RESUMO
The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases.
Assuntos
Infecções Bacterianas/genética , Doença Granulomatosa Crônica/genética , Glicoproteínas de Membrana/genética , NADPH Oxidases/genética , Sequência de Aminoácidos , Animais , Povo Asiático , Bactérias/enzimologia , Infecções Bacterianas/complicações , Infecções Bacterianas/enzimologia , Infecções Bacterianas/etnologia , Proteínas de Bactérias/metabolismo , População Negra , Catalase/metabolismo , Evolução Molecular , Variação Genética , Doença Granulomatosa Crônica/complicações , Doença Granulomatosa Crônica/enzimologia , Doença Granulomatosa Crônica/etnologia , Haplótipos , Interações Hospedeiro-Patógeno , Humanos , Glicoproteínas de Membrana/classificação , Dados de Sequência Molecular , Mutação , NADPH Oxidase 2 , NADPH Oxidases/classificação , Filogenia , Seleção Genética , População BrancaRESUMO
CYBB encodes the gp91-phox protein of the phagocytic NADPH oxidase; the innate immunity-related enzymatic complex responsible for the respiratory burst. Mutations in CYBB can cause chronic granulomatous disease (CGD), a primary immunodeficiency characterized by ineffective microbicidal activity, for which over 150 family-specific mutations have been described. It is also plausible that common SNPs in CYBB alter the expression or function of gp91-phox, determining differences in susceptibility to complex disorders such as autoimmune or infectious diseases. We have resequenced the exons, UTRs, and intronic regions of CYBB in 102 ethnically diverse individuals and genotyped nine tag-SNPs in 942 individuals from 52 worldwide populations. The 28 observed SNPs (none of which nonsynonymous) reside on 28 haplotypes that can be collapsed into five clades. CYBB shows lower diversity than other X-chromosome genes and most of the between-population genetic variance was observed among Africans and non-Africans. The African population shows the highest diversity and the lowest linkage disequilibrium (LD). Because there is extensive shared LD among non-Africans, tag-SNPs can be effectively employed in gene-centric association studies and are portable across Eurasian and Native American populations. Comparison of CYBB coding sequences among mammals evidences the action of long-term purifying selection, which is stronger on the C-terminal cytosolic domain than on the N-terminal transmembrane domain of gp91-phox.
Assuntos
Glicoproteínas de Membrana/genética , NADPH Oxidases/genética , Animais , Membrana Celular/enzimologia , Cromossomos Humanos X , Citosol/enzimologia , Haplótipos , Humanos , Imunidade Inata , Desequilíbrio de Ligação , NADPH Oxidase 2 , Polimorfismo de Nucleotídeo Único , Especificidade da EspécieRESUMO
A molecular phylogeny of the genus Artibeus using 19 of the 20 recognized species, many with samples from a broad geographic range, is presented. The analysis shows a clear distinction between the two subgenera (or genera), the 'large'Artibeus and the 'small'Dermanura, in both mitochondrial and nuclear genes. The placement and status of A. concolor remains inconclusive and is presented as the third subgenus Koopmania. The phylogenies and divergence time estimates show a marked influence of the Andes in the formation of the subgenera and the main lineages inside each subgenus. Nuclear genes showed a highly incomplete lineage sorting among species inside subgenera Artibeus and Dermanura. Indeed, shared alleles were also found between Artibeus and Koopmania, which are presumed to have split apart during the Miocene, showing that great care should be taken in using these markers. Cytochrome-b gene divergences and monophyly analyses suggest that A. lituratus and A. intermedius are indeed conspecifics. These analyses also suggested the existence of at least four 'new' species revealing a significant cryptic diversity inside the genus.
Assuntos
Quirópteros/classificação , Quirópteros/genética , Evolução Molecular , Filogenia , Animais , Teorema de Bayes , Citocromos b/genética , DNA Mitocondrial/genética , Genes Mitocondriais , Marcadores Genéticos , Especiação Genética , Haplótipos , Funções Verossimilhança , Mitocôndrias/genética , Alinhamento de Sequência , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
Sequence variation among different hepatitis C virus (HCV) isolates has adaptive significance and reflects the modes and intensities of selection mechanisms operating on the virus. In this work, we sought to investigate using classical population genetics parameters, the genetic variability of HCV genotype 1 using the 5' UTR and NS5A regions from treatment non-responding and responding groups of patients. Both regions showed low genetic variability and the 5' UTR showed neutral deviation. No differences were observed in the nonsynonymous/synonymous nucleotide substitution ratio among groups for NS5A. The analysis of molecular variance test of the 5' UTR region showed an 11.94% variation among groups. Phylogenetic analysis showed no correlation between sequence variations and therapeutic responses.
Assuntos
Regiões 5' não Traduzidas/genética , Variação Genética/genética , Hepacivirus/genética , Hepatite C Crônica/virologia , Proteínas não Estruturais Virais/genética , Antivirais/uso terapêutico , Genótipo , Hepatite C Crônica/tratamento farmacológico , Humanos , Interferon alfa-2 , Interferon-alfa/uso terapêutico , Filogenia , Polietilenoglicóis/uso terapêutico , RNA Viral/genética , Proteínas Recombinantes , Ribavirina/uso terapêuticoRESUMO
Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ÏX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.
Assuntos
Bacteriófago phi X 174 , Proteínas do Capsídeo/genética , Evolução Molecular , Seleção Genética , Bacteriófago phi X 174/classificação , Bacteriófago phi X 174/genéticaRESUMO
Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus.
RESUMO
Comparative studies of salivary glands showed that they maybe related to the adaptive radiation of bats, especially in the family Phylostomidae. In this study we have been searching for a likely relationship between different feeding habits found in bats and possible adaptive changes in a coding segment of the alpha-amylase enzyme. We have also tested some hypothesis about the phylogenetic relationship of bats and other mammals. A 663 bp segment of the alpha-amylase gene, corresponding to the exon 4 and part of the intron c, was sequenced in nine bat species. The exon 4 was also sequenced in further ten mammalian species. The phylogenetic trees generated with different methods produced the same results. When the intron c and the exon 4 were independently analyzed, they showed distinct topologies involving the bat species Sturnira lilium, different from the traditional bat phylogeny. Phylogenetic analysis of bats, primates and rodents supports the Euarchontoglires-Laurasiatheria hypothesis about the relationship among these groups. Selection tests showed that the alpha-amylase exon 4 is under strong purifying selection, probably caused by functional constraints. The conflicting bat phylogenies could not be explained by evolutionary convergence due to adaptive forces, and the different topologies may be likely due to the retention of plesiomorphic characters or the independent acquisition by evolutionary parallelism.
Assuntos
Quirópteros/genética , Evolução Molecular , alfa-Amilases/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Brasil , Quirópteros/metabolismo , Humanos , Funções Verossimilhança , Camundongos , Dados de Sequência Molecular , Pan troglodytes , Filogenia , Ratos , Alinhamento de Sequência , Análise de Sequência de DNARESUMO
The first and second internal transcribed spacer regions (ITS1 and ITS2) of the ribosomal DNA of Biomphalaria tenagophila complex (B. tenagophila, B. occidentalis, and B. t. guaibensis) were sequenced and compared. The alignment lengths of these regions were about 655 bp and 481 bp, respectively. Phylogenetic relationships among the Biomphalaria species were inferred by Maximum Parsimony and Neighbor-joining methods. The phylogenetic trees produced, in most of the cases, were in accordance with morphological systematics and other molecular data previously obtained by polymerase chain reaction and restriction fragment length polymorphism analysis. The present results provide support for the proposal that B. tenagophila represents a complex comprising B. tenagophila, B. occidentalis and B. t. guaibensis.
Assuntos
Biomphalaria/genética , DNA de Helmintos/genética , DNA Espaçador Ribossômico/genética , Filogenia , Animais , Sequência de Bases , Biomphalaria/classificação , Dados de Sequência Molecular , Reação em Cadeia da PolimeraseRESUMO
Sequence variation among different hepatitis C virus (HCV) isolates has adaptive significance and reflects the modes and intensities of selection mechanisms operating on the virus. In this work, we sought to investigate using classical population genetics parameters, the genetic variability of HCV genotype 1 using the 5' UTR and NS5A regions from treatment non-responding and responding groups of patients. Both regions showed low genetic varia-bility and the 5' UTR showed neutral deviation. No differences were observed in the nonsynonymous/synonymous nucleotide substitution ratio among groups for NS5A. The analysis of molecular variance test of the 5' UTR region showed an 11.94 percent variation among groups. Phylogenetic analysis showed no correlation between sequence variations and therapeutic responses.
Assuntos
Humanos , /genética , Variação Genética/genética , Hepacivirus/genética , Hepatite C Crônica/virologia , Proteínas não Estruturais Virais/genética , Antivirais/uso terapêutico , Genótipo , Hepatite C Crônica/tratamento farmacológico , Interferon-alfa , Filogenia , Polietilenoglicóis/uso terapêutico , RNA Viral/genética , Ribavirina/uso terapêuticoRESUMO
The first and second internal transcribed spacer regions (ITS1 and ITS2) of the ribosomal DNA of Biomphalaria tenagophila complex (B. tenagophila, B. occidentalis, and B. t. guaibensis) were sequenced and compared. The alignment lengths of these regions were about 655 bp and 481 bp, respectively. Phylogenetic relationships among the Biomphalaria species were inferred by Maximum Parsimony and Neighbor-joining methods. The phylogenetic trees produced, in most of the cases, were in accordance with morphological systematics and other molecular data previously obtained by polymerase chain reaction and restriction fragment length polymorphism analysis. The present results provide support for the proposal that B. tenagophila represents a complex comprising B. tenagophila, B. occidentalis and B. t. guaibensis.