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1.
Chembiochem ; : e202400187, 2024 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-38639212

RESUMO

Understanding the mechanisms of drug action in malarial parasites is crucial for the development of new drugs to combat infection and to counteract drug resistance. Proteomics is a widely used approach to study host-pathogen systems and to identify drug protein targets. Plasmodione is an antiplasmodial early-lead drug exerting potent activities against young asexual and sexual blood stages in vitro with low toxicity to host cells. To elucidate its molecular mechanisms, an affinity-based protein profiling (AfBPP) approach was applied to yeast and P. falciparum proteomes. New (pro-) AfBPP probes based on the 3-benz(o)yl-6-fluoro-menadione scaffold were synthesized. With optimized conditions of both photoaffinity labeling and click reaction steps, the AfBPP protocol was then applied to a yeast proteome, yielding 11 putative drug-protein targets. Among these, we found four proteins associated with oxidoreductase activities, the hypothesized type of targets for plasmodione and its metabolites, and other proteins associated with the mitochondria. In Plasmodium parasites, the MS analysis revealed 44 potential plasmodione targets that need to be validated in further studies. Finally, the localization of a 3-benzyl-6-fluoromenadione AfBPP probe was studied in the subcellular structures of the parasite at the trophozoite stage.

2.
Proc Natl Acad Sci U S A ; 115(47): E11033-E11042, 2018 11 20.
Artigo em Inglês | MEDLINE | ID: mdl-30397120

RESUMO

The nuclear receptor REV-ERBα integrates the circadian clock with hepatic glucose and lipid metabolism by nucleating transcriptional comodulators at genomic regulatory regions. An interactomic approach identified O-GlcNAc transferase (OGT) as a REV-ERBα-interacting protein. By shielding cytoplasmic OGT from proteasomal degradation and favoring OGT activity in the nucleus, REV-ERBα cyclically increased O-GlcNAcylation of multiple cytoplasmic and nuclear proteins as a function of its rhythmically regulated expression, while REV-ERBα ligands mostly affected cytoplasmic OGT activity. We illustrate this finding by showing that REV-ERBα controls OGT-dependent activities of the cytoplasmic protein kinase AKT, an essential relay in insulin signaling, and of ten-of-eleven translocation (TET) enzymes in the nucleus. AKT phosphorylation was inversely correlated to REV-ERBα expression. REV-ERBα enhanced TET activity and DNA hydroxymethylated cytosine (5hmC) levels in the vicinity of REV-ERBα genomic binding sites. As an example, we show that the REV-ERBα/OGT complex modulates SREBP-1c gene expression throughout the fasting/feeding periods by first repressing AKT phosphorylation and by epigenomically priming the Srebf1 promoter for a further rapid response to insulin. Conclusion: REV-ERBα regulates cytoplasmic and nuclear OGT-controlled processes that integrate at the hepatic SREBF1 locus to control basal and insulin-induced expression of the temporally and nutritionally regulated lipogenic SREBP-1c transcript.


Assuntos
Insulina/metabolismo , N-Acetilglucosaminiltransferases/metabolismo , Membro 1 do Grupo D da Subfamília 1 de Receptores Nucleares/metabolismo , Proteína de Ligação a Elemento Regulador de Esterol 1/biossíntese , Animais , Linhagem Celular Tumoral , Relógios Circadianos/fisiologia , Regulação da Expressão Gênica/genética , Glucose/metabolismo , Células HEK293 , Células Hep G2 , Humanos , Metabolismo dos Lipídeos/fisiologia , Fígado/metabolismo , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , N-Acetilglucosaminiltransferases/genética , Membro 1 do Grupo D da Subfamília 1 de Receptores Nucleares/genética , Fosforilação , Proteínas Proto-Oncogênicas c-akt/metabolismo , Transdução de Sinais , Proteína de Ligação a Elemento Regulador de Esterol 1/genética
3.
Cell Microbiol ; 19(2)2017 02.
Artigo em Inglês | MEDLINE | ID: mdl-27385072

RESUMO

Apicomplexan parasites are responsible for some of the most deadly parasitic diseases affecting humans and livestock. There is an urgent need for new medicines that will target apicomplexan-specific pathways. We characterized a Toxoplasma gondii C2H2 zinc finger protein, named TgZNF2, which is conserved among eukaryotes. We constructed an inducible KO strain (iKO-TgZNF2) for this gene where the tgznf2 gene expression is repressed in the presence of a tetracycline analog (ATc). We showed that the iKO-TgZNF2 parasites are unable to proliferate after depletion of the TgZNF2 protein. Complementation with a full length copy of the gene restores the phenotype Moreover, the homolog of this protein in the related apicomplexan Plasmodium falciparum was shown to efficiently rescue the phenotype, suggesting that this pathway is likely conserved among apicomplexan parasites. We demonstrated that the iKO-mutant lacking TgZNF2 are arrested during the cell cycle during the G1 phase. We identified potential protein partners of this protein among which are spliceosomal complex and mRNA nuclear export components. We confirmed that TgZNF2 is able to bind in vivo to transcripts but splicing is not perturbed in the ATc-treated parasites. Instead, we demonstrated that TgZNF2 depletion leads to the sequestration of polyA+ mRNAs in the nucleus while ribosomal RNAs are not affected. We discovered a conserved protein with specific apicomplexan functional properties that is essential for the survival of T. gondii. TgZNF2 may be crucial to ensure the correct polyA+ mRNA nuclear export, a function that is conserved in P. falciparum.


Assuntos
Transporte Ativo do Núcleo Celular , Dedos de Zinco CYS2-HIS2 , Fatores de Transcrição Kruppel-Like/metabolismo , RNA Mensageiro/metabolismo , RNA Viral/metabolismo , Toxoplasma/crescimento & desenvolvimento , Pontos de Checagem do Ciclo Celular , Técnicas de Silenciamento de Genes , Teste de Complementação Genética , Humanos , Fatores de Transcrição Kruppel-Like/deficiência , Plasmodium falciparum/genética , Plasmodium falciparum/crescimento & desenvolvimento , Toxoplasma/genética
4.
Int J Mol Sci ; 15(6): 9644-69, 2014 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-24886812

RESUMO

Botryosphaeria dieback is a fungal grapevine trunk disease that currently represents a threat for viticulture worldwide because of the important economical losses due to reduced yield of affected plants and their premature death. Neofusicoccum parvum and Diplodia seriata are among the causal agents. Vine green stems were artificially infected with N. parvum or D. seriata at the onset of three different phenological stages (G stage (separated clusters), flowering and veraison). Highest mean lesion lengths were recorded at flowering. Major proteome changes associated to artificial infections during the three different phenological stages were also reported using two dimensional gel electrophoresis (2D)-based analysis. Twenty (G stage), 15 (flowering) and 13 (veraison) differentially expressed protein spots were subjected to nanoLC-MS/MS and a total of 247, 54 and 25 proteins were respectively identified. At flowering, a weaker response to the infection was likely activated as compared to the other stages, and some defense-related proteins were even down regulated (e.g., superoxide dismutase, major latex-like protein, and pathogenesis related protein 10). Globally, the flowering period seemed to represent the period of highest sensitivity of grapevine to Botryosphaeria dieback agent infection, possibly being related to the high metabolic activity in the inflorescences.


Assuntos
Ascomicetos/fisiologia , Doenças das Plantas/microbiologia , Proteínas de Plantas/análise , Vitis/microbiologia , Vitis/fisiologia , Eletroforese em Gel Bidimensional , Proteínas de Plantas/metabolismo , Proteoma/análise , Proteoma/metabolismo , Proteômica , Espectrometria de Massas em Tandem , Vitis/crescimento & desenvolvimento
5.
PLoS Pathog ; 7(3): e1001328, 2011 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-21483487

RESUMO

In Toxoplasma gondii, cis-acting elements present in promoter sequences of genes that are stage-specifically regulated have been described. However, the nuclear factors that bind to these cis-acting elements and regulate promoter activities have not been identified. In the present study, we performed affinity purification, followed by proteomic analysis, to identify nuclear factors that bind to a stage-specific promoter in T. gondii. This led to the identification of several nuclear factors in T. gondii including a novel factor, designated herein as TgNF3. The N-terminal domain of TgNF3 shares similarities with the N-terminus of yeast nuclear FK506-binding protein (FKBP), known as a histone chaperone regulating gene silencing. Using anti-TgNF3 antibodies, HA-FLAG and YFP-tagged TgNF3, we show that TgNF3 is predominantly a parasite nucleolar, chromatin-associated protein that binds specifically to T. gondii gene promoters in vivo. Genome-wide analysis using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified promoter occupancies by TgNF3. In addition, TgNF3 has a direct role in transcriptional control of genes involved in parasite metabolism, transcription and translation. The ectopic expression of TgNF3 in the tachyzoites revealed dynamic changes in the size of the nucleolus, leading to a severe attenuation of virulence in vivo. We demonstrate that TgNF3 physically interacts with H3, H4 and H2A/H2B assembled into bona fide core and nucleosome-associated histones. Furthermore, TgNF3 interacts specifically to histones in the context of stage-specific gene silencing of a promoter that lacks active epigenetic acetylated histone marks. In contrast to virulent tachyzoites, which express the majority of TgNF3 in the nucleolus, the protein is exclusively located in the cytoplasm of the avirulent bradyzoites. We propose a model where TgNF3 acts essentially to coordinate nucleolus and nuclear functions by modulating nucleosome activities during the intracellular proliferation of the virulent tachyzoites of T. gondii.


Assuntos
Nucléolo Celular/metabolismo , Cromatina/metabolismo , Proteínas Nucleares/metabolismo , Regiões Promotoras Genéticas , Proteínas de Protozoários/metabolismo , Toxoplasma/patogenicidade , Anticorpos Antiprotozoários , Nucléolo Celular/genética , Imunoprecipitação da Cromatina , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Inativação Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Histonas/metabolismo , Espectrometria de Massas , Microscopia Eletrônica , Proteínas Nucleares/biossíntese , Proteínas Nucleares/química , Proteínas Nucleares/genética , Proteômica , Proteínas de Protozoários/biossíntese , Proteínas de Protozoários/química , Proteínas de Protozoários/genética , Sequências Reguladoras de Ácido Nucleico , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Ribossomos/metabolismo , Análise de Sequência de Proteína , Coloração e Rotulagem , Proteínas de Ligação a Tacrolimo/química , Toxoplasma/genética , Toxoplasma/metabolismo
6.
Mol Cell Proteomics ; 10(9): M111.008953, 2011 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-21610105

RESUMO

Toxoplasma gondii motility, which is essential for host cell entry, migration through host tissues, and invasion, is a unique form of actin-dependent gliding. It is powered by a motor complex mainly composed of myosin heavy chain A, myosin light chain 1, gliding associated proteins GAP45, and GAP50, the only integral membrane anchor so far described. In the present study, we have combined glycomic and proteomic approaches to demonstrate that all three potential N-glycosylated sites of GAP50 are occupied by unusual N-glycan structures that are rarely found on mature mammalian glycoproteins. Using site-directed mutagenesis, we show that N-glycosylation is a prerequisite for GAP50 transport from the endoplasmic reticulum to the Golgi apparatus and for its subsequent delivery into the inner complex membrane. Assembly of key partners into the gliding complex, and parasite motility are severely impaired in the unglycosylated GAP50 mutants. Furthermore, comparative affinity purification using N-glycosylated and unglycosylated GAP50 as bait identified three novel hypothetical proteins including the recently described gliding associated protein GAP40, and we demonstrate that N-glycans are required for efficient binding to gliding partners. Collectively, these results provide the first detailed analyses of T. gondii N-glycosylation functions that are vital for parasite motility and host cell entry.


Assuntos
Movimento Celular , Retículo Endoplasmático/metabolismo , Glicoproteínas/química , Complexo de Golgi/metabolismo , Proteínas de Membrana/metabolismo , Proteínas Motores Moleculares/metabolismo , Proteínas de Protozoários/metabolismo , Toxoplasma/metabolismo , Membrana Celular/genética , Membrana Celular/metabolismo , Movimento Celular/fisiologia , Fibroblastos/citologia , Fibroblastos/parasitologia , Glicômica , Glicoproteínas/genética , Glicoproteínas/metabolismo , Glicosilação , Interações Hospedeiro-Parasita/genética , Humanos , Espectrometria de Massas , Proteínas de Membrana/genética , Proteínas Motores Moleculares/genética , Mutagênese Sítio-Dirigida , Plasmídeos , Ligação Proteica , Transporte Proteico/fisiologia , Proteômica , Proteínas de Protozoários/genética , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Toxoplasma/genética , Transfecção
7.
Exp Gerontol ; 164: 111811, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35472570

RESUMO

In humans, hyperglycemia is associated with protein glycation, which may contribute to aging. Strikingly, birds usually outlive mammals of the same body mass, while exhibiting high plasma glucose levels. However, how birds succeed in escaping pro-aging effects of glycation remains unknown. Using a specific mass spectrometry-based approach in captive zebra finches of known age, we recorded high glycaemia values but no glycated hemoglobin form was found. Still, we showed that zebra finch hemoglobin can be glycated in vitro, albeit only to a limited extent compared to its human homologue. This may be due to peculiar structural features, as supported by the unusual presence of three different tetramer populations with balanced proportions and a still bound cofactor that could be inositol pentaphosphate. High levels of the glycated forms of zebra finch plasma serotransferrin, carbonic anhydrase 2, and albumin were measured. Glucose, age or body mass correlations with either plasma glycated proteins or hemoglobin isoforms suggest that those variables may be future molecular tools of choice to monitor glycation and its link with individual fitness. Our molecular advance may help determine how evolution succeeded in associating flying ability, high blood glucose and long lifespan in birds.


Assuntos
Tentilhões , Hiperglicemia , Envelhecimento , Animais , Hemoglobinas Glicadas/metabolismo , Mamíferos , Espectrometria de Massas
8.
Nat Cardiovasc Res ; 1(11): 990-1005, 2022 Nov 03.
Artigo em Inglês | MEDLINE | ID: mdl-38229609

RESUMO

Myocardial ischemia-reperfusion injury (MIRI) induces life-threatening damages to the cardiac tissue and pharmacological means to achieve cardioprotection are sorely needed. MIRI severity varies along the day-night cycle and is molecularly linked to components of the cellular clock including the nuclear receptor REV-ERBα, a transcriptional repressor. Here we show that digoxin administration in mice is cardioprotective when timed to trigger REV-ERBα protein degradation. In cardiomyocytes, digoxin increases REV-ERBα ubiquitinylation and proteasomal degradation, which depend on REV-ERBα ability to bind its natural ligand, heme. Inhibition of the membrane-bound Src tyrosine-kinase partially alleviated digoxin-induced REV-ERBα degradation. In untreated cardiomyocytes, REV-ERBα proteolysis is controlled by known (HUWE1, FBXW7, SIAH2) or novel (CBL, UBE4B) E3 ubiquitin ligases and the proteasome subunit PSMB5. Only SIAH2 and PSMB5 contributed to digoxin-induced degradation of REV-ERBα. Thus, controlling REV-ERBα proteostasis through the ubiquitin-proteasome system is an appealing cardioprotective strategy. Our data support the timed use of clinically-approved cardiotonic steroids in prophylactic cardioprotection.

9.
Mol Cell Proteomics ; 7(5): 891-910, 2008 May.
Artigo em Inglês | MEDLINE | ID: mdl-18187410

RESUMO

The apicomplexan parasite Toxoplasma gondii recognizes, binds, and penetrates virtually any kind of mammalian cell using a repertoire of proteins released from late secretory organelles and a unique form of gliding motility (also named glideosome) that critically depends on actin filaments and myosin. How T. gondii glycosylated proteins mediate host-parasite interactions remains elusive. To date, only limited evidence is available concerning N-glycosylation in apicomplexans. Here we report comprehensive proteomics and glycomics analyses showing that several key components required for host cell-T. gondii interactions are N-glycosylated. Detailed structural characterization confirmed that N-glycans from T. gondii total protein extracts consist of oligomannosidic (Man(5-8)(GlcNAc)2) and paucimannosidic (Man(3-4)(GlcNAc)2) sugars, which are rarely present on mature eukaryotic glycoproteins. In situ fluorescence using concanavalin A and Pisum sativum agglutinin predominantly stained the entire parasite body. Visualization of Toxoplasma glycoproteins purified by affinity chromatography followed by detailed proteomics and glycan analyses identified components involved in gliding motility, moving junction, and other additional functions implicated in intracellular development. Importantly tunicamycin-treated parasites were considerably reduced in motility, host cell invasion, and growth. Collectively these results indicate that N-glycosylation probably participates in modifying key proteins that are essential for host cell invasion by T. gondii.


Assuntos
Glicômica , Glicoproteínas/metabolismo , Interações Hospedeiro-Parasita , Proteômica , Proteínas de Protozoários/metabolismo , Toxoplasma/fisiologia , Animais , Sequência de Carboidratos , Células Cultivadas , Glicoproteínas/análise , Glicosilação , Humanos , Microscopia Confocal , Dados de Sequência Molecular , Oligossacarídeos/análise , Peptídeo-N4-(N-acetil-beta-glucosaminil) Asparagina Amidase/química , Lectinas de Plantas/química , Polissacarídeos/química , Proteínas de Protozoários/análise , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Toxoplasma/química , Toxoplasma/metabolismo
10.
Life Sci Alliance ; 2(1)2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30760556

RESUMO

During platelet biogenesis, microtubules (MTs) are arranged into submembranous structures (the marginal band) that encircle the cell in a single plane. This unique MT array has no equivalent in any other mammalian cell, and the mechanisms responsible for this particular mode of assembly are not fully understood. One possibility is that platelet MTs are composed of a particular set of tubulin isotypes that carry specific posttranslational modifications. Although ß1-tubulin is known to be essential, no equivalent roles of α-tubulin isotypes in platelet formation or function have so far been reported. Here, we identify α4A-tubulin as a predominant α-tubulin isotype in platelets. Similar to ß1-tubulin, α4A-tubulin expression is up-regulated during the late stages of megakaryocyte differentiation. Missense mutations in the α4A-tubulin gene cause macrothrombocytopenia in mice and humans. Defects in α4A-tubulin lead to changes in tubulin tyrosination status of the platelet tubulin pool. Ultrastructural defects include reduced numbers and misarranged MT coils in the platelet marginal band. We further observed defects in megakaryocyte maturation and proplatelet formation in Tuba4a-mutant mice. We have, thus, discovered an α-tubulin isotype with specific and essential roles in platelet biogenesis.


Assuntos
Plaquetas/fisiologia , Trombocitopenia/genética , Trombopoese/fisiologia , Tubulina (Proteína)/genética , Tubulina (Proteína)/metabolismo , Alquilantes/administração & dosagem , Alquilantes/farmacologia , Animais , Antígenos CD34/metabolismo , Células Cultivadas , Etilnitrosoureia/administração & dosagem , Etilnitrosoureia/farmacologia , Humanos , Masculino , Megacariócitos/metabolismo , Camundongos , Camundongos Endogâmicos BALB C , Microtúbulos/metabolismo , Mutação de Sentido Incorreto , Contagem de Plaquetas , Doadores de Tecidos
11.
Artigo em Inglês | MEDLINE | ID: mdl-18644751

RESUMO

A new delta-chain variant, delta143 (H21) His-->Tyr or Hb Noah Mehmet Oeztuerk, was discovered during the investigation of the cause of hemolytic anaemia in a 6-month-old infant of Turkish descent. It was detected by Cation exchange high-performance liquid chromatography (CE-HPLC) using PolyCAT A column. P(50) was 20.6+/-0.60 mmHg and 29.3+/-0.40 mmHg for the carrier and the wild-type, respectively. This suggests an increase in oxygen affinity. On routine CE-HPLC Hb A(2) was low (1.2%) and the variant was not detected. An extended family study revealed that the variant was not associated with the anaemia or with any other clinical abnormality.


Assuntos
Hemoglobinas Anormais/genética , Anemia Hemolítica/sangue , Sítios de Ligação , Humanos , Lactente , Masculino , Espectrometria de Massas
12.
J Proteomics ; 156: 113-125, 2017 03 06.
Artigo em Inglês | MEDLINE | ID: mdl-28153682

RESUMO

Elicitors are known to trigger plant defenses in response to biotic stress, but do not systematically lead to effective resistance to pathogens. The reasons explaining such differences remain misunderstood. Therefore, elicitation and induced resistance (IR) were investigated through the comparison of two modified ß-1,3 glucans applied on grapevine (Vitis vinifera) leaves before and after inoculation with Plasmopara viticola, the causal agent of downy mildew. The sulfated (PS3) and the shortened (H13) forms of laminarin are both known to elicit defense responses whereas only PS3 induces resistance against downy mildew. The analysis of the 2-DE gel electrophoresis revealed that PS3 and H13 induced distinct proteomic profiles after treatment and pathogen inoculation. Our results point out that the PS3-induced resistance is associated with the activation of the primary metabolism especially on amino acids and carbohydrates pathways. In addition, few proteins, such as the 12-oxophytodienoate reductase (OPR-like) related to the OPDA pathway, and an Arsenite-resistance protein (Serrate-like protein) could be considered as useful markers of induced resistance. SIGNIFICANCE: One strategy to reduce the application of fungicides is the use of elicitors which induce plant defense responses. Nonetheless, the elicitors do not systematically lead to resistance against pathogens. The lack of correlation between plant defense activation and induced resistance (IR) requires the investigation of what makes the specificity of elicitor-IR. In this study, the two ß-glucans elicitors, sulfated (PS3) and short (H13) laminarins, were used in the grapevine/Plasmopara viticola interaction since only the first one leads to resistance against downy mildew. To disclose IR specificity, proteomic approach has been employed to compare the two treatments before and after P. viticola inoculation. The analysis of the 2-DE revealed that PS3 and H13 induced distinct proteomic profiles after treatment and pathogen inoculation. Significant increase of the number of proteins regulated by PS3, relative to both H13 and time-points, is correlated with the resistance process establishment. Our results point that the PS3-induced resistance requires the activation of the primary metabolism especially on amino acids and carbohydrates pathways. In addition, few proteins, such as the 12-oxophytodienoate reductase (OPR-like) related to the OPDA pathway, and an Arsenite-resistance protein (Serrate-like protein) could constitute useful markers of PS3 induced resistance.


Assuntos
Resistência à Doença , Peronospora/patogenicidade , Doenças das Plantas/microbiologia , Proteômica/métodos , Vitis/microbiologia , Eletroforese em Gel de Poliacrilamida , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Glucanos/farmacologia , Folhas de Planta/efeitos dos fármacos , Folhas de Planta/microbiologia , Proteínas de Plantas/efeitos dos fármacos , Vitis/fisiologia
13.
Food Chem ; 200: 237-44, 2016 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-26830584

RESUMO

Vacuolar invertase is a key enzyme of sugar metabolism in grape berries. A full characterisation of this highly N-glycosylated protein is required to help understand its biological and biochemical significance in grapes. We have developed a mass spectrometry (MS)-based glycoproteomic approach wherein deglycosylated peptides are analysed by LC-MS/MS, while intact glycopeptides are characterised using a dedicated MS method to determine the attachment sites and micro-heterogeneity. For grape invertase, in parallel with deglycosylated peptides analysis, different enzymatic digestions were performed and glycopeptide detection was improved by enrichment method, nanoLC-MS and oxonium glycan ions. This MS-based glycoproteomic approach demonstrates that vacuolar invertase is glycosylated at all twelve potential N-glycosylation sites. Glycosylation is heterogeneous, with twelve glycoforms identified at six of the sites. The identification of several types of N-glycans is a major result to correlate with the surface and foaming properties of wine, the solubility, allergenicity, and protease resistance of wine proteins.


Assuntos
Glicopeptídeos/análise , Espectrometria de Massas em Tandem/métodos , Vitis/enzimologia , beta-Frutofuranosidase/metabolismo , Sequência de Aminoácidos , Dados de Sequência Molecular , beta-Frutofuranosidase/química
14.
Front Cell Dev Biol ; 4: 3, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26870729

RESUMO

The acid mine drainage (AMD) impacted creek of the Carnoulès mine (Southern France) is characterized by acid waters with a high heavy metal content. The microbial community inhabiting this AMD was extensively studied using isolation, metagenomic and metaproteomic methods, and the results showed that a natural arsenic (and iron) attenuation process involving the arsenite oxidase activity of several Thiomonas strains occurs at this site. A sensitive quantitative Selected Reaction Monitoring (SRM)-based proteomic approach was developed for detecting and quantifying the two subunits of the arsenite oxidase and RpoA of two different Thiomonas groups. Using this approach combined with FISH and pyrosequencing-based 16S rRNA gene sequence analysis, it was established here for the first time that these Thiomonas strains are ubiquitously present in minor proportions in this AMD and that they express the key enzymes involved in natural remediation processes at various locations and time points. In addition to these findings, this study also confirms that targeted proteomics applied at the community level can be used to detect weakly abundant proteins in situ.

15.
Nat Commun ; 7: 11191, 2016 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-27064065

RESUMO

Membrane trafficking pathways play critical roles in Apicomplexa, a phylum of protozoan parasites that cause life-threatening diseases worldwide. Here we report the first retromer-trafficking interactome in Toxoplasma gondii. This retromer complex includes a trimer Vps35-Vps26-Vps29 core complex that serves as a hub for the endosome-like compartment and parasite-specific proteins. Conditional ablation of TgVps35 reveals that the retromer complex is crucial for the biogenesis of secretory organelles and for maintaining parasite morphology. We identify TgHP12 as a parasite-specific and retromer-associated protein with functions unrelated to secretory organelle formation. Furthermore, the major facilitator superfamily homologue named TgHP03, which is a multiple spanning and ligand transmembrane transporter, is maintained at the parasite membrane by retromer-mediated endocytic recycling. Thus, our findings highlight that both evolutionarily conserved and unconventional proteins act in concert in T. gondii by controlling retrograde transport that is essential for parasite integrity and host infection.


Assuntos
Compartimento Celular , Endossomos/metabolismo , Interações Hospedeiro-Parasita , Complexos Multiproteicos/metabolismo , Parasitos/metabolismo , Proteínas de Protozoários/metabolismo , Toxoplasma/metabolismo , Sequência de Aminoácidos , Animais , Membrana Celular/metabolismo , Endocitose , Inativação Gênica , Genes de Protozoários , Dados de Sequência Molecular , Biogênese de Organelas , Fenótipo , Mapeamento de Interação de Proteínas , Proteínas de Protozoários/química , Especificidade da Espécie , Toxoplasma/genética , Proteínas de Transporte Vesicular/metabolismo
16.
J Proteomics ; 132: 51-62, 2016 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-26585461

RESUMO

Proteomic workflows based on nanoLC-MS/MS data-dependent-acquisition analysis have progressed tremendously in recent years. High-resolution and fast sequencing instruments have enabled the use of label-free quantitative methods, based either on spectral counting or on MS signal analysis, which appear as an attractive way to analyze differential protein expression in complex biological samples. However, the computational processing of the data for label-free quantification still remains a challenge. Here, we used a proteomic standard composed of an equimolar mixture of 48 human proteins (Sigma UPS1) spiked at different concentrations into a background of yeast cell lysate to benchmark several label-free quantitative workflows, involving different software packages developed in recent years. This experimental design allowed to finely assess their performances in terms of sensitivity and false discovery rate, by measuring the number of true and false-positive (respectively UPS1 or yeast background proteins found as differential). The spiked standard dataset has been deposited to the ProteomeXchange repository with the identifier PXD001819 and can be used to benchmark other label-free workflows, adjust software parameter settings, improve algorithms for extraction of the quantitative metrics from raw MS data, or evaluate downstream statistical methods. BIOLOGICAL SIGNIFICANCE: Bioinformatic pipelines for label-free quantitative analysis must be objectively evaluated in their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. This can be done through the use of complex spiked samples, for which the "ground truth" of variant proteins is known, allowing a statistical evaluation of the performances of the data processing workflow. We provide here such a controlled standard dataset and used it to evaluate the performances of several label-free bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, for detection of variant proteins with different absolute expression levels and fold change values. The dataset presented here can be useful for tuning software tool parameters, and also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods.


Assuntos
Benchmarking/normas , Cromatografia Líquida/normas , Espectrometria de Massas/normas , Proteoma/análise , Proteoma/normas , Fluxo de Trabalho , Benchmarking/métodos , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Software , Validação de Programas de Computador , Coloração e Rotulagem
17.
Data Brief ; 6: 286-94, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26862574

RESUMO

This data article describes a controlled, spiked proteomic dataset for which the "ground truth" of variant proteins is known. It is based on the LC-MS analysis of samples composed of a fixed background of yeast lysate and different spiked amounts of the UPS1 mixture of 48 recombinant proteins. It can be used to objectively evaluate bioinformatic pipelines for label-free quantitative analysis, and their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. More specifically, it can be useful for tuning software tools parameters, but also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods. The raw MS files can be downloaded from ProteomeXchange with identifier PXD001819. Starting from some raw files of this dataset, we also provide here some processed data obtained through various bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, to exemplify the use of such data in the context of software benchmarking, as discussed in details in the accompanying manuscript [1]. The experimental design used here for data processing takes advantage of the different spike levels introduced in the samples composing the dataset, and processed data are merged in a single file to facilitate the evaluation and illustration of software tools results for the detection of variant proteins with different absolute expression levels and fold change values.

19.
Cell Host Microbe ; 11(5): 515-27, 2012 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-22607804

RESUMO

Apicomplexan parasites have an assortment of unique apical secretory organelles (rhoptries and micronemes), which have crucial functions in host infection. Here, we show that a Toxoplasma gondii sortilin-like receptor (TgSORTLR) is required for the subcellular localization and formation of apical secretory organelles. TgSORTLR is a transmembrane protein that resides within Golgi-endosomal related compartments. The lumenal domain specifically interacts with rhoptry and microneme proteins, while the cytoplasmic tail of TgSORTLR recruits cytosolic sorting machinery involved in anterograde and retrograde protein transport. Ectopic expression of the N-terminal TgSORTLR lumenal domain results in dominant negative effects with the mislocalization of both endogenous TgSORTLR as well as rhoptry and microneme proteins. Conditional ablation of TgSORTLR disrupts rhoptry and microneme biogenesis, inhibits parasite motility, and blocks both invasion into and egress from host cells. Thus, the sortilin-like receptor is essential for protein trafficking and the biogenesis of key secretory organelles in Toxoplasma.


Assuntos
Proteínas Adaptadoras de Transporte Vesicular/metabolismo , Organelas/metabolismo , Toxoplasma/metabolismo , Toxoplasma/patogenicidade , Animais , Células Cultivadas , Feminino , Humanos , Proteínas de Membrana , Camundongos , Camundongos Endogâmicos BALB C , Modelos Biológicos , Ligação Proteica , Mapeamento de Interação de Proteínas , Transporte Proteico , Análise de Sobrevida , Toxoplasmose Animal
20.
J Chromatogr B Analyt Technol Biomed Life Sci ; 879(28): 2952-6, 2011 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-21937289

RESUMO

A new ß variant was found in a German diabetic patient whose blood samples appeared to contain 45% Hb A(1c) using Bio-Rad Variant V-II A1c-analyzer but 7.6% on boronate affinity chromatography. Structural studies using, HPLC, mass spectrometry, and the genomic DNA analysis revealed a new substitution in which the cysteine residue at position ß93 was replaced by serine. The variant was named Hb Riesa or ß93 (F9) Cys→Ser and accounted for 54.3% of the total haemoglobin. This suggests that the protein-synthesis processes for the mutant could be slightly more promoted than those of the wild-type. Hb Riesa is clinically and electrophoretically silent.


Assuntos
Diabetes Mellitus Tipo 1/sangue , Variação Genética , Hemoglobinas Glicadas/química , Hemoglobinas Glicadas/genética , Mutação de Sentido Incorreto , Sequência de Aminoácidos , Substituição de Aminoácidos , Cromatografia Líquida de Alta Pressão , Cisteína/genética , Cisteína/metabolismo , Diabetes Mellitus Tipo 1/genética , Humanos , Masculino , Pessoa de Meia-Idade , Dados de Sequência Molecular , Serina/genética , Serina/metabolismo , Espectrometria de Massas por Ionização por Electrospray , Globinas beta/genética , Globinas beta/metabolismo
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