoribonuclease RNase R from the bacterial pathogen Helicobacter pylori. The 'prototypical' Escherichia coli RNase R displays both exoribonuclease and helicase activities, but whether this latter RNA unwinding function is a general feature of bacterial RNase R had not been addressed. We observed that H. pylori HpRNase R protein does not carry the domains responsible for helicase activity and accordingly the purified protein is unable to degrade in vitro RNA molecules with secondary structures. The lack of RNase R helicase domains is widespread among the Campylobacterota, which include Helicobacter and Campylobacter genera, and this loss occurred gradually during their evolution. An in vivo interaction between HpRNase R and RhpA, the sole DEAD-box RNA helicase of H. pylori was discovered. Purified RhpA facilitates the degradation of double stranded RNA by HpRNase R, showing that this complex is functional. HpRNase R has a minor role in 5S rRNA maturation and few targets in H. pylori, all included in the RhpA regulon. We concluded that during evolution, HpRNase R has co-opted the RhpA helicase to compensate for its lack of helicase activity.


Subject(s)
DEAD-box RNA Helicases/metabolism , Exoribonucleases/metabolism , Helicobacter pylori/enzymology , Amino Acid Motifs , Epsilonproteobacteria/enzymology , Exoribonucleases/chemistry , RNA, Double-Stranded/metabolism , RNA, Ribosomal, 5S/metabolism
14.
Data Brief ; 35: 106818, 2021 Apr.
Article in English | MEDLINE | ID: mdl-33604433

ABSTRACT

This article provides experimental data describing the cell wall protein profiles of stems and leaves of Brachypodium distachyon at two different stages of development. The cell wall proteomics data have been obtained from (i) stem internodes at young and mature stages of development, and (ii) leaves at young and mature stages of development. The proteins have been extracted from purified cell walls using buffers containing calcium chloride (0.2 M) or lithium chloride (2 M). They have been identified by LC-MS/MS and bioinformatics. These data allow deepening our knowledge of these cell wall proteomes. They are a valuable resource for people interested in plant cell wall biology to understand the roles of cell wall proteins during the growth of vegetative organs.

15.
PLoS One ; 16(1): e0243992, 2021.
Article in English | MEDLINE | ID: mdl-33428654

ABSTRACT

Insecticide resistance is a worldwide threat for vector control around the world, and Aedes aegypti, the main vector of several arboviruses, is a particular concern. To better understand the mechanisms of resistance, four isofemale strains originally from French Guiana were isolated and analysed using combined approaches. The activity of detoxification enzymes involved in insecticide resistance was assayed, and mutations located at positions 1016 and 1534 of the sodium voltage-gated channel gene, which have been associated with pyrethroid resistance in Aedes aegypti populations in Latin America, were monitored. Resistance to other insecticide families (organophosphates and carbamates) was evaluated. A large-scale proteomic analysis was performed to identify proteins involved in insecticide resistance. Our results revealed a metabolic resistance and resistance associated with a mutation of the sodium voltage-gated channel gene at position 1016. Metabolic resistance was mediated through an increase of esterase activity in most strains but also through the shifts in the abundance of several cytochrome P450 (CYP450s). Overall, resistance to deltamethrin was linked in the isofemale strains to resistance to other class of insecticides, suggesting that cross- and multiple resistance occur through selection of mechanisms of metabolic resistance. These results give some insights into resistance to deltamethrin and into multiple resistance phenomena in populations of Ae. aegypti.


Subject(s)
Aedes/metabolism , Cytochrome P-450 Enzyme System/genetics , Insect Proteins/genetics , Insecticide Resistance/genetics , Voltage-Gated Sodium Channels/genetics , Aedes/drug effects , Aedes/genetics , Animals , Esterases/metabolism , Female , French Guiana , Gene Knockdown Techniques , Genotype , Inactivation, Metabolic/genetics , Insect Proteins/antagonists & inhibitors , Insect Proteins/metabolism , Insecticides/pharmacology , Intestinal Mucosa/metabolism , Nitriles/pharmacology , Oligonucleotides/metabolism , Polymorphism, Single Nucleotide , Proteome/analysis , Proteomics , Pyrethrins/pharmacology , Voltage-Gated Sodium Channels/chemistry , Voltage-Gated Sodium Channels/metabolism
16.
Mol Cell Proteomics ; 20: 100049, 2021.
Article in English | MEDLINE | ID: mdl-33515806

ABSTRACT

Viruses manipulate the central machineries of host cells to their advantage. They prevent host cell antiviral responses to create a favorable environment for their survival and propagation. Measles virus (MV) encodes two nonstructural proteins MV-V and MV-C known to counteract the host interferon response and to regulate cell death pathways. Several molecular mechanisms underlining MV-V regulation of innate immunity and cell death pathways have been proposed, whereas MV-C host-interacting proteins are less studied. We suggest that some cellular factors that are controlled by MV-C protein during viral replication could be components of innate immunity and the cell death pathways. To determine which host factors are targeted by MV-C, we captured both direct and indirect host-interacting proteins of MV-C protein. For this, we used a strategy based on recombinant viruses expressing tagged viral proteins followed by affinity purification and a bottom-up mass spectrometry analysis. From the list of host proteins specifically interacting with MV-C protein in different cell lines, we selected the host targets that belong to immunity and cell death pathways for further validation. Direct protein interaction partners of MV-C were determined by applying protein complementation assay and the bioluminescence resonance energy transfer approach. As a result, we found that MV-C protein specifically interacts with p65-iASPP protein complex that controls both cell death and innate immunity pathways and evaluated the significance of these host factors on virus replication.


Subject(s)
Intracellular Signaling Peptides and Proteins/metabolism , Repressor Proteins/metabolism , Transcription Factor RelA/metabolism , Viral Nonstructural Proteins/metabolism , Animals , Cell Death , Cell Line , Chlorocebus aethiops , Host-Pathogen Interactions , Humans , Intracellular Signaling Peptides and Proteins/genetics , Measles virus/genetics , Measles virus/physiology , Protein Interaction Maps , Proteomics , Repressor Proteins/genetics , Transcription Factor RelA/genetics , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism , Viral Nonstructural Proteins/genetics , Virus Replication
17.
Nat Commun ; 11(1): 1941, 2020 04 22.
Article in English | MEDLINE | ID: mdl-32321914

ABSTRACT

Cytokinesis requires the constriction of ESCRT-III filaments on the side of the midbody, where abscission occurs. After ESCRT recruitment at the midbody, it is not known how the ESCRT-III machinery localizes to the abscission site. To reveal actors involved in abscission, we obtained the proteome of intact, post-abscission midbodies (Flemmingsome) and identified 489 proteins enriched in this organelle. Among these proteins, we further characterized a plasma membrane-to-ESCRT module composed of the transmembrane proteoglycan syndecan-4, ALIX and syntenin, a protein that bridges ESCRT-III/ALIX to syndecans. The three proteins are highly recruited first at the midbody then at the abscission site, and their depletion delays abscission. Mechanistically, direct interactions between ALIX, syntenin and syndecan-4 are essential for proper enrichment of the ESCRT-III machinery at the abscission site, but not at the midbody. We propose that the ESCRT-III machinery must be physically coupled to a membrane protein at the cytokinetic abscission site for efficient scission, uncovering common requirements in cytokinesis, exosome formation and HIV budding.


Subject(s)
Calcium-Binding Proteins/metabolism , Cell Cycle Proteins/metabolism , Cell Membrane/metabolism , Cytokinesis , Endosomal Sorting Complexes Required for Transport/metabolism , Organelles/metabolism , Syndecan-4/metabolism , Syntenins/metabolism , Calcium-Binding Proteins/genetics , Cell Cycle Proteins/genetics , Cell Membrane/genetics , Endosomal Sorting Complexes Required for Transport/genetics , Endosomes/genetics , Endosomes/metabolism , HeLa Cells , Humans , Organelles/genetics , Protein Binding , Syndecan-4/genetics , Syntenins/genetics
18.
FASEB J ; 33(9): 10065-10076, 2019 09.
Article in English | MEDLINE | ID: mdl-31226003

ABSTRACT

The adenylate cyclase (CyaA) toxin is a major virulence factor of Bordetella pertussis, the causative agent of whooping cough. CyaA is synthetized as a pro-toxin, pro-CyaA, and converted into its cytotoxic form upon acylation of two lysines. After secretion, CyaA invades eukaryotic cells and produces cAMP, leading to host defense subversion. To gain further insights into the effect of acylation, we compared the functional and structural properties of pro-CyaA and CyaA proteins. HDX-MS results show that the refolding process of both proteins upon progressive urea removal is initiated by calcium binding to the C-terminal RTX domain. We further identified a critical hydrophobic segment, distal from the acylation region, that folds at higher urea concentration in CyaA than in pro-CyaA. Once refolded into monomers, CyaA is more compact and stable than pro-CyaA, due to a complex set of interactions between domains. Our HDX-MS data provide direct evidence that the presence of acyl chains in CyaA induces a significant stabilization of the apolar segments of the hydrophobic domain and of most of the acylation region. We propose a refolding model dependent on calcium and driven by local and distal acylation-dependent interactions within CyaA. Therefore, CyaA acylation is not only critical for cell intoxication, but also for protein refolding into its active conformation. Our data shed light on the complex relationship between post-translational modifications, structural disorder and protein folding. Coupling calcium-binding and acylation-driven folding is likely pertinent for other repeat-in-toxin cytolysins produced by many Gram-negative bacterial pathogens.-O'Brien, D. P., Cannella, S. E., Voegele, A., Raoux-Barbot, D., Davi, M., Douché, T., Matondo, M., Brier, S., Ladant, D., Chenal, A. Post-translational acylation controls the folding and functions of the CyaA RTX toxin.


Subject(s)
Adenylate Cyclase Toxin/chemistry , Bordetella pertussis/metabolism , Protein Processing, Post-Translational , Acylation , Adenylate Cyclase Toxin/metabolism , Amino Acid Sequence , Anilino Naphthalenesulfonates/pharmacology , Animals , Bordetella pertussis/genetics , Erythrocytes/drug effects , Hydrophobic and Hydrophilic Interactions , Lysine/chemistry , Protein Conformation , Protein Domains , Protein Folding , Protein Stability , Recombinant Proteins/chemistry , Sheep , Structure-Activity Relationship , Tandem Mass Spectrometry , Urea
19.
Infect Immun ; 87(8)2019 08.
Article in English | MEDLINE | ID: mdl-31085703

ABSTRACT

Clostridium difficile is the leading cause of antibiotic-associated diarrhea in adults. During infection, C. difficile must detect the host environment and induce an appropriate survival strategy. Signal transduction networks involving serine/threonine kinases (STKs) play key roles in adaptation, as they regulate numerous physiological processes. PrkC of C. difficile is an STK with two PASTA domains. We showed that PrkC is membrane associated and is found at the septum. We observed that deletion of prkC affects cell morphology with an increase in mean size, cell length heterogeneity, and presence of abnormal septa. A ΔprkC mutant was able to sporulate and germinate but was less motile and formed more biofilm than the wild-type strain. Moreover, a ΔprkC mutant was more sensitive to antimicrobial compounds that target the cell envelope, such as the secondary bile salt deoxycholate, cephalosporins, cationic antimicrobial peptides, and lysozyme. This increased susceptibility was not associated with differences in peptidoglycan or polysaccharide II composition. However, the ΔprkC mutant had less peptidoglycan and released more polysaccharide II into the supernatant. A proteomic analysis showed that the majority of C. difficile proteins associated with the cell wall were less abundant in the ΔprkC mutant than the wild-type strain. Finally, in a hamster model of infection, the ΔprkC mutant had a colonization delay that did not significantly affect overall virulence.


Subject(s)
Bacterial Proteins/physiology , Clostridioides difficile/drug effects , Protein Serine-Threonine Kinases/physiology , Animals , Cell Wall/metabolism , Clostridioides difficile/metabolism , Clostridioides difficile/pathogenicity , Cricetinae , Drug Resistance, Bacterial , Homeostasis , Mesocricetus , Microbial Sensitivity Tests , Peptidoglycan/metabolism , Protein Serine-Threonine Kinases/genetics , Virulence
20.
Toxins (Basel) ; 11(2)2019 02 13.
Article in English | MEDLINE | ID: mdl-30781809

ABSTRACT

The adenylate cyclase (CyaA) toxin produced in Bordetella pertussis is the causative agent of whooping cough. CyaA exhibits the remarkable capacity to translocate its N-terminal adenyl cyclase domain (ACD) directly across the plasma membrane into the cytosol of eukaryotic cells. Once translocated, calmodulin binds and activates ACD, leading to a burst of cAMP that intoxicates the target cell. Previously, Gonzalez-Bullon et al. reported that CyaA exhibits a phospholipase A activity that could destabilize the membrane to facilitate ACD membrane translocation. However, Bumba and collaborators lately reported that they could not replicate these results. To clarify this controversy, we assayed the putative PLA activity of two CyaA samples purified in two different laboratories by using two distinct fluorescent probes reporting either PLA2 or both PLA1 and PLA2 activities, as well as in various experimental conditions (i.e., neutral or negatively charged membranes in different buffers.) However, we could not detect any PLA activity in these CyaA batches. Thus, our data independently confirm that CyaA does not possess any PLA activity.


Subject(s)
Adenylate Cyclase Toxin/chemistry , Phospholipases A1/chemistry , Phospholipases A2/chemistry , Bordetella pertussis , Fluorescent Dyes
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