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2.
Cytogenet Genome Res ; 160(6): 295-308, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32683365

RESUMO

Intramolecular coevolution of amino acid sites has repeatedly been studied to improve predictions on protein structure and function. Thereby, the focus was on bacterial proteins with available crystallographic data. However, intramolecular coevolution has not yet been compared between protein sets along a gradient of functional proximity to fertilization. This is especially true for the potential effect of external selective forces on intraprotein coevolution. In this study, we investigated both aspects in equally sized sets of mammalian proteins representing spermatozoa, testis, entire body, and liver. For coevolutionary analyses, we derived the proportion of covarying sites per protein from amino acid alignments of 10 mammalian orthologues each. In confirmation of the validity of our coevolution proxy, we found positive associations with the nonsynonymous or amino acid substitution rate in all protein sets. However, our coevolution proxy negatively correlated with the number of protein interactants (node degree) in male reproductive protein sets alone. In addition, a negative association of our coevolution proxy with protein hydrophobicity was significant in sperm proteins only. Accordingly, the restrictive effect of protein interactants was most pronounced in male reproductive proteins, and the tendency of sperm proteins to form internal structures decreased the more coevolutionary sites they had. Both aspects illustrate that the share of outward and thus functional coevolution increases with greater proximity to fertilization. We found this conclusion confirmed by additional comparisons within sperm proteins. Thus, sperm proteins with high hydrophobicity had the lowest proportions of covarying sites and, according to gene annotations, localized more frequently to internal cellular structures. They should therefore be less exposed to postcopulatory forms of sexual selection. Their counterparts with low hydrophobicity had larger proportions of covarying sites and more often resided at the cell membrane or were secreted. At the cellular level, they are thus closer to externally induced forces of postcopulatory selection which are known for their potential to increase substitution rates. In addition, we show that the intermediary status of the testicular protein set in correlation analyses is probably due to a special combination of reproductive and somatic involvements.


Assuntos
Evolução Molecular , Fertilização , Proteínas/química , Proteínas/metabolismo , Espermatozoides/química , Espermatozoides/metabolismo , Animais , Doença , Fertilização/genética , Humanos , Interações Hidrofóbicas e Hidrofílicas , Masculino , Proteínas de Membrana/química , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Camundongos , Proteínas/genética , Proteoma/química , Proteoma/metabolismo , Suínos
3.
Nature ; 582(7813): 592-596, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32555458

RESUMO

Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported1, advances in mass-spectrometry-based proteomics2 have enabled increasingly comprehensive identification and quantification of the human proteome3-6. However, there have been few comparisons across species7,8, in stark contrast with genomics initiatives9. Here we use an advanced proteomics workflow-in which the peptide separation step is performed by a microstructured and extremely reproducible chromatographic system-for the in-depth study of 100 taxonomically diverse organisms. With two million peptide and 340,000 stringent protein identifications obtained in a standardized manner, we double the number of proteins with solid experimental evidence known to the scientific community. The data also provide a large-scale case study for sequence-based machine learning, as we demonstrate by experimentally confirming the predicted properties of peptides from Bacteroides uniformis. Our results offer a comparative view of the functional organization of organisms across the entire evolutionary range. A remarkably high fraction of the total proteome mass in all kingdoms is dedicated to protein homeostasis and folding, highlighting the biological challenge of maintaining protein structure in all branches of life. Likewise, a universally high fraction is involved in supplying energy resources, although these pathways range from photosynthesis through iron sulfur metabolism to carbohydrate metabolism. Generally, however, proteins and proteomes are remarkably diverse between organisms, and they can readily be explored and functionally compared at www.proteomesoflife.org.


Assuntos
Classificação , Aprendizado Profundo , Peptídeos/química , Peptídeos/isolamento & purificação , Proteoma/química , Proteoma/isolamento & purificação , Proteômica/métodos , Animais , Bacteroides/química , Bacteroides/classificação , Metabolismo dos Carboidratos , Cromatografia , Glicólise , Homeostase , Transporte de Íons , Proteínas com Ferro-Enxofre/metabolismo , Oxirredução , Fotossíntese , Biossíntese de Proteínas , Dobramento de Proteína , Proteólise , Especificidade da Espécie
4.
Mol Immunol ; 123: 7-17, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32387766

RESUMO

The identification of T cell epitopes derived from tumour specific antigens remains a significant challenge for the development of peptide-based vaccines and immunotherapies. The use of mass spectrometry-based approaches (immunopeptidomics) can provide powerful new avenues for the identification of such epitopes. In this study we report the use of complementary peptide antigen enrichment methods and a comprehensive mass spectrometric acquisition strategy to provide in-depth immunopeptidome data for the THP-1 cell line, a cell line used widely as a model of human leukaemia. To accomplish this, we combined robust experimental workflows that incorporated ultrafiltration or off-line reversed phase chromatography to enrich peptide ligand as well as a multifaceted data acquisition strategy using an Orbitrap Fusion LC-MS instrument. Using the combined datasets from the two ligand enrichment methods we gained significant depth in immunopeptidome coverage by identifying a total of 41,816 HLA class I peptides from THP-1 cells, including a significant number of peptides derived from different oncogenes or over expressed proteins associated with cancer. The physicochemical properties of the HLA-bound peptides dictated their recovery using the two ligand enrichment approaches and their distribution across the different precursor charge states considered in the data acquisition strategy. The data highlight the complementarity of the two enrichment procedures, and in cases where sample is not limiting, suggest that the combination of both approaches will yield the most comprehensive immunopeptidome information.


Assuntos
Antígenos de Neoplasias/análise , Mineração de Dados/métodos , Epitopos de Linfócito T/imunologia , Leucemia Mieloide Aguda/metabolismo , Peptídeos/análise , Proteoma/análise , Antígenos de Neoplasias/química , Antígenos de Neoplasias/imunologia , Células Cultivadas , Cromatografia Líquida/métodos , Bases de Dados de Proteínas , Humanos , Imunoterapia/métodos , Leucemia Mieloide Aguda/imunologia , Leucemia Mieloide Aguda/patologia , Leucemia Mieloide Aguda/terapia , Ligantes , Espectrometria de Massas/métodos , Biblioteca de Peptídeos , Peptídeos/química , Proteoma/química , Proteômica/métodos , Células THP-1
5.
Food Chem ; 321: 126712, 2020 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-32247179

RESUMO

Zein, a class of prolamine proteins extracted from maize, is extensively used in the food and pharmaceutical industries. Characterization of its components is essential for quality control and safety evaluation. We performed in silico digestion of zein proteins using tandem combinations of different proteinases, to improve protein sequence coverage and subsequent identification by nano-LC-MS/MS analysis. Trypsin/chymotrypsin yielded the highest protein sequence coverage of up to 79.5% and increased the number of proteins from 11 to 35 compared to trypsin/Lys-C. Besides, SDS-PAGE analysis revealed 37 proteins in the zein extract, as well as the possibility of protein polymers. Also, 420 peptides originating from 71 proteins were identified, of which 116 were predicted as bioactive by in silico approach. In conclusion, in silico prediction coupled with multi-enzyme digestion can significantly improve the coverage of complex zein protein proteome, and the potential function of zein proteins and peptides need be further investigated.


Assuntos
Excipientes/química , Peptídeos/química , Zea mays/química , Zeína/química , Sequência de Aminoácidos , Cromatografia Líquida de Alta Pressão , Excipientes/metabolismo , Peptídeos/metabolismo , Proteoma/química , Proteoma/metabolismo , Espectrometria de Massas em Tandem , Zea mays/metabolismo , Zeína/metabolismo
6.
Nature ; 580(7802): 235-238, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32269345

RESUMO

The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1-5. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge6-8. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)9,10 and Homo erectus from Dmanisi (Georgia)1, two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor-that is, similar to that of modern humans-may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.


Assuntos
Esmalte Dentário/química , Esmalte Dentário/metabolismo , Fósseis , Hominidae , Proteoma/análise , Proteoma/metabolismo , Sequência de Aminoácidos , Animais , República da Geórgia , Humanos , Masculino , Dente Molar/química , Dente Molar/metabolismo , Homem de Neandertal , Fosfoproteínas/análise , Fosfoproteínas/química , Fosfoproteínas/metabolismo , Fosforilação , Filogenia , Proteoma/química , Espanha
7.
Nat Rev Mol Cell Biol ; 21(6): 327-340, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32235894

RESUMO

The ability of living systems to adapt to changing conditions originates from their capacity to change their molecular constitution. This is achieved by multiple mechanisms that modulate the quantitative composition and the diversity of the molecular inventory. Molecular diversification is particularly pronounced on the proteome level, at which multiple proteoforms derived from the same gene can in turn combinatorially form different protein complexes, thus expanding the repertoire of functional modules in the cell. The study of molecular and modular diversity and their involvement in responses to changing conditions has only recently become possible through the development of new 'omics'-based screening technologies. This Review explores our current knowledge of the mechanisms regulating functional diversification along the axis of gene expression, with a focus on the proteome and interactome. We explore the interdependence between different molecular levels and how this contributes to functional diversity. Finally, we highlight several recent techniques for studying molecular diversity, with specific focus on mass spectrometry-based analysis of the proteome and its organization into functional modules, and examine future directions for this rapidly growing field.


Assuntos
Proteoma/química , Proteoma/metabolismo , Proteômica , Animais , Redes Reguladoras de Genes , Humanos , Complexos Multiproteicos , Mapas de Interação de Proteínas , Isoformas de Proteínas , Proteínas/química , Proteínas/genética , Proteínas/metabolismo , Proteoma/genética , Transcriptoma
8.
Nature ; 579(7799): 409-414, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32188942

RESUMO

Plants are essential for life and are extremely diverse organisms with unique molecular capabilities1. Here we present a quantitative atlas of the transcriptomes, proteomes and phosphoproteomes of 30 tissues of the model plant Arabidopsis thaliana. Our analysis provides initial answers to how many genes exist as proteins (more than 18,000), where they are expressed, in which approximate quantities (a dynamic range of more than six orders of magnitude) and to what extent they are phosphorylated (over 43,000 sites). We present examples of how the data may be used, such as to discover proteins that are translated from short open-reading frames, to uncover sequence motifs that are involved in the regulation of protein production, and to identify tissue-specific protein complexes or phosphorylation-mediated signalling events. Interactive access to this resource for the plant community is provided by the ProteomicsDB and ATHENA databases, which include powerful bioinformatics tools to explore and characterize Arabidopsis proteins, their modifications and interactions.


Assuntos
Proteínas de Arabidopsis/análise , Proteínas de Arabidopsis/química , Arabidopsis/química , Espectrometria de Massas , Proteoma/análise , Proteoma/química , Proteômica , Motivos de Aminoácidos , Arabidopsis/anatomia & histologia , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/biossíntese , Proteínas de Arabidopsis/genética , Bases de Dados de Proteínas , Conjuntos de Dados como Assunto , Regulação da Expressão Gênica de Plantas , Anotação de Sequência Molecular , Fases de Leitura Aberta , Especificidade de Órgãos , Fosfoproteínas/análise , Fosfoproteínas/química , Fosfoproteínas/genética , Fosforilação , Proteoma/biossíntese , Proteoma/genética , RNA Mensageiro/análise , RNA Mensageiro/biossíntese , RNA Mensageiro/genética , Transcriptoma
9.
Adv Exp Med Biol ; 1248: 425-430, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32185720

RESUMO

It is well established that palmitoylation plays a key role in the regulation of immune checkpoints, but the technical challenges in detecting protein palmitoylation have significantly prohibited further researches in this field. Till now, different approaches have been proposed, such as mutagenesis, antibody-based methods, bioinformatic prediction, "palmitate-centric" approaches, and "cysteine-centric" approaches. Of specific importance, high-throughput methods that allow the unbiased discovery of palmitoylation in the whole proteome should be further improved and employed. This chapter will summarize the methodological progresses for detecting protein palmitoylation, aiming to facilitate future researches in the lipid modification of immune checkpoint proteins.


Assuntos
Lipoilação , Palmitatos/metabolismo , Processamento de Proteína Pós-Traducional , Pontos de Checagem do Ciclo Celular/imunologia , Biologia Computacional , Cisteína/metabolismo , Humanos , Proteoma/química , Proteoma/metabolismo
10.
Mol Biol (Mosk) ; 54(1): 164-176, 2020.
Artigo em Russo | MEDLINE | ID: mdl-32163400

RESUMO

Lysine succinylation of proteins has potential impacts on protein structure and function, which occurs on post-translation level. However, the information about the succinylation of proteins in tea plants is limited. In the present study, the significant signal of succinylation in tea plants was found by western blot. Subsequently, we performed a qualitative analysis to globally identify the lysine succinylation of proteins using high accuracy nano LC-MS/MS combined with affinity purification. As a result, a total of 142 lysine succinylation sites were identified on 86 proteins in tea leaves. The identified succinylated proteins were involved in various biological processes and a large proportion of the succinylation sites were presented on proteins in the primary metabolism, including glyoxylate and dicarboxylate metabolism, TCA cycle and glycine, serine and threonine metabolism. Moreover, 10 new succinylation sites were detected on histones in tea leaves. The results suggest that succinylated proteins in tea plants might play critical regulatory roles in biological processes, especially in the primary metabolism. This study not only comprehensively analyzed the lysine succinylome in tea plants, but also provided valuable information for further investigating the functions of lysine succinylation in tea plants.


Assuntos
Lisina/química , Lisina/metabolismo , Processamento de Proteína Pós-Traducional , Proteoma/metabolismo , Chá/química , Chá/metabolismo , Cromatografia Líquida , Proteoma/química , Espectrometria de Massas em Tandem
11.
Nat Methods ; 17(4): 399-404, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32203386

RESUMO

Isobaric labeling empowers proteome-wide expression measurements simultaneously across multiple samples. Here an expanded set of 16 isobaric reagents based on an isobutyl-proline immonium ion reporter structure (TMTpro) is presented. These reagents have similar characteristics to existing tandem mass tag reagents but with increased fragmentation efficiency and signal. In a proteome-scale example dataset, we compared eight common cell lines with and without Torin1 treatment with three replicates, quantifying more than 8,800 proteins (mean of 7.5 peptides per protein) per replicate with an analysis time of only 1.1 h per proteome. Finally, we modified the thermal stability assay to examine proteome-wide melting shifts after treatment with DMSO, 1 or 20 µM staurosporine with five replicates. This assay identified and dose-stratified staurosporine binding to 228 cellular kinases in just one, 18-h experiment. TMTpro reagents allow complex experimental designs-all with essentially no missing values across the 16 samples and no loss in quantitative integrity.


Assuntos
Peptídeos/química , Proteoma/química , Proteômica/métodos , Espectrometria de Massas em Tandem/métodos , Linhagem Celular , Humanos , Marcação por Isótopo
12.
Curr Opin Chem Biol ; 54: 70-75, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-32131038

RESUMO

Protein-RNA interactions regulate all aspects of RNA metabolism and are crucial to the function of catalytic ribonucleoproteins. Until recently, the available technologies to capture RNA-bound proteins have been biased toward poly(A) RNA-binding proteins (RBPs) or involve molecular labeling, limiting their application. With the advent of organic-aqueous phase separation-based methods, we now have technologies that efficiently enrich the complete suite of RBPs and enable quantification of RBP dynamics. These flexible approaches to study RBPs and their bound RNA open up new research avenues for systems-level interrogation of protein-RNA interactions.


Assuntos
Proteoma/metabolismo , Proteínas de Ligação a RNA/metabolismo , RNA/metabolismo , Proteoma/química , Proteômica/métodos , RNA/química , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/isolamento & purificação
13.
Food Chem ; 319: 126531, 2020 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-32169763

RESUMO

Postmortem changes of sarcoplasmic and myofibrillar protein phosphorylation in pectoralis major (PM) muscle of broilers under pre-slaughter stress were investigated. Broiler chickens were randomly distributed to unstressed control and transport under high environmental temperature groups. PM muscle samples of transport-stressed broilers were classified into normal or pale, soft and exudative (PSE)-like. Sarcoplasmic fraction in PSE-like meat had a higher global phosphorylation level than that in normal meat at the early postmortem stage. The myofibrillar proteins showed diverse phosphorylation patterns at different postmortem times. The stress-induced highly phosphorylated sarcoplasmic proteins were glycometabolic enzymes, which partially contributed to accelerated glycolysis rate. The phosphorylation levels of most sarcomeric proteins identified in the myofibrillar fraction were affected by postmortem time, implying their roles in regulating muscle rigor mortis development. This work contributes to a deeper understanding of the biochemical processes that may lead to stress-induced changes in meat quality.


Assuntos
Proteínas Musculares/química , Músculos Peitorais/química , Proteoma/química , Animais , Galinhas , Glicólise , Temperatura Alta , Carne/análise , Células Musculares/química , Músculos Peitorais/lesões , Fosforilação , Estresse Fisiológico
14.
PLoS Biol ; 18(3): e3000631, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32150533

RESUMO

Endocytic recycling of internalized transmembrane proteins is essential for many important physiological processes. Recent studies have revealed that retromer-related Sorting Nexin family (SNX)-Bin/Amphiphysin/Rvs (BAR) proteins can directly recognize cargoes like cation-independent mannose 6-phosphate receptor (CI-MPR) and Insulin-like growth factor 1 receptor (IGF1R); however, it remains poorly understood how SNX-BARs select specific cargo proteins and whether they recognize additional ligands. Here, we discovered that the binding between SNX-BARs and CI-MPR or IGF1R is mediated by the phox-homology (PX) domain of SNX5 or SNX6 and a bipartite motif, termed SNX-BAR-binding motif (SBM), in the cargoes. Using this motif, we identified over 70 putative SNX-BAR ligands, many of which play critical roles in apoptosis, cell adhesion, signal transduction, or metabolite homeostasis. Remarkably, SNX-BARs could cooperate with both SNX27 and retromer in the recycling of ligands encompassing the SBM, PDZ-binding motif, or both motifs. Overall, our studies establish that SNX-BARs function as a direct cargo-selecting module for a large set of transmembrane proteins transiting the endosome, in addition to their roles in phospholipid recognition and biogenesis of tubular structures.


Assuntos
Proteoma/metabolismo , Receptor IGF Tipo 2/metabolismo , Nexinas de Classificação/química , Nexinas de Classificação/metabolismo , Motivos de Aminoácidos , Sítios de Ligação , Transporte Biológico , Simulação por Computador , Técnicas de Inativação de Genes , Células HeLa , Humanos , Domínios Proteicos , Proteoma/química , Receptor IGF Tipo 2/química , Semaforinas/metabolismo , Nexinas de Classificação/genética
15.
Nat Rev Drug Discov ; 19(6): 414-426, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32139903

RESUMO

Most therapeutics are designed to alter the activities of proteins. From metabolic enzymes to cell surface receptors, connecting the function of a protein to a cellular phenotype, to the activity of a drug and to a clinical outcome represents key mechanistic milestones during drug development. Yet, even for therapeutics with exquisite specificity, the sequence of events following target engagement can be complex. Interconnected communities of structural, metabolic and signalling proteins modulate diverse downstream effects that manifest as interindividual differences in efficacy, adverse effects and resistance to therapy. Recent advances in mass spectrometry proteomics have made it possible to decipher these complex relationships and to understand how factors such as genotype, cell type, local environment and external perturbations influence them. In this Review, we explore how proteomic technologies are expanding our understanding of protein communities and their responses to large- and small-molecule therapeutics.


Assuntos
Descoberta de Drogas/métodos , Proteoma , Proteômica/métodos , Animais , Anticorpos Monoclonais/química , Anticorpos Monoclonais/farmacologia , Humanos , Espectrometria de Massas , Proteoma/química , Proteoma/genética , Proteoma/metabolismo , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/farmacologia
16.
Nat Commun ; 11(1): 1548, 2020 03 25.
Artigo em Inglês | MEDLINE | ID: mdl-32214105

RESUMO

Data-independent acquisition approaches typically rely on experiment-specific spectrum libraries, requiring offline fractionation and tens to hundreds of injections. We demonstrate a library generation workflow that leverages fragmentation and retention time prediction to build libraries containing every peptide in a proteome, and then refines those libraries with empirical data. Our method specifically enables rapid, experiment-specific library generation for non-model organisms, which we demonstrate using the malaria parasite Plasmodium falciparum, and non-canonical databases, which we show by detecting missense variants in HeLa.


Assuntos
Cromatografia Líquida/métodos , Peptídeos/análise , Proteômica/métodos , Espectrometria de Massas em Tandem/métodos , Algoritmos , Bases de Dados de Proteínas , Células HeLa , Humanos , Biblioteca de Peptídeos , Peptídeos/química , Proteoma/análise , Proteoma/química , Reprodutibilidade dos Testes , Fluxo de Trabalho
17.
PLoS Negl Trop Dis ; 14(2): e0007758, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-32049966

RESUMO

Amblyomma americanum ticks transmit more than a third of human tick-borne disease (TBD) agents in the United States. Tick saliva proteins are critical to success of ticks as vectors of TBD agents, and thus might serve as targets in tick antigen-based vaccines to prevent TBD infections. We describe a systems biology approach to identify, by LC-MS/MS, saliva proteins (tick = 1182, rabbit = 335) that A. americanum ticks likely inject into the host every 24 h during the first 8 days of feeding, and towards the end of feeding. Searching against entries in GenBank grouped tick and rabbit proteins into 27 and 25 functional categories. Aside from housekeeping-like proteins, majority of tick saliva proteins belong to the tick-specific (no homology to non-tick organisms: 32%), protease inhibitors (13%), proteases (8%), glycine-rich proteins (6%) and lipocalins (4%) categories. Global secretion dynamics analysis suggests that majority (74%) of proteins in this study are associated with regulating initial tick feeding functions and transmission of pathogens as they are secreted within 24-48 h of tick attachment. Comparative analysis of the A. americanum tick saliva proteome to five other tick saliva proteomes identified 284 conserved tick saliva proteins: we speculate that these regulate critical tick feeding functions and might serve as tick vaccine antigens. We discuss our findings in the context of understanding A. americanum tick feeding physiology as a means through which we can find effective targets for a vaccine against tick feeding.


Assuntos
Proteínas de Artrópodes/química , Ixodidae/fisiologia , Proteoma/química , Saliva/química , Animais , Proteínas de Artrópodes/genética , Proteínas de Artrópodes/metabolismo , Cromatografia Líquida , Comportamento Alimentar , Feminino , Ixodidae/química , Ixodidae/genética , Masculino , Proteoma/genética , Proteoma/metabolismo , Coelhos , Saliva/metabolismo , Proteínas e Peptídeos Salivares/química , Proteínas e Peptídeos Salivares/genética , Proteínas e Peptídeos Salivares/metabolismo , Espectrometria de Massas em Tandem , Infestações por Carrapato/parasitologia
18.
Life Sci ; 248: 117444, 2020 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-32084433

RESUMO

AIMS: Nonhuman primates have been used to investigate pathogenic mechanisms and evaluate immune responses following Chlamydia trachomatis inoculation. This study aimed to systemically profile antibody responses to C. trachomatis infection in nonhuman primates. MATERIALS AND METHODS: Sera were obtained from 4 pig-tailed and 8 long-tailed macaques which were intravaginally or ocularly infected with live C. trachomatis organisms, and analyzed by C. trachomatis proteome array of antigens. KEY FINDINGS: The sera from 12 macaques recognized total 172 C. trachomatis antigens. While 84 antigens were recognized by pig-tailed macaques intravaginally infected with serovar D strain, 125 antigens were recognized by long-tailed macaques ocularly infected with serovar A, and 37 antigens were recognized by both. Ocular inoculation with virulent A2497 strain induced antibodies to more antigens. Among the antigens uniquely recognized by A2497 strain infected macaques, outer membrane complex B antigen (OmcB) induced robust antibody response. Although macaques infected by less virulent A/HAR-13 strain failed to develop antibodies to OmcB, reinfection by A2497 strain induced high levels of antibodies to OmcB. SIGNIFICANCE: Proteome array has revealed a correlation of chlamydial infection invasiveness with chlamydial antigen immunogenicity, and identified antibody responses to OmcB potentially as biomarkers for invasive infection with C. trachomatis.


Assuntos
Anticorpos Antibacterianos/biossíntese , Antígenos de Bactérias/sangue , Infecções por Chlamydia/imunologia , Chlamydia trachomatis/imunologia , Infecções do Sistema Genital/imunologia , Tracoma/imunologia , Animais , Anticorpos Antibacterianos/classificação , Antígenos de Bactérias/classificação , Proteínas da Membrana Bacteriana Externa/sangue , Infecções por Chlamydia/sangue , Infecções por Chlamydia/microbiologia , Chlamydia trachomatis/patogenicidade , Olho/imunologia , Olho/microbiologia , Feminino , Soros Imunes/química , Macaca fascicularis , Macaca nemestrina , Masculino , Análise Serial de Proteínas , Proteoma/química , Proteoma/imunologia , Infecções do Sistema Genital/sangue , Infecções do Sistema Genital/microbiologia , Tracoma/sangue , Tracoma/microbiologia , Vagina/imunologia , Vagina/microbiologia
19.
BMC Evol Biol ; 20(1): 28, 2020 02 13.
Artigo em Inglês | MEDLINE | ID: mdl-32054457

RESUMO

BACKGROUND: Temperature exerts a strong influence on protein evolution: species living in thermally distinct environments often exhibit adaptive differences in protein structure and function. However, previous research on protein temperature adaptation has focused on small numbers of proteins and on proteins adapted to extreme temperatures. Consequently, less is known about the types and quantity of evolutionary change that occurs to proteins when organisms adapt to small shifts in environmental temperature. In this study, these uncertainties were addressed by developing software that enabled comparison of structural changes associated with temperature adaptation (hydrogen bonding, salt bridge formation, and amino acid use) among large numbers of proteins from warm- and cold-adapted species of marine mussels, Mytilus galloprovincialis and Mytilus trossulus, respectively. RESULTS: Small differences in habitat temperature that characterize the evolutionary history of Mytilus mussels were sufficient to cause protein structural changes consistent with temperature adaptation. Hydrogen bonds and salt bridges that increase stability and protect against heat-induced denaturation were more abundant in proteins from warm-adapted M. galloprovincialis compared with proteins from cold-adapted M. trossulus. These structural changes were related to deviations in the use of polar and charged amino acids that facilitate formation of hydrogen bonds and salt bridges within proteins, respectively. Enzymes, in particular those within antioxidant and cell death pathways, were over-represented among proteins with the most hydrogen bonds and salt bridges in warm-adapted M. galloprovincialis. Unlike extremophile proteins, temperature adaptation in Mytilus proteins did not involve substantial changes in the number of hydrophobic or large volume amino acids, nor in the content of glycine or proline. CONCLUSIONS: Small shifts in organism temperature tolerance, such as that needed to cope with climate warming, may result from structural and functional changes to a small percentage of the proteome. Proteins in which function is dependent on large conformational change, notably enzymes, may be particularly sensitive to temperature perturbation and represent foci for natural selection. Protein temperature adaptation can occur through different types and frequencies of structural change, and adaptive mechanisms used to cope with small shifts in habitat temperature appear different from mechanisms used to retain protein function at temperature extremes.


Assuntos
Aclimatação , Mytilus/metabolismo , Proteínas/química , Proteínas/metabolismo , Temperatura , Aclimatação/genética , Adaptação Fisiológica/fisiologia , Sequência de Aminoácidos , Animais , Regulação da Temperatura Corporal/fisiologia , Ensaios de Triagem em Larga Escala/veterinária , Temperatura Alta , Ligação de Hidrogênio , Modelos Moleculares , Conformação Proteica , Processamento de Proteína Pós-Traducional/fisiologia , Proteoma/química , Proteoma/metabolismo , Relação Estrutura-Atividade
20.
Biochim Biophys Acta Proteins Proteom ; 1868(5): 140391, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32058072

RESUMO

Transcriptomic analysis of cone snail venom duct tissue has permitted the identification of diverse conopressin/conophysin precursor sequences from seven distinct Conus species. Multiple precursor isoforms are present in C.monile, C.lividus and C.loroisii. Aqueous extracts of the venom duct tissue from C.monile yield a band, at ~ 15-20 kDa on SDS-PAGE. In-gel trypsin digestion, followed by mass spectrometry establishes the presence of two distinct conopressin/conophysin isoforms that differ at position 8 in the predicted conopressin nonapeptide sequence. Mass spectrometric analysis of aqueous extracts revealed the presence of four conopressin related peptides, whose sequences could be deduced from MS/MS fragmentation patterns. The four sequences determined in this study are CFIRNCPKG*, CFIRNCPEG*, CFIRNCPK* and CFIRNCPE* (∗ indicates amide), which were further confirmed by comparison with chemically synthesized peptides. A conophysin with a mass of 9419.7 Da was also detected, corresponding to one of the isoforms revealed by the transcriptome data. Complete conservation of fourteen Cys residues and the key residues involved in peptide hormone binding is established by comparison of conophysin sequences, with the crystallographically characterized sequence of bovine neurophysin, in complex with vasopressin. A survey of available sequences for oxytocin/vasopressin peptides in both vertebrates and invertebrates establishes the conopressins as a distinct group in this family. C-terminal amidated, truncated conopressin analogs may arise by alternate post-translational processing.


Assuntos
Caramujo Conus/metabolismo , Venenos de Moluscos/química , Neurofisinas/química , Ocitocina/análogos & derivados , Vasopressinas/química , Animais , Caramujo Conus/genética , Venenos de Moluscos/genética , Proteoma/química , Homologia de Sequência de Aminoácidos , Transcriptoma
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