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1.
Arch Virol ; 164(12): 2995-3006, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31576460

RESUMO

Reticuloendotheliosis virus (REV) is an important representative avian retrovirus. To improve our understanding of the host cellular responses to virus infection and the pathogenesis of REV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with multidimensional liquid chromatography-tandem mass spectrometry to detect changes in protein levels in chicken embryo fibroblast cells (CEFs) that were infected with REV or mock infected. In total, 605 cellular proteins were differentially expressed, among which 196, 345, and 286 were differentially expressed in REV-infected CEFs at 1, 3, and 5 days postinfection, respectively. Gene Ontology analysis indicated that the biological processes of the differentially expressed proteins were primarily related to cellular processes, metabolic processes, biological regulation, response to stimulus, and immune system processes and that the molecular functions in which the differentially expressed proteins were mainly involved were binding, catalytic activity, and enzyme regulator activity. Pathway analysis showed that a total of 143, 167, and 179 pathways, including protein digestion and absorption, focal adhesion, ECM-receptor interaction, cytokine-cytokine receptor interaction, Toll-like receptors, and JAK-STAT signaling, were enriched in REV-infected CEFs at 1, 3, and 5 days postinfection, respectively. In conclusion, this study is the first to analyze the protein profile of REV-infected CEFs using an iTRAQ approach. The results of this study provide valuable information for better understanding the host response to REV infection.


Assuntos
Fibroblastos/metabolismo , Doenças das Aves Domésticas/genética , Proteoma/genética , Vírus da Reticuloendoteliose/fisiologia , Infecções por Retroviridae/veterinária , Animais , Embrião de Galinha , Galinhas , Fibroblastos/química , Fibroblastos/virologia , Doenças das Aves Domésticas/metabolismo , Doenças das Aves Domésticas/virologia , Proteoma/química , Proteoma/metabolismo , Proteômica , Vírus da Reticuloendoteliose/genética , Infecções por Retroviridae/genética , Infecções por Retroviridae/metabolismo , Infecções por Retroviridae/virologia , Espectrometria de Massas em Tandem
2.
Nature ; 574(7776): 103-107, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31511700

RESUMO

The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5-although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7-9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.


Assuntos
DNA Antigo/análise , Esmalte Dentário/metabolismo , Fósseis , Perissodáctilos/classificação , Perissodáctilos/genética , Filogenia , Proteoma/genética , Proteômica , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Teorema de Bayes , História Antiga , Humanos , Masculino , Perissodáctilos/metabolismo , Fosforilação/genética , Proteoma/análise
3.
Vet Parasitol ; 272: 44-52, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31395204

RESUMO

In the present study, a quantitative proteomic approach to study changes in saliva proteins associated with canine leishmaniosis (CanL) was performed. For this, canine salivary proteins were analysed and compared between dogs before (T0) and after (T1) experimental infection with Leishmania infantum by high-throughput label-based quantitative LC-MS/MS proteomic approach and bioinformatic analysis of the in silico inferred interactome protein network was created from the initial list of differential proteins. More than 2000 proteins were identified, and of the 90 differentially expressed proteins between T0 and T1, 12 were down-regulated with log2 fold change lower than -0.5849, and 19 were up-regulated with log2 fold change greater than 0.5849. This study provides evidence of changes in salivary proteome that can occur in canine leishmaniosis and revealed biological pathways in saliva modulated in canine leishmaniosis with potential for further targeted research.


Assuntos
Doenças do Cão/fisiopatologia , Leishmaniose/veterinária , Saliva , Proteínas e Peptídeos Salivares/genética , Proteínas e Peptídeos Salivares/metabolismo , Animais , Cromatografia Líquida , Simulação por Computador , Cães , Regulação da Expressão Gênica , Leishmaniose/fisiopatologia , Proteoma/genética , Proteoma/metabolismo , Proteômica , Saliva/química , Saliva/metabolismo , Espectrometria de Massas em Tandem
4.
Nat Commun ; 10(1): 3035, 2019 07 10.
Artigo em Inglês | MEDLINE | ID: mdl-31292443

RESUMO

Mycobacterium tuberculosis readily adapts to survive a wide range of assaults by modifying its physiology and establishing a latent tuberculosis (TB) infection. Here we report a sophisticated mode of regulation by a tRNA-cleaving toxin that enlists highly selective ribosome stalling to recalibrate the transcriptome and remodel the proteome. This toxin, MazF-mt9, exclusively inactivates one isoacceptor tRNA, tRNALys43-UUU, through cleavage at a single site within its anticodon (UU↓U). Because wobble rules preclude compensation for loss of tRNALys43-UUU by the second M. tuberculosis lysine tRNA, tRNALys19-CUU, ribosome stalling occurs at in-frame cognate AAA Lys codons. Consequently, the transcripts harboring these stalled ribosomes are selectively cleaved by specific RNases, leading to their preferential deletion. This surgically altered transcriptome generates concomitant changes to the proteome, skewing synthesis of newly synthesized proteins away from those rich in AAA Lys codons toward those harboring few or no AAA codons. This toxin-mediated proteome reprogramming may work in tandem with other pathways to facilitate M. tuberculosis stress survival.


Assuntos
Proteínas de Bactérias/metabolismo , Endorribonucleases/metabolismo , Mycobacterium tuberculosis/fisiologia , Proteoma/genética , Ribossomos/metabolismo , Sistemas Toxina-Antitoxina/fisiologia , Toxinas Bacterianas/metabolismo , Tuberculose Latente/microbiologia , Mycobacterium tuberculosis/patogenicidade , Proteoma/metabolismo , RNA Bacteriano/metabolismo , RNA de Transferência/metabolismo , Transcriptoma/genética
5.
Gene ; 714: 143984, 2019 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-31330237

RESUMO

Intrinsically disordered proteins (IDPs) are highly abundant in eukaryotic proteomes and involved in key biological and cellular processes. Although some resources of disordered protein predictions are available from animal and plant proteomes, those related to cereals are largely unknown. Here, we present an overview of IDPomes from Oryza sativa, Zea mays, Sorghum bicolor and Brachypodium distachyon. The work includes a comparative analysis with the model plant Arabidopsis thaliana. The data show that the intrinsic disorder content increases with the proteome size. Gene Ontology analysis reveals that IDPs in the studied species are involved mainly in regulation of cellular and metabolic processes and responses to stimulus. Our findings strongly suggest that higher plants may use common cellular and regulatory mechanisms for adaptation to various environmental constraints.


Assuntos
Grão Comestível/genética , Proteínas Intrinsicamente Desordenadas/genética , Adaptação Biológica/genética , Arabidopsis/genética , Brachypodium/genética , Ontologia Genética , Genômica/métodos , Oryza/genética , Proteínas de Plantas/genética , Proteoma/genética , Sorghum/genética , Zea mays/genética
6.
Nat Commun ; 10(1): 2682, 2019 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-31213602

RESUMO

RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. We devise CAPRI, a method to map RNA-binding domains (RBDs) by simultaneous identification of RNA interacting crosslinked peptides and peptides adjacent to such crosslinked sites. CAPRI identifies more than 3000 RNA proximal peptides in Drosophila and human proteins with more than 45% of them forming new interaction interfaces. The comparison of orthologous proteins enables the identification of evolutionary conserved RBDs in globular domains and intrinsically disordered regions (IDRs). By comparing the sequences of IDRs through evolution, we classify them based on the type of motif, accumulation of tandem repeats, conservation of amino acid composition and high sequence divergence.


Assuntos
Evolução Molecular , Proteômica/métodos , Motivos de Ligação ao RNA/genética , Proteínas de Ligação a RNA/genética , RNA/metabolismo , Sequência de Aminoácidos/genética , Animais , Linhagem Celular , Sequência Conservada/genética , Reagentes para Ligações Cruzadas/química , Drosophila , Humanos , Peptídeos/química , Peptídeos/genética , Ligação Proteica/genética , Proteoma/genética , RNA/química , Proteínas de Ligação a RNA/química
7.
BMC Plant Biol ; 19(1): 280, 2019 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-31242871

RESUMO

BACKGROUND: The xylem sap of vascular plants primarily transports water and mineral nutrients from the roots to the shoots and also transports heavy metals such as cadmium (Cd). Proteomic changes in xylem sap is an important mechanism for detoxifying Cd by plants. However, it is unclear how proteins in xylem sap respond to Cd. Here, we investigated the effects of Cd stress on the xylem sap proteome of Brassica napus using a label-free shotgun proteomic approach to elucidate plant response mechanisms to Cd toxicity. RESULTS: We identified and quantified 672 proteins; 67% were predicted to be secretory, and 11% (73 proteins) were unique to Cd-treated samples. Cd stress caused statistically significant and biologically relevant abundance changes in 28 xylem sap proteins. Among these proteins, the metabolic pathways that were most affected were related to cell wall modifications, stress/oxidoreductases, and lipid and protein metabolism. We functionally validated a plant defensin-like protein, BnPDFL, which belongs to the stress/oxidoreductase category, that was unique to the Cd-treated samples and played a positive role in Cd tolerance. Subcellular localization analysis revealed that BnPDFL is cell wall-localized. In vitro Cd-binding assays revealed that BnPDFL has Cd-chelating activity. BnPDFL heterologous overexpression significantly enhanced Cd tolerance in E. coli and Arabidopsis. Functional disruption of Arabidopsis plant defensin genes AtPDF2.3 and AtPDF2.2, which are mainly expressed in root vascular bundles, significantly decreased Cd tolerance. CONCLUSIONS: Several xylem sap proteins in Brassica napus are differentially induced in response to Cd treatment, and plant defensin plays a positive role in Cd tolerance.


Assuntos
Brassica napus/genética , Cádmio/efeitos adversos , Proteoma/efeitos dos fármacos , Poluentes do Solo/efeitos adversos , Xilema/fisiologia , Brassica napus/efeitos dos fármacos , Brassica napus/metabolismo , Proteoma/genética , Proteoma/metabolismo , Xilema/efeitos dos fármacos
8.
Mol Biol (Mosk) ; 53(3): 524-528, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31184618

RESUMO

Proteins with homo-repeats of more than 4 amino acid residues in length were examined to understand whether some splicing sites in pre-mRNA may be attributed to homo-repeats in human proteins. The human proteome was found to contain a total of 404 proteins with homo-repeats that account for at least one splicing site in pre-mRNA. Pre-mRNA splicing sites were more often found in the C-terminal part (67%) than in the middle orN-terminal part of a homo-repeat. Ten homo-repeats were identified to have two splicing sites per repeat. The repeats were lysine homo-repeats in all but one case.


Assuntos
Proteínas/análise , Proteínas/química , Precursores de RNA/genética , Sítios de Splice de RNA/genética , Sequências Repetitivas de Aminoácidos/genética , Humanos , Lisina/genética , Lisina/metabolismo , Proteínas/genética , Proteoma/análise , Proteoma/química , Proteoma/genética , Processamento de RNA/genética
9.
J Sci Food Agric ; 99(13): 5760-5770, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31162844

RESUMO

BACKGROUND: It has been reported that antagonistic microorganisms could effectively control the infection of Fusarium graminearum. However, there is limited information on the control of F. graminearum by Saccharomyces cerevisiae, while the possible control mechanisms involved through proteomic and transcriptomic techniques have also not been reported. RESULTS: The results of this study showed that S. cerevisiae Y-912 could significantly inhibit the growth of F. graminearum Fg1, and the spore germination rate and germ tube length of F. graminearum Fg1 were also significantly inhibited by S. cerevisiae Y-912. Proteomic analysis revealed that differentially expressed proteins which were made of some basic proteins and enzymes related to basal metabolism, such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate mutase (PGAM), enolase (ENO), fructose diphosphate aldolase (FBA) and so on, were all down-regulated. The transcriptomics of F. graminearum control by S. cerevisiae was also analyzed. CONCLUSION: The control mechanism of S. cerevisiae Y-912 on F. graminearum Fg1 was a very complex material and energy metabolic process in which the related proteins and genes involved in the glycolytic pathway, tricarboxylic acid (TCA) cycle and amino acid metabolism were all down-regulated. © 2019 Society of Chemical Industry.


Assuntos
Fusarium/genética , Saccharomyces cerevisiae/genética , Transcriptoma , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Fusarium/crescimento & desenvolvimento , Fusarium/metabolismo , Proteoma/genética , Proteoma/metabolismo , Saccharomyces cerevisiae/crescimento & desenvolvimento , Saccharomyces cerevisiae/metabolismo , Esporos Fúngicos/genética , Esporos Fúngicos/crescimento & desenvolvimento , Esporos Fúngicos/metabolismo
10.
J Biosci ; 44(2)2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31180067

RESUMO

Proteins in a proteome can be identified from a sequence of K integers equal to the digitized volumes of subsequences with L residues from the primary sequence of a stretched protein. Exhaustive computations on the proteins of Helicobacter pylori (UniProt id UP000000210) with L and K in the range 4-8 show that approx. 90% of the proteins can be identified uniquely in this manner. This computational result can be translated into practice with a nanopore, an emerging technology that does not require analyte immobilization, proteolysis or labeling. Unlike other methods, most of which focus on a specific target protein, nanopore-based methods enable the identification of multiple proteins from a sample in a single run. Recent work by Kennedy, Kolmogorov and associates shows that the blockade current due to a protein molecule translocating through a nanopore is roughly proportional to one or more contiguous residues. The present study points to a modified version in which the volumes of subsequences (rather than of single residues) may be obtained by integrating the blockade current due to L contiguous residues. The advantages arising from this include lower detector bandwidth, elimination of the homopolymer problem and reduced noise. Because an identifier is based on near as well as distant (up to 2KL-L) residues, this approach uses more global information than an approach based on single residues and short-range correlations. The results of the study, which are available in a data supplement, are discussed in detail. Potential implementation issues are addressed.


Assuntos
Proteínas de Bactérias/isolamento & purificação , Helicobacter pylori/genética , Modelos Estatísticos , Mapeamento de Peptídeos/estatística & dados numéricos , Proteoma/isolamento & purificação , Sequência de Aminoácidos , Aminoácidos , Proteínas de Bactérias/genética , Bases de Dados de Proteínas , Helicobacter pylori/química , Nanoporos , Fragmentos de Peptídeos/análise , Mapeamento de Peptídeos/métodos , Proteoma/genética
11.
PLoS Pathog ; 15(6): e1007828, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31242261

RESUMO

The protozoan parasite Leishmania possesses a single flagellum, which is remodelled during the parasite's life cycle from a long motile flagellum in promastigote forms in the sand fly to a short immotile flagellum in amastigotes residing in mammalian phagocytes. This study examined the protein composition and in vivo function of the promastigote flagellum. Protein mass spectrometry and label free protein enrichment testing of isolated flagella and deflagellated cell bodies defined a flagellar proteome for L. mexicana promastigote forms (available via ProteomeXchange with identifier PXD011057). This information was used to generate a CRISPR-Cas9 knockout library of 100 mutants to screen for flagellar defects. This first large-scale knockout screen in a Leishmania sp. identified 56 mutants with altered swimming speed (52 reduced and 4 increased) and defined distinct mutant categories (faster swimmers, slower swimmers, slow uncoordinated swimmers and paralysed cells, including aflagellate promastigotes and cells with curled flagella and disruptions of the paraflagellar rod). Each mutant was tagged with a unique 17-nt barcode, providing a simple barcode sequencing (bar-seq) method for measuring the relative fitness of L. mexicana mutants in vivo. In mixed infections of the permissive sand fly vector Lutzomyia longipalpis, paralysed promastigotes and uncoordinated swimmers were severely diminished in the fly after defecation of the bloodmeal. Subsequent examination of flies infected with a single paralysed mutant lacking the central pair protein PF16 or an uncoordinated swimmer lacking the axonemal protein MBO2 showed that these promastigotes did not reach anterior regions of the fly alimentary tract. These data show that L. mexicana need directional motility for successful colonisation of sand flies.


Assuntos
Flagelos/metabolismo , Leishmania/metabolismo , Proteoma/metabolismo , Proteínas de Protozoários/metabolismo , Psychodidae/parasitologia , Animais , Flagelos/genética , Leishmania/genética , Proteoma/genética , Proteínas de Protozoários/genética
12.
PLoS Comput Biol ; 15(6): e1007066, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31158228

RESUMO

Growth rate and yield are fundamental features of microbial growth. However, we lack a mechanistic and quantitative understanding of the rate-yield relationship. Studies pairing computational predictions with experiments have shown the importance of maintenance energy and proteome allocation in explaining rate-yield tradeoffs and overflow metabolism. Recently, adaptive evolution experiments of Escherichia coli reveal a phenotypic diversity beyond what has been explained using simple models of growth rate versus yield. Here, we identify a two-dimensional rate-yield tradeoff in adapted E. coli strains where the dimensions are (A) a tradeoff between growth rate and yield and (B) a tradeoff between substrate (glucose) uptake rate and growth yield. We employ a multi-scale modeling approach, combining a previously reported coarse-grained small-scale proteome allocation model with a fine-grained genome-scale model of metabolism and gene expression (ME-model), to develop a quantitative description of the full rate-yield relationship for E. coli K-12 MG1655. The multi-scale analysis resolves the complexity of ME-model which hindered its practical use in proteome complexity analysis, and provides a mechanistic explanation of the two-dimensional tradeoff. Further, the analysis identifies modifications to the P/O ratio and the flux allocation between glycolysis and pentose phosphate pathway (PPP) as potential mechanisms that enable the tradeoff between glucose uptake rate and growth yield. Thus, the rate-yield tradeoffs that govern microbial adaptation to new environments are more complex than previously reported, and they can be understood in mechanistic detail using a multi-scale modeling approach.


Assuntos
Proteínas de Bactérias/metabolismo , Escherichia coli/metabolismo , Evolução Molecular , Proteínas de Bactérias/genética , Escherichia coli/genética , Genoma Bacteriano/genética , Modelos Biológicos , Proteoma/genética , Proteoma/metabolismo , Biologia de Sistemas
13.
Fish Shellfish Immunol ; 92: 438-449, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31229644

RESUMO

To understand the homeostasis mechanism of crustacean hepatopancreas to cold stress, iTRAQ proteomics based on the genome database of Litopenaeus vannamei (L. vannamei) was applied to investigate proteins changes and variety of the hepatopancreas during cold stress stage in this study. A total of 4062 distinct proteins were identified, 137 differentially expressed proteins (DEPs) including 62 differentially up-regulated proteins (DUPs) and 75 differentially down-regulated proteins (DDPs) were identified in G1 (18 °C) compared with CK (28 °C), 359 DEPs including 131 DUPs and 228 DDPs were identified in G2 (13 °C for 24 h) compared with CK. Based on bioinformatics analysis, the cold tolerance of L. vannamei might be related to energy metabolism such as amino acid, carbohydrate, lipid, and oxidative phosphorylation. Moreover, shrimp immunity was declined during cold stress stage. However, L. vannamei could cope with cold stress by enhancing the production of ATP and UFA. Notably, arginine kinase, heat shock proteins, and histones may act as positive regulators in L. vannamei under cold stress. Ten randomly selected proteins were used for validation using qRT-PCR and the expressions on the transcription level for most of the genes were similar to the results of iTRAQ. These results indicated that L. vannamei can maintain the organism homeostasis by a series of orderly regulatory process during cold stress. Furthermore, the results can provide guidance for shrimp farming.


Assuntos
Temperatura Baixa/efeitos adversos , Hepatopâncreas/imunologia , Imunidade Inata/genética , Penaeidae/imunologia , Proteoma/genética , Animais , Proteínas de Artrópodes/genética , Proteínas de Artrópodes/imunologia , Perfilação da Expressão Gênica , Histonas/metabolismo , Homeostase/imunologia , Penaeidae/genética , Proteoma/imunologia , Regulação para Cima/imunologia
14.
Int J Mol Sci ; 20(11)2019 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-31181633

RESUMO

The growth and development of maize roots are closely related to drought tolerance. In order to clarify the molecular mechanisms of drought tolerance between different maize (Zea mays L.) varieties at the protein level, the isobaric tags for relative and absolute quantitation (iTRAQ) quantitative proteomics were used for the comparative analysis of protein expression in the seedling roots of the drought-tolerant Chang 7-2 and drought-sensitive TS141 maize varieties under 20% polyethylene glycol 6000 (PEG 6000)-simulated drought stress. We identified a total of 7723 differentially expressed proteins (DEPs), 1243 were significantly differentially expressed in Chang 7-2 following drought stress, 572 of which were up-regulated and 671 were down-regulated; 419 DEPs were identified in TS141, 172 of which were up-regulated and 247 were down-regulated. In Chang 7-2, the DEPs were associated with ribosome pathway, glycolysis/gluconeogenesis pathway, and amino sugar and nucleotide sugar metabolism. In TS141, the DEPs were associated with metabolic pathway, phenylpropanoid biosynthesis pathway, and starch and sucrose metabolism. Compared with TS141, the higher drought tolerance of Chang 7-2 root system was attributed to a stronger water retention capacity; the synergistic effect of antioxidant enzymes; the strengthen cell wall; the osmotic stabilization of plasma membrane proteins; the effectiveness of recycling amino acid; and an improvement in the degree of lignification. The common mechanisms of the drought stress response between the two varieties included: The promotion of enzymes in the glycolysis/gluconeogenesis pathway; cross-protection against the toxicity of aldehydes and ammonia; maintenance of the cell membrane stability. Based on the proteome sequencing information, the coding region sequences of eight DEP-related genes were analyzed at the mRNA level by quantitative real-time PCR (qRT-PCR). The findings of this study can inform the future breeding of drought-tolerant maize varieties.


Assuntos
Secas , Pressão Osmótica , Proteínas de Plantas/metabolismo , Proteoma/metabolismo , Zea mays/genética , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Raízes de Plantas/genética , Raízes de Plantas/metabolismo , Proteoma/genética , Zea mays/metabolismo
15.
Arch Virol ; 164(7): 1889-1895, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31087191

RESUMO

Singapore grouper iridovirus (SGIV) is a lethal grouper virus containing 162 predicted ORFs. Previous proteomic studies led to identification of 73 SGIV structural proteins. Here, SDS-assisted tube-gel digestion and DOC-assisted in-solution digestion coupled with LC-ESI-MS/MS were applied to further profile the SGIV structural proteome. We identified a total of 90 SGIV structural proteins including 24 newly reported proteins. Additionally, several PTMs were identified, including 26 N-terminal acetylated proteins, three phosphorylated proteins, and one myristoylated protein. Importantly, 47 of the proteins that were identified are predicted to contain conserved domains. Our work greatly expands the repertoire of the SGIV structural proteome and provides more insight into the biology of SGIV.


Assuntos
Bass/virologia , Doenças dos Peixes/virologia , Iridovirus/genética , Iridovirus/isolamento & purificação , Proteínas Estruturais Virais/genética , Animais , Perfilação da Expressão Gênica , Fases de Leitura Aberta/genética , Proteoma/genética , Proteômica , Espectrometria de Massas em Tandem
16.
BMC Plant Biol ; 19(1): 212, 2019 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-31113380

RESUMO

BACKGROUND: Manganese (Mn), an essential element for plants, can be toxic when present in excess. Stylo (Stylosanthes) is a pioneer tropical legume with great potential for Mn tolerance, but its Mn tolerance mechanisms remain poorly understood. RESULTS: In this study, variations in Mn tolerance were observed among nine stylo genotypes. Stylo genotype 'RY5' exhibited the highest Mn tolerance compared to the other tested genotypes, whereas 'TF2001' was a Mn-sensitive genotype. The mechanisms underlying the response of stylo to Mn toxicity were further investigated using these two genotypes with contrasting Mn tolerance. Results showed that stylo genotype RY5 exhibited Mn tolerance superior to that of genotype TF2001, showing lower reductions in leaf chlorophyll concentration, chlorophyll fluorescence parameters, photosynthetic indexes and plant dry weight under Mn toxicity. A label-free quantitative proteomic analysis was conducted to investigate the protein profiles in the leaves and roots of RY5 in response to Mn toxicity. A total of 356 differentially expressed proteins (DEPs) were identified, including 206 proteins from leaves and 150 proteins from roots, which consisted of 71 upregulated, 62 downregulated, 127 strongly induced and 96 completely suppressed proteins. These DEPs were mainly involved in defense response, photosynthesis, carbon fixation, metabolism, cell wall modulation and signaling. The qRT-PCR analysis verified that 10 out of 12 corresponding gene transcription patterns correlated with their encoding proteins after Mn exposure. Finally, a schematic was constructed to reveal insights into the molecular processes in the leaves and roots of stylo in response to Mn toxicity. CONCLUSIONS: These findings suggest that stylo plants may cope with Mn toxicity by enhancing their defense response and phenylpropanoid pathways, adjusting photosynthesis and metabolic processes, and modulating protein synthesis and turnover. This study provides a platform for the future study of Mn tolerance mechanisms in stylo and may lead to a better understanding of the potential mechanisms underlying tropical legume adaptation to Mn toxicity.


Assuntos
Fabaceae/fisiologia , Manganês/toxicidade , Proteínas de Plantas/genética , Proteoma/genética , Fabaceae/genética , Genótipo , Proteínas de Plantas/metabolismo , Proteoma/metabolismo
17.
Int J Mol Sci ; 20(10)2019 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-31137823

RESUMO

The rubber grass Taraxacum kok-saghyz (TKS) contains large amounts of natural rubber (cis-1,4-polyisoprene) in its enlarged roots and it is an alternative crop source of natural rubber. Natural rubber biosynthesis (NRB) and storage in the mature roots of TKS is a cascade process involving many genes, proteins and their cofactors. The TKS genome has just been annotated and many NRB-related genes have been determined. However, there is limited knowledge about the protein regulation mechanism for NRB in TKS roots. We identified 371 protein species from the mature roots of TKS by combining two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). Meanwhile, a large-scale shotgun analysis of proteins in TKS roots at the enlargement stage was performed, and 3545 individual proteins were determined. Subsequently, all identified proteins from 2-DE gel and shotgun MS in TKS roots were subject to gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses and most proteins were involved in carbon metabolic process with catalytic activity in membrane-bounded organelles, followed by proteins with binding ability, transportation and phenylpropanoid biosynthesis activities. Fifty-eight NRB-related proteins, including eight small rubber particle protein (SRPP) and two rubber elongation factor(REF) members, were identified from the TKS roots, and these proteins were involved in both mevalonate acid (MVA) and methylerythritol phosphate (MEP) pathways. To our best knowledge, it is the first high-resolution draft proteome map of the mature TKS roots. Our proteomics of TKS roots revealed both MVA and MEP pathways are important for NRB, and SRPP might be more important than REF for NRB in TKS roots. These findings would not only deepen our understanding of the TKS root proteome, but also provide new evidence on the roles of these NRB-related proteins in the mature TKS roots.


Assuntos
Hemiterpenos/biossíntese , Látex/biossíntese , Proteínas de Plantas/metabolismo , Raízes de Plantas/metabolismo , Proteoma/metabolismo , Taraxacum/metabolismo , Hemiterpenos/genética , Proteínas de Plantas/genética , Proteoma/genética , Taraxacum/genética
18.
Science ; 364(6439): 480-484, 2019 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-31048489

RESUMO

Mutationally constrained epitopes of variable pathogens represent promising targets for vaccine design but are not reliably identified by sequence conservation. In this study, we employed structure-based network analysis, which applies network theory to HIV protein structure data to quantitate the topological importance of individual amino acid residues. Mutation of residues at important network positions disproportionately impaired viral replication and occurred with high frequency in epitopes presented by protective human leukocyte antigen (HLA) class I alleles. Moreover, CD8+ T cell targeting of highly networked epitopes distinguished individuals who naturally control HIV, even in the absence of protective HLA alleles. This approach thereby provides a mechanistic basis for immune control and a means to identify CD8+ T cell epitopes of topological importance for rational immunogen design, including a T cell-based HIV vaccine.


Assuntos
Vacinas contra a AIDS/genética , Vacinas contra a AIDS/imunologia , Síndrome de Imunodeficiência Adquirida/prevenção & controle , Linfócitos T CD8-Positivos/imunologia , Epitopos de Linfócito T/genética , Epitopos de Linfócito T/imunologia , HIV-1/imunologia , Alelos , Sequência Conservada , Antígenos HLA-B/genética , Antígenos HLA-B/imunologia , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/imunologia , Humanos , Mutação , Proteoma/genética , Proteoma/imunologia , Replicação Viral , Produtos do Gene gag do Vírus da Imunodeficiência Humana
19.
PLoS Negl Trop Dis ; 13(5): e0007362, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31091291

RESUMO

BACKGROUND: Schistosomiasis is a neglected disease affecting hundreds of millions worldwide. Of the three main species affecting humans, Schistosoma haematobium is the most common, and is the leading cause of urogenital schistosomiasis. S. haematobium infection can cause different urogenital clinical complications, particularly in the bladder, and furthermore, this parasite has been strongly linked with squamous cell carcinoma. A comprehensive analysis of the molecular composition of its different proteomes will contribute to developing new tools against this devastating disease. METHODS AND FINDINGS: By combining a comprehensive protein fractionation approach consisting of OFFGEL electrophoresis with high-throughput mass spectrometry, we have performed the first in-depth characterisation of the different discrete proteomes of S. haematobium that are predicted to interact with human host tissues, including the secreted and tegumental proteomes of adult flukes and secreted and soluble egg proteomes. A total of 662, 239, 210 and 138 proteins were found in the adult tegument, adult secreted, soluble egg and secreted egg proteomes, respectively. In addition, we probed these distinct proteomes with urine to assess urinary antibody responses from naturally infected human subjects with different infection intensities, and identified adult fluke secreted and tegument extracts as being the best predictors of infection. CONCLUSION: We provide a comprehensive dataset of proteins from the adult and egg stages of S. haematobium and highlight their utility as diagnostic markers of infection intensity. Protein composition was markedly different between the different extracts, highlighting the distinct subsets of proteins that different development stages present in their different niches. Furthermore, we have identified adult fluke ES and tegument extracts as best predictors of infection using urine antibodies of naturally infected people. This study provides the first steps towards the development of novel tools to control this important neglected tropical disease.


Assuntos
Proteínas de Helminto/metabolismo , Proteoma/metabolismo , Schistosoma haematobium/metabolismo , Esquistossomose Urinária/parasitologia , Animais , Feminino , Proteínas de Helminto/química , Proteínas de Helminto/genética , Humanos , Masculino , Proteoma/química , Proteoma/genética , Proteômica , Schistosoma haematobium/química , Schistosoma haematobium/classificação , Schistosoma haematobium/genética
20.
Genome Biol Evol ; 11(6): 1618-1629, 2019 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-31124562

RESUMO

Nucleomorphs are small nuclei that evolved from the nucleus of former eukaryotic endosymbionts of cryptophytes and chlorarachniophytes. These enigmatic organelles reside in their complex plastids and harbor the smallest and most compacted eukaryotic genomes investigated so far. Although the coding capacity of the nucleomorph genomes is small, a significant percentage of the encoded proteins (predicted nucleomorph-encoded proteins, pNMPs) is still not functionally annotated. We have analyzed pNMPs with unknown functions via Phyre2, a bioinformatic tool for prediction and modeling of protein structure, resulting in a functional annotation of 215 pNMPs out of 826 uncharacterized open reading frames of cryptophytes. The newly annotated proteins are predicted to participate in nucleomorph-specific functions such as chromosome organization and expression, as well as in modification and degradation of nucleomorph-encoded proteins. Additionally, we have functionally assigned nucleomorph-encoded, putatively plastid-targeted proteins among the reinvestigated pNMPs. Hints for a putative function in the periplastid compartment, the cytoplasm surrounding the nucleomorphs, emerge from the identification of pNMPs that might be homologs of endomembrane system-related proteins. These proteins are discussed in respect to their putative functions.


Assuntos
Criptófitas/citologia , Criptófitas/genética , Cromatina , Cromossomos , Fases de Leitura Aberta , Proteoma/genética
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