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1.
bioRxiv ; 2024 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-38798513

RESUMO

The antiviral protein kinase R (PKR) is activated by viral double-stranded RNA and phosphorylates translation initiation factor eIF2α, thereby inhibiting translation and virus replication. Most poxviruses contain two PKR inhibitors, called E3 and K3 in vaccinia virus (VACV), which are determinants of viral host range. The prevailing model for E3 function is that it inhibits PKR through the non-specific sequestration of double-stranded (ds) RNA. Our data revealed that Syrian hamster PKR was resistant to E3, which is at odds with the sequestration model. However, Syrian hamster PKR was still sensitive to K3 inhibition. In contrast, Armenian hamster PKR showed opposite sensitivities, being sensitive to E3 and resistant to K3 inhibition. Mutational analyses of hamster PKRs showed that sensitivity to E3 inhibition was largely determined by the region linking the dsRNA-binding domains and the kinase domain of PKR, whereas two amino acid residues in the kinase domain (helix αG) determined sensitivity to K3. Expression of PKRs in congenic cells showed that Syrian hamster PKR containing the two Armenian hamster PKR residues in helix-αG was resistant to wild type VACV infection, and that cells expressing either hamster PKR recapitulated the phenotypes observed in species-derived cell lines. The observed resistance of Syrian hamster PKR to E3 explains its host range function and challenges the paradigm that dsRNA-binding PKR inhibitors mainly act by the sequestration of dsRNA. Significance: The molecular mechanisms that govern the host range of viruses are incompletely understood. A small number of poxvirus genes have been identified that influence the host range of poxviruses. We show that the host range functions of E3 and K3, two host range factors from vaccinia virus, are a result of species-specific interactions with the antiviral protein kinase R (PKR) and that PKR from closely related species displayed dramatic differences in their sensitivities to these viral inhibitors. While there is a substantial body of work demonstrating host-specific interactions with K3, the current model for E3-mediated PKR inhibition is that E3 non-specifically sequesters dsRNA to prevent PKR activation. This model does not predict species-specific sensitivity to E3; therefore, our data suggest that the current model is incomplete, and that dsRNA sequestration is not the primary mechanism for E3 activity.

2.
Biomolecules ; 13(2)2023 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-36830694

RESUMO

Cowpox viruses (CPXVs) exhibit the broadest known host range among the Poxviridae family and have caused lethal outbreaks in various zoo animals and pets across 12 Eurasian countries, as well as an increasing number of human cases. Herein, we review the history of how the cowpox name has evolved since the 1700s up to modern times. Despite early documentation of the different properties of CPXV isolates, only modern genetic analyses and phylogenies have revealed the existence of multiple Orthopoxvirus species that are currently constrained under the CPXV designation. We further chronicle modern outbreaks in zoos, domesticated animals, and humans, and describe animal models of experimental CPXV infections and how these can help shaping CPXV species distinctions. We also describe the pathogenesis of modern CPXV infections in animals and humans, the geographic range of CPXVs, and discuss CPXV-host interactions at the molecular level and their effects on pathogenicity and host range. Finally, we discuss the potential threat of these viruses and the future of CPXV research to provide a comprehensive review of CPXVs.


Assuntos
Vírus da Varíola Bovina , Varíola Bovina , Animais , Humanos , Vírus da Varíola Bovina/genética , Varíola Bovina/epidemiologia , Filogenia , Surtos de Doenças
3.
mBio ; 14(1): e0152622, 2023 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-36515529

RESUMO

Poxviruses are often thought to evolve relatively slowly because they are double-stranded DNA pathogens with proofreading polymerases. However, poxviruses have highly adaptable genomes and can undergo relatively rapid genotypic and phenotypic change, as illustrated by the recent increase in human-to-human transmission of monkeypox virus. Advances in deep sequencing technologies have demonstrated standing nucleotide variation in poxvirus populations, which has been underappreciated. There is also an emerging understanding of the role genomic architectural changes play in shaping poxvirus evolution. These mechanisms include homologous and nonhomologous recombination, gene duplications, gene loss, and the acquisition of new genes through horizontal gene transfer. In this review, we discuss these evolutionary mechanisms and their potential roles for adaption to novel host species and modulating virulence.


Assuntos
Evolução Molecular , Poxviridae , Humanos , Poxviridae/genética , Especificidade de Hospedeiro , Duplicação Gênica
4.
Viruses ; 14(7)2022 07 19.
Artigo em Inglês | MEDLINE | ID: mdl-35891544

RESUMO

Crocodilepox virus (CRV) belongs to the Poxviridae family and mainly infects hatchling and juvenile Nile crocodiles. Most poxviruses encode inhibitors of the host antiviral protein kinase R (PKR), which is activated by viral double-stranded (ds) RNA formed during virus replication, resulting in the phosphorylation of eIF2α and the subsequent shutdown of general mRNA translation. Because CRV lacks orthologs of known poxviral PKR inhibitors, we experimentally characterized one candidate (CRV157), which contains a predicted dsRNA-binding domain. Bioinformatic analyses indicated that CRV157 evolved independently from other poxvirus PKR inhibitors. CRV157 bound to dsRNA, co-localized with PKR in the cytosol, and inhibited PKR from various species. To analyze whether CRV157 could inhibit PKR in the context of a poxvirus infection, we constructed recombinant vaccinia virus strains that contain either CRV157, or a mutant CRV157 deficient in dsRNA binding in a strain that lacks PKR inhibitors. The presence of wild-type CRV157 rescued vaccinia virus replication, while the CRV157 mutant did not. The ability of CRV157 to inhibit PKR correlated with virus replication and eIF2α phosphorylation. The independent evolution of CRV157 demonstrates that poxvirus PKR inhibitors evolved from a diverse set of ancestral genes in an example of convergent evolution.


Assuntos
Poxviridae , eIF-2 Quinase , Fator de Iniciação 2 em Eucariotos/genética , Fator de Iniciação 2 em Eucariotos/metabolismo , Fosforilação , Poxviridae/genética , Poxviridae/metabolismo , RNA de Cadeia Dupla/genética , Vaccinia virus/genética , Proteínas Virais/metabolismo , Replicação Viral , eIF-2 Quinase/metabolismo
5.
Proc Natl Acad Sci U S A ; 119(20): e2115354119, 2022 05 17.
Artigo em Inglês | MEDLINE | ID: mdl-35549551

RESUMO

Myxoma virus (MYXV) causes localized cutaneous fibromas in its natural hosts, tapeti and brush rabbits; however, in the European rabbit, MYXV causes the lethal disease myxomatosis. Currently, the molecular mechanisms underlying this increased virulence after cross-species transmission are poorly understood. In this study, we investigated the interaction between MYXV M156 and the host protein kinase R (PKR) to determine their crosstalk with the proinflammatory nuclear factor kappa B (NF-κB) pathway. Our results demonstrated that MYXV M156 inhibits brush rabbit PKR (bPKR) more strongly than European rabbit PKR (ePKR). This moderate ePKR inhibition could be improved by hyperactive M156 mutants. We hypothesized that the moderate inhibition of ePKR by M156 might incompletely suppress the signal transduction pathways modulated by PKR, such as the NF-κB pathway. Therefore, we analyzed NF-κB pathway activation with a luciferase-based promoter assay. The moderate inhibition of ePKR resulted in significantly higher NF-κB­dependent reporter activity than complete inhibition of bPKR. We also found a stronger induction of the NF-κB target genes TNFα and IL-6 in ePKR-expressing cells than in bPKR-expressing cells in response to M156 in both transfection and infections assays. Furthermore, a hyperactive M156 mutant did not cause ePKR-dependent NF-κB activation. These observations indicate that M156 is maladapted for ePKR inhibition, only incompletely blocking translation in these hosts, resulting in preferential depletion of short­half-life proteins, such as the NF-κB inhibitor IκBα. We speculate that this functional activation of NF-κB induced by the intermediate inhibition of ePKR by M156 may contribute to the increased virulence of MYXV in European rabbits.


Assuntos
Interações Hospedeiro-Patógeno , Myxoma virus , Mixomatose Infecciosa , NF-kappa B , Coelhos , eIF-2 Quinase , Animais , Redes e Vias Metabólicas , Myxoma virus/genética , Myxoma virus/patogenicidade , Mixomatose Infecciosa/metabolismo , Mixomatose Infecciosa/virologia , Inibidor de NF-kappaB alfa/metabolismo , NF-kappa B/metabolismo , Coelhos/virologia , eIF-2 Quinase/metabolismo
6.
PLoS Pathog ; 17(1): e1009183, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33444388

RESUMO

The antiviral protein kinase R (PKR) is an important host restriction factor, which poxviruses must overcome to productively infect host cells. To inhibit PKR, many poxviruses encode a pseudosubstrate mimic of the alpha subunit of eukaryotic translation initiation factor 2 (eIF2), designated K3 in vaccinia virus. Although the interaction between PKR and eIF2α is highly conserved, some K3 orthologs from host-restricted poxviruses were previously shown to inhibit PKR in a species-specific manner. To better define this host range function, we compared the sensitivity of PKR from 17 mammals to inhibition by K3 orthologs from closely related orthopoxviruses, a genus with a generally broader host range. The K3 orthologs showed species-specific inhibition of PKR and exhibited three distinct inhibition profiles. In some cases, PKR from closely related species showed dramatic differences in their sensitivity to K3 orthologs. Vaccinia virus expressing the camelpox virus K3 ortholog replicated more than three orders of magnitude better in human and sheep cells than a virus expressing vaccinia virus K3, but both viruses replicated comparably well in cow cells. Strikingly, in site-directed mutagenesis experiments between the variola virus and camelpox virus K3 orthologs, we found that different amino acid combinations were necessary to mediate improved or diminished inhibition of PKR derived from different host species. Because there is likely a limited number of possible variations in PKR that affect K3-interactions but still maintain PKR/eIF2α interactions, it is possible that by chance PKR from some potential new hosts may be susceptible to K3-mediated inhibition from a virus it has never previously encountered. We conclude that neither the sensitivity of host proteins to virus inhibition nor the effectiveness of viral immune antagonists can be inferred from their phylogenetic relatedness but must be experimentally determined.


Assuntos
Antivirais/antagonistas & inibidores , Especificidade de Hospedeiro , Orthopoxvirus/classificação , Orthopoxvirus/fisiologia , Infecções por Poxviridae/virologia , Replicação Viral , eIF-2 Quinase/antagonistas & inibidores , Sequência de Aminoácidos , Animais , Antivirais/metabolismo , Células HeLa , Humanos , Fosforilação , Filogenia , Infecções por Poxviridae/genética , Infecções por Poxviridae/metabolismo , Homologia de Sequência , eIF-2 Quinase/genética , eIF-2 Quinase/metabolismo
7.
Oncotarget ; 7(19): 27185-98, 2016 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-27034009

RESUMO

In an era where mutational profiles inform treatment options, it is critical to know the extent to which tumor biopsies represent the molecular profile of the primary and metastatic tumor. Head and neck squamous cell carcinoma (HNSCC) arise primarily in the mucosal lining of oral cavity and oropharynx. Despite aggressive therapy the 5-year survival rate is at 50%. The primary objective of this study is to characterize the degree of intratumor mutational heterogeneity in HNSCC. We used multi-region sequencing of paired primary and metastatic tumor DNA of 24 spatially distinct samples from seven patients with HNSCC of larynx, floor of the mouth (FOM) or oral tongue. Full length, in-depth sequencing of 202 genes implicated in cancer was carried out. Larynx and FOM tumors had more than 69.2% unique SNVs between the paired primary and metastatic lesions. In contrast, the oral tongue HNSCC had only 33.3% unique SNVs across multiple sites. In addition, HNSCC of the oral tongue had fewer mutations than larynx and FOM tumors. These findings were validated on the Affymetrix whole genome 6.0 array platform and were consistent with data from The Cancer Genome Atlas (TCGA). This is the first report demonstrating differences in mutational heterogeneity varying by subsite in HNSCC. The heterogeneity within laryngeal tumor specimens may lead to an underestimation of the genetic abnormalities within tumors and may foster resistance to standard treatment protocols. These findings are relevant to investigators and clinicians developing personalized cancer treatments based on identification of specific mutations in tumor biopsies.


Assuntos
Carcinoma de Células Escamosas/genética , Heterogeneidade Genética , Neoplasias de Cabeça e Pescoço/genética , Mutação , Adulto , Carcinoma de Células Escamosas/patologia , Variações do Número de Cópias de DNA , Feminino , Neoplasias de Cabeça e Pescoço/patologia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Neoplasias Laríngeas/genética , Neoplasias Laríngeas/patologia , Perda de Heterozigosidade , Masculino , Pessoa de Meia-Idade , Neoplasias Bucais/genética , Neoplasias Bucais/patologia , Neoplasias da Língua/genética , Neoplasias da Língua/patologia
8.
Artigo em Inglês | MEDLINE | ID: mdl-26773880

RESUMO

Dextran sulfate is a polyanionic derivative of dextran, produced by esterification of dextran with chlorosulphonic acid. Dextran sulfate with an average molecular weight of 8000Da can be added to the cell culture to inhibit binding of proteins to cells, increasing cellular growth and productivity. Residual dextran sulfate levels must be monitored during the purification process development to insure clearance. A size-exclusion chromatography based HPLC assay has been developed for the separation and quantitation of dextran sulfate in a highly concentrated purified protein drug substance sample. Trichloroacetic acid (TCA) was used to precipitate the protein and separate the dextran sulfate. Detection and quantitation of dextran sulfate was achieved by post column reaction with dimethylene blue to form a metachromatic complex that absorbs visible light at 530nm. The quantitation limit (LOQ) was determined to be 1.5µg/mL dextran sulfate in high concentration protein samples.


Assuntos
Cromatografia em Gel/métodos , Cromatografia Líquida de Alta Pressão/métodos , Sulfato de Dextrana/análise , Proteínas/química , Sulfato de Dextrana/química , Limite de Detecção , Modelos Lineares , Reprodutibilidade dos Testes
9.
Nucleic Acids Res ; 42(16): 10321-30, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25147208

RESUMO

Translational control of transcription factor ATF4 through paired upstream ORFs (uORFs) plays an important role in eukaryotic gene regulation. While it is typically induced by phosphorylation of eIF2α, ATF4 translation can be also induced by expression of a translational inhibitor protein, eIF5-mimic protein 1 (5MP1, also known as BZW2) in mammals. Here we show that the 5MP gene is maintained in eukaryotes under strong purifying selection, but is uniquely missing in two major phyla, nematoda and ascomycota. The common function of 5MP from protozoa, plants, fungi and insects is to control translation by inhibiting eIF2. The affinity of human 5MP1 to eIF2ß was measured as being equivalent to the published value of human eIF5 to eIF2ß, in agreement with effective competition of 5MP with eIF5 for the main substrate, eIF2. In the red flour beetle, Tribolium castaneum, RNA interference studies indicate that 5MP facilitates expression of GADD34, a downstream target of ATF4. Furthermore, both 5MP and ATF4 are essential for larval development. Finally, 5MP and the paired uORFs allowing ATF4 control are conserved in the entire metazoa except nematoda. Based on these findings, we discuss the phylogenetic and functional linkage between ATF4 regulation and 5MP expression in this group of eukaryotes.


Assuntos
Fator 4 Ativador da Transcrição/genética , Proteínas de Ligação a DNA/metabolismo , Regulação da Expressão Gênica , Biossíntese de Proteínas , Fator 4 Ativador da Transcrição/biossíntese , Animais , Proteínas de Ligação a DNA/classificação , Proteínas de Ligação a DNA/fisiologia , Fator de Iniciação 2 em Eucariotos/antagonistas & inibidores , Fator de Iniciação 2 em Eucariotos/metabolismo , Fator de Iniciação 5 em Eucariotos/metabolismo , Humanos , Proteínas de Insetos/metabolismo , Fases de Leitura Aberta , Filogenia , Proteína Fosfatase 1/metabolismo , Saccharomyces cerevisiae/metabolismo , Tribolium/enzimologia , Tribolium/genética , Tribolium/crescimento & desenvolvimento
10.
Extremophiles ; 18(3): 525-35, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24682608

RESUMO

Great Salt Lake (GSL) represents one of the world's most hypersaline environments. In this study, the archaeal and bacterial communities at the North and South arms of the lake were surveyed by cloning and sequencing the 16S rRNA gene. The sampling locations were chosen for high salt concentration and the presence of unique environmental gradients, such as petroleum seeps and high sulfur content. Molecular techniques have not been systematically applied to this extreme environment, and thus the composition and the genetic diversity of microbial communities at GSL remain mostly unknown. This study led to the identification of 58 archaeal and 42 bacterial operational taxonomic units. Our phylogenetic and statistical analyses displayed a high biodiversity of the microbial communities in this environment. In this survey, we also showed that the majority of the 16S rRNA gene sequences within the clone library were distantly related to previously described environmental halophilic archaeal and bacterial taxa and represent novel phylotypes.


Assuntos
Archaea/genética , Bactérias/genética , Lagos/microbiologia , Microbiota , Archaea/classificação , Archaea/isolamento & purificação , Bactérias/classificação , Bactérias/isolamento & purificação , Lagos/química , Filogenia , Salinidade , Tolerância ao Sal , Utah
11.
BMC Evol Biol ; 11: 62, 2011 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-21385447

RESUMO

BACKGROUND: Replicate experiments are often difficult to find in evolutionary biology, as this field is inherently an historical science. However, viruses, bacteria and phages provide opportunities to study evolution in both natural and experimental contexts, due to their accelerated rates of evolution and short generation times. Here we investigate HIV-1 evolution by using a natural model represented by monozygotic twins infected synchronically at birth with an HIV-1 population from a shared blood transfusion source. We explore the evolutionary processes and population dynamics that shape viral diversity of HIV in these monozygotic twins. RESULTS: Despite the identical host genetic backdrop of monozygotic twins and the identical source and timing of the HIV-1 inoculation, the resulting HIV populations differed in genetic diversity, growth rate, recombination rate, and selection pressure between the two infected twins. CONCLUSIONS: Our study shows that the outcome of evolution is strikingly different between these two "replicates" of viral evolution. Given the identical starting points at infection, our results support the impact of random epigenetic selection in early infection dynamics. Our data also emphasize the need for a better understanding of the impact of host-virus interactions in viral evolution.


Assuntos
Doenças em Gêmeos/virologia , Infecções por HIV/virologia , HIV-1/genética , Gêmeos Monozigóticos , Evolução Molecular , Variação Genética , Humanos , Masculino , Filogenia , Dinâmica Populacional , RNA Viral/genética , Análise de Sequência de RNA
12.
Infect Genet Evol ; 11(1): 209-21, 2011 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-20849978

RESUMO

The evolutionary history of two human malaria parasites, Plasmodium vivax and Plasmodium malariae, remains unresolved. The near genetic identity between human P. vivax and P. malariae, and primate P. simium and P. brasilianum, respectively, suggests that recent host transfers occurred, but questions remain, such as whether the transfer was from humans to New World monkeys or vice versa, and when the transfers occurred. Here, we investigate the phylogenies, haplotype networks, positive selection and genetic diversity among these parasite species by means of four genes. Human P. vivax and primate P. simium recently derived one from the other; at least two host transfers have occurred. Human P. malariae and primate P. brasilianum also have recently derived one from the other by lateral host transfer. The direction of the host transfer cannot be decided in either one of the two pairs of species, owing to the scarcity of available strains from the primate parasites.


Assuntos
Plasmodium/genética , Animais , Genes de Protozoários , Variação Genética , Haplótipos , Filogenia , Plasmodium/classificação , Especificidade da Espécie
13.
BMC Infect Dis ; 10: 13, 2010 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-20092631

RESUMO

BACKGROUND: Gonorrhea is a major sexually transmitted disease (STD) in many countries worldwide. The emergence of fluoroquinolone resistance has complicated efforts to control and treat this disease. We report the first study of the evolutionary processes acting on transmission dynamics of a resistant gonococcal population from Shanghai, China. We compare these findings with our previous study of the evolution of a fluoroquinolone sensitive gonococcal population from Baltimore, MD. METHODS: Ninety six gonococcal samples were collected from male patients in Shanghai, China. All samples were fluoroquinolone resistant. Seven MLST housekeeping genes, two fluoroquinolone resistance genes (gyrA and parC) and the porB gene were sequenced and subjected to population genetic and evolutionary analyses. We estimated genetic diversity, recombination, growth, and selective pressure. The evolutionary history and population dynamics of the Shanghai population were also inferred and compared with that observed in a fluoroquinolone sensitive gonococcal population from Baltimore. RESULTS: For both populations, mutation plays a larger role than recombination in the evolution of the porB gene, whereas the latter seems to be the main force driving the evolution of housekeeping and fluoroquinolone resistance genes. In both populations there was evidence for positively selected sites in all genes analyzed. The phylogenetic analyses showed no temporal clustering in the Shanghai gonococcal population, nor did we detect shared allelic profiles between the Shanghai and the Baltimore populations. Past population dynamics of gonococcal strains from Shanghai showed a rising relative effective population size (Ne) in MLST genes with a declining relative Ne for gyrA and parC, whereas among sensitive strains from Baltimore we previously observed concordance among these genes. In both Shanghai and Baltimore, the past population dynamics of gonococcal strains tracked changes in the prevalence of gonorrhea. CONCLUSIONS: Our study illustrates both similarities and differences in the evolutionary processes acting on gonococcal populations in different geographic areas. An explanation of this pattern that may apply in China is the continued use of quinolone antibiotics despite widespread resistance. Population genetic analysis of gonococcal strains in conjunction with epidemiological surveillance may provide insights into the epidemic behavior of antibiotic resistant strains and help to design control measures.


Assuntos
Evolução Molecular , Genética Populacional , Gonorreia/epidemiologia , Neisseria gonorrhoeae/classificação , Adolescente , Adulto , Antibacterianos/uso terapêutico , Baltimore/epidemiologia , Teorema de Bayes , China , DNA Bacteriano/genética , Farmacorresistência Bacteriana , Fluoroquinolonas/uso terapêutico , Variação Genética , Geografia , Humanos , Funções Verossimilhança , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Mutação , Neisseria gonorrhoeae/efeitos dos fármacos , Neisseria gonorrhoeae/genética , Filogenia , Dinâmica Populacional , Recombinação Genética , Seleção Genética , Análise de Sequência de DNA , Adulto Jovem
14.
J Virol ; 82(11): 5548-61, 2008 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-18385252

RESUMO

Throughout the natural course of human immunodeficiency virus (HIV) infection, follicular dendritic cells (FDCs) trap and retain large quantities of particle-associated HIV RNA in the follicles of secondary lymphoid tissue. We have previously found that murine FDCs in vivo could maintain trapped virus particles in an infectious state for at least 9 months. Here we sought to determine whether human FDCs serve as an HIV reservoir, based on the criteria that virus therein must be replication competent, genetically diverse, and archival in nature. We tested our hypothesis using postmortem cells and tissues obtained from three HIV-infected subjects and antemortem blood samples obtained from one of these subjects. Replication competence was determined using coculture, while genetic diversity and the archival nature of virus were established using phylogenetic and population genetics methods. We found that FDC-trapped virus was replication competent and demonstrated greater genetic diversity than that of virus found in most other tissues and cells. Antiretrovirus-resistant variants that were not present elsewhere were also detected on FDCs. Furthermore, genetic similarity was observed between FDC-trapped HIV and viral species recovered from peripheral blood mononuclear cells obtained 21 and 22 months antemortem, but was not present in samples obtained 4 and 18 months prior to the patient's death, indicating that FDCs can archive HIV. These data indicate that FDCs represent a significant reservoir of infectious and diverse HIV, thereby providing a mechanism for viral persistence for months to years.


Assuntos
Células Dendríticas Foliculares/imunologia , Células Dendríticas Foliculares/metabolismo , Infecções por HIV/imunologia , HIV-1/imunologia , Linfócitos T CD4-Positivos/imunologia , Linfócitos T CD4-Positivos/metabolismo , Técnicas de Cocultura , Genótipo , HIV-1/genética , HIV-1/metabolismo , Humanos , Mutação/genética , Filogenia , Proteínas Virais/genética , Proteínas Virais/metabolismo , Replicação Viral
15.
BMC Biol ; 6: 12, 2008 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-18312693

RESUMO

BACKGROUND: Double-stranded (ds) RNA, generated during viral infection, binds and activates the mammalian anti-viral protein kinase PKR, which phosphorylates the translation initiation factor eIF2alpha leading to the general inhibition of protein synthesis. Although PKR-like activity has been described in fish cells, the responsible enzymes eluded molecular characterization until the recent discovery of goldfish and zebrafish PKZ, which contain Z-DNA-binding domains instead of dsRNA-binding domains (dsRBDs). Fish and amphibian PKR genes have not been described so far. RESULTS: Here we report the cloning and identification of 13 PKR genes from 8 teleost fish and amphibian species, including zebrafish, demonstrating the coexistence of PKR and PKZ in this latter species. Analyses of their genomic organization revealed up to three tandemly arrayed PKR genes, which are arranged in head-to-tail orientation. At least five duplications occurred independently in fish and amphibian lineages. Phylogenetic analyses reveal that the kinase domains of fish PKR genes are more closely related to those of fish PKZ than to the PKR kinase domains of other vertebrate species. The duplication leading to fish PKR and PKZ genes occurred early during teleost fish evolution after the divergence of the tetrapod lineage. While two dsRBDs are found in mammalian and amphibian PKR, one, two or three dsRBDs are present in fish PKR. In zebrafish, both PKR and PKZ were strongly upregulated after immunostimulation with some tissue-specific expression differences. Using genetic and biochemical assays we demonstrate that both zebrafish PKR and PKZ can phosphorylate eIF2alpha in yeast. CONCLUSION: Considering the important role for PKR in host defense against viruses, the independent duplication and fixation of PKR genes in different lineages probably provided selective advantages by leading to the recognition of an extended spectrum of viral nucleic acid structures, including both dsRNA and Z-DNA/RNA, and perhaps by altering sensitivity to viral PKR inhibitors. Further implications of our findings for the evolution of the PKR family and for studying PKR/PKZ interactions with viral gene products and their roles in viral infections are discussed.


Assuntos
Anfíbios/genética , Peixes/genética , Duplicação Gênica , RNA de Cadeia Dupla/genética , eIF-2 Quinase/genética , Substituição de Aminoácidos , Anfíbios/metabolismo , Animais , Sítios de Ligação , Clonagem Molecular , Ativação Enzimática , Peixes/metabolismo , Regulação Enzimológica da Expressão Gênica , Immunoblotting , Fosforilação , Filogenia , Saccharomyces cerevisiae/enzimologia , Saccharomyces cerevisiae/genética , Especificidade da Espécie , Especificidade por Substrato , Tetraodontiformes/genética , Tetraodontiformes/metabolismo , Xenopus laevis/genética , Xenopus laevis/metabolismo , Peixe-Zebra/genética , Peixe-Zebra/metabolismo , eIF-2 Quinase/metabolismo
16.
Infect Genet Evol ; 7(5): 636-44, 2007 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-17689298

RESUMO

Like in most developing countries, tuberculosis represents a major public health problem in Morocco. This paper describes the first study combining molecular and conventional epidemiology of tuberculosis in Casablanca, the economic capital of this country. Molecular fingerprinting of the genomic DNA recovered from cultures of sputum of 150 patients was performed by MIRU-VNTR. This molecular marker revealed that 53.1% of the total cases were clustered. These cases were classified into 23 clusters ranging in size from 2 to 13 patients, suggesting a rate of 37% of recent transmission in the sample under study. In a multivariate analysis, there were no independent predictors of clustering. However, the clinical form was associated with drug resistance (odds ratio=9.9; P value=0.0006). The phylogenetic analysis showed that the heterogeneity found in this population includes also the members from a same patient family, and that the 2 major families distributed in Casablanca were the Latin-American-Mediterranean (LAM) and Haarlem families. All the results of this work allow to understand better the tuberculosis transmission in Casablanca, and suggest that different clones of M. tuberculosis seem to circulate in this city, and that the reactivation of latent infections would be mainly responsible for the endemic situation of this disease. These findings indicate also that the transmission of TB in Morocco is not optimally controlled, and that efforts for control strategies should be sustained in all developing countries where the incidence of TB is high and still raising.


Assuntos
Mycobacterium tuberculosis/genética , Tuberculose/microbiologia , Tuberculose/transmissão , Antituberculosos/farmacologia , DNA Bacteriano/genética , Farmacorresistência Bacteriana Múltipla , Humanos , Incidência , Marrocos/epidemiologia , Filogenia , Prevalência , Estudos Retrospectivos , Fatores de Risco , Tuberculose/epidemiologia
17.
Infect Genet Evol ; 7(1): 24-43, 2007 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-16627010

RESUMO

The reduced cost of high throughput sequencing, increasing automation, and the amenability of sequence data for evolutionary analysis are making DNA data (or the corresponding amino acid sequences) the molecular marker of choice for studying microbial population genetics and phylogenetics. Concomitantly, due to the ever-increasing computational power, new, more accurate (and sometimes faster), sequence-based analytical approaches are being developed and applied to these new data. Here we review some commonly used, recently improved, and newly developed methodologies for inferring population dynamics and evolutionary relationships using nucleotide and amino acid sequence data, including: alignment, model selection, bifurcating and network phylogenetic approaches, and methods for estimating demographic history, population structure, and population parameters (recombination, genetic diversity, growth, and natural selection). Because of the extensive literature published on these topics this review cannot be comprehensive in its scope. Instead, for all the methods discussed we introduce the approaches we think are particularly useful for analyses of microbial sequences and where possible, include references to recent and more inclusive reviews.


Assuntos
Bactérias/genética , Variação Genética , Genômica/métodos , Filogenia , Análise de Sequência de DNA
18.
Proc Natl Acad Sci U S A ; 102(43): 15523-8, 2005 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-16227436

RESUMO

Plasmodium vivax causes the most geographically widespread human malaria, accounting annually for 70-80 million clinical cases throughout the tropical and subtropical regions of the world's continents. We have analyzed the DNA sequences of the Csp (circumsporozoite protein) gene in 24 geographically representative strains of P. vivax and 2 of P. simium, which parasitizes several species of New World monkeys. The Csp sequences are of two types, VK210 and VK247, which differ by three diagnostic amino acid replacements, one in each of the 5' and 3' terminal regions [5' nonrepeat (NR) and 3' NR] of the gene and in an insertion sequence that precedes the 3' NR region. The central region of the gene consists of approximately 38 repetitive "motifs," which are alternatively four and five amino acids long, which also are diagnostically different between the VK210 and VK247 types. There are very few synonymous substitutions within and between the two types of strains, which we hypothesize reflects that the worldwide spread of P. vivax is very recent. The two P. simium Csp sequences belong one to each of the two VK types and are genetically indistinguishable from the corresponding P. vivax strains, suggesting that at least two host transfers have occurred between humans and New World monkeys. We exclude as unlikely the possibility that the two types of sequences could have independently arisen in humans and platyrrhines by natural selection. There are reasons favoring each of the two possible directions of host transfer between humans and monkeys.


Assuntos
Plasmodium vivax/genética , Plasmodium/genética , Proteínas de Protozoários/genética , Animais , Haplorrinos/parasitologia , Humanos , Plasmodium/classificação , Plasmodium vivax/classificação , Polimorfismo Genético , Análise de Sequência de DNA
19.
J Clin Microbiol ; 42(1): 461-6, 2004 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-14715806

RESUMO

Although lower-resource countries have by far the highest burden of tuberculosis, knowledge of Mycobacterium tuberculosis population structure and genetic diversity in these regions remains almost nonexistent. In this paper, 150 Moroccan M. tuberculosis isolates circulating in Casablanca were genotyped by random amplified polymorphic DNA analysis using 10 different primers and by mycobacterial interspersed repetitive units-variable number of tandem repeats typing at 12 loci. The population genetic tests revealed a basically clonal structure for this population, without excluding rare genetic exchanges. Genetic analysis also showed a notable genetic polymorphism for the species M. tuberculosis, a weak cluster individualization, and an unexpected genetic diversity for a population in such a high-incidence community. Phylogenetic analyses of this Moroccan sample also supported that these isolates are genetically heterogeneous.


Assuntos
Mycobacterium tuberculosis/genética , Variação Genética , Humanos , Incidência , Marrocos/epidemiologia , Filogenia , Polimorfismo Genético , Técnica de Amplificação ao Acaso de DNA Polimórfico , Sequências Repetitivas de Ácido Nucleico , Tuberculose/epidemiologia , Tuberculose/microbiologia
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