Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 7.299
Filtrar
1.
Phytopathology ; 110(1): 146-152, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31559902

RESUMO

Cucumber green mottle mosaic virus (CGMMV), a member of the genus Tobamovirus, is a major threat to economically important cucurbit crops worldwide. An attenuated strain (SH33b) derived from a severe strain (SH) of CGMMV caused a reduction in the viral RNA accumulation and the attenuation of symptoms, and it has been successfully used to protect muskmelon plants against severe strains in Japan. In this study, we compared GFP-induced silencing suppression by the 129K protein and the methyltransferase domain plus intervening region (MTIR) of the 129K protein between the SH and SH33b strains, respectively. As a result, silencing suppression activity (SSA) in the GFP-silenced plants was inhibited efficiently by the MTIR and 129K protein of SH strain, and it coincided with drastically reduced accumulation of GFP-specific small interfering RNAs (siRNAs) but not by that of SH33b strain. Furthermore, analyses of siRNA binding capability (SBC) by the MTIR of 129K protein and 129K protein using electrophoretic mobility shift assay revealed that SBC was found with the MTIR and 129K protein of SH but not with that of SH33b, suggesting that a single amino acid mutation (E to G) in the MTIR is responsible for impaired SSA and SBC of SH33b. These data suggest that a single amino acid substitution in the intervening region of 129K protein of CGMMV resulted in attenuated symptoms by affecting RNA silencing suppression.


Assuntos
Substituição de Aminoácidos , Cucurbitaceae , Doenças das Plantas , Tobamovirus , Substituição de Aminoácidos/genética , Cucurbitaceae/virologia , Japão , Doenças das Plantas/virologia , Tobamovirus/genética , Tobamovirus/patogenicidade
2.
Med Sci (Paris) ; 35(8-9): 651-658, 2019.
Artigo em Francês | MEDLINE | ID: mdl-31532377

RESUMO

BCR-ABL negative myeloproliferative neoplasms are acquired hematologic diseases characterized by blood cell proliferation and that include polycythemia vera (PV), essential thrombocytemia (ET) and primary myelofibrosis (PMF). Occurring of venous and arterial thrombosis is the main complication of these diseases. Risk factors for thrombosis are individuals older than 60 and history of thrombosis. The mechanisms leading to thrombosis are complex and involve several blood compartments, plasmatic factors and endothelial cells. Over the last years, new actors of thrombosis have been discovered.


Assuntos
Janus Quinase 2/genética , Mutação de Sentido Incorreto , Transtornos Mieloproliferativos/complicações , Transtornos Mieloproliferativos/genética , Trombose/etiologia , Substituição de Aminoácidos/genética , Animais , Plaquetas/fisiologia , Humanos , Transtornos Mieloproliferativos/sangue , Transtornos Mieloproliferativos/fisiopatologia , Fenilalanina/genética , Trombose/sangue , Trombose/genética , Trombose/patologia , Valina/genética
3.
Clin Biochem ; 74: 80-85, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31493379

RESUMO

Hb variants are structurally abnormal haemoglobins which can originate a wide range of phenotypes from clinically silent conditions to very severe disorders. In many cases, diagnosis is very difficult due to the instability of Hb mutants or the occurrence of misleading symptoms, such as cyanosis or hypoxia. Here we report the case of a young female with undiagnosed chronic haemolytic anaemia and low oxygen saturation in the absence of respiratory distress. High performance liquid chromatography showed the occurrence of an abnormal peak in the HbA2 region, which disappeared few days after blood sampling. Genetic analysis of both α genes revealed the -α3.7 deletion in heterozygous state and a novel mutation c.130 T > C leading to the substitution of Phenylalanine at codon 43 with Leucine in the α1 gene. This substitution originated a new Hb variant, named Hb Vanvitelli, with a molecular mass of 15,092.2 ±â€¯0.4 Da. Biochemical and laboratory tests described a hyper unstable Hb variant with altered oxygen affinity that was clinically significant only when co-inherited with genetic defects affecting the α2 locus. This case highlights the genetic complexity and diagnostic pitfalls of Hb variants, defined "experiments of nature" which can generate severe clinical conditions.


Assuntos
Anemia Hemolítica/diagnóstico , Anemia Hemolítica/genética , Hemoglobinas Anormais/genética , Deleção de Sequência , alfa-Globinas/genética , Adolescente , Sequência de Aminoácidos/genética , Substituição de Aminoácidos/genética , Anemia Hemolítica/sangue , Cromatografia Líquida , Doença Crônica , Códon/genética , Feminino , Testes Genéticos , Heterozigoto , Humanos , Itália , Espectrometria de Massas , Oximetria , Oxigênio/sangue , Linhagem , Fenótipo
4.
Genetics ; 213(2): 411-429, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31391264

RESUMO

Telomeres progressively shorten at every round of DNA replication in the absence of telomerase. When they become critically short, telomeres trigger replicative senescence by activating a DNA damage response that is governed by the Mec1/ATR and Tel1/ATM protein kinases. While Mec1/ATR is known to block cell division when extended single-stranded DNA (ssDNA) accumulates at eroded telomeres, the molecular mechanism by which Tel1/ATM promotes senescence is still unclear. By characterizing a Tel1-hy184 mutant variant that compensates for the lack of Mec1 functions, we provide evidence that Tel1 promotes senescence by signaling to a Rad9-dependent checkpoint. Tel1-hy184 anticipates senescence onset in telomerase-negative cells, while the lack of Tel1 or the expression of a kinase-defective (kd) Tel1 variant delays it. Both Tel1-hy184 and Tel1-kd do not alter ssDNA generation at telomeric DNA ends. Furthermore, Rad9 and (only partially) Mec1 are responsible for the precocious senescence promoted by Tel1-hy184. This precocious senescence is mainly caused by the F1751I, D1985N, and E2133K amino acid substitutions, which are located in the FRAP-ATM-TRAPP domain of Tel1 and also increase Tel1 binding to DNA ends. Altogether, these results indicate that Tel1 induces replicative senescence by directly signaling dysfunctional telomeres to the checkpoint machinery.


Assuntos
Peptídeos e Proteínas de Sinalização Intracelular/genética , Proteínas Serina-Treonina Quinases/genética , Proteínas de Saccharomyces cerevisiae/genética , Encurtamento do Telômero/genética , Telômero/genética , Substituição de Aminoácidos/genética , Proteínas Mutadas de Ataxia Telangiectasia/genética , Pontos de Checagem do Ciclo Celular/genética , Divisão Celular/genética , Senescência Celular/genética , Dano ao DNA/genética , Replicação do DNA/genética , DNA de Cadeia Simples/genética , Proteínas de Ligação a DNA/genética , Proteínas Mutantes/genética , Saccharomyces cerevisiae/genética , Telomerase/genética
5.
J Hum Genet ; 64(11): 1127-1132, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31420595

RESUMO

RAC3 is a member of the Rho GTPases family, which has important regulatory functions in aspects of neuronal morphogenesis. Rho GTPases show a conformational change in two regions (switch I and II) through GTP binding, which provides a platform for selective interactions with functionally diverse proteins. Missense variants in the switch I and II regions of RAC3 were recently suggested to cause severe intellectual disability and brain malformations. Here, we report an individual with a novel de novo RAC3 variant (c.101 C>G, p.(Pro34Arg)), which substitutes for an evolutionarily conserved amino acid within the switch I region. The patient showed severe global developmental delay, intellectual disability, epilepsy, and laryngeal dystonia. An imaging study revealed characteristic brain dysplasia, including coexistence of the middle interhemispheric variant of holoprosencephaly and brainstem dysmorphism. Our study supports that RAC3 variants cause syndromic neurodevelopmental disorders and brain structural abnormality, and expands the phenotypic spectrum of RAC3-related disorders.


Assuntos
Deficiências do Desenvolvimento/genética , Holoprosencefalia/genética , Deficiência Intelectual/genética , Proteínas rac de Ligação ao GTP/genética , Substituição de Aminoácidos/genética , Criança , Pré-Escolar , Sequência Conservada/genética , Deficiências do Desenvolvimento/fisiopatologia , Predisposição Genética para Doença , Holoprosencefalia/fisiopatologia , Humanos , Recém-Nascido , Deficiência Intelectual/fisiopatologia , Masculino , Mutação de Sentido Incorreto/genética , Fenótipo
6.
Bull Exp Biol Med ; 167(3): 384-387, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31346883

RESUMO

We studied the constellation of genes encoding polymerase complex proteins of master donor viruses for Russian live attenuated influenza vaccine type B. Reassortants of the reserve attenuation donor B/Leningrad/14/17/55 with B/USSR/60/69 master donor virus currently used for manufacturing seasonal influenza vaccine were prepared and examined. Most reassortants obtained by the classical reassortment method inherited all genes from the B/Leningrad/14/17/55 virus except the gene encoding PB1 subunit of the polymerase complex. One reassortant was selected for further evaluation of the role of PB1 gene. Greater attenuation of the strain for experimental animals (mice) in comparison with the original strains was demonstrated. This indicates high degree of constellation of genes of cold-adapted master donor viruses and the important compensating role of amino acid substitutions in the PB1 protein of B/Leningrad/14/17/55 donor virus in preventing viral hyperattenuation.


Assuntos
Influenza Humana/prevenção & controle , Influenzavirus B/genética , Proteínas Virais/genética , Substituição de Aminoácidos/genética , Animais , Embrião de Galinha , Temperatura Baixa , Humanos , Vacinas contra Influenza/imunologia , Influenzavirus B/imunologia , Camundongos , Vírus Reordenados/genética , Vírus Reordenados/imunologia , Vacinas Atenuadas/imunologia
7.
Mol Cell ; 75(3): 427-441.e5, 2019 08 08.
Artigo em Inglês | MEDLINE | ID: mdl-31353208

RESUMO

The translation machinery and the genes it decodes co-evolved to achieve production throughput and accuracy. Nonetheless, translation errors are frequent, and they affect physiology and protein evolution. Mapping translation errors in proteomes and understanding their causes is hindered by lack of a proteome-wide experimental methodology. We present the first methodology for systematic detection and quantification of errors in entire proteomes. Following proteome mass spectrometry, we identify, in E. coli and yeast, peptides whose mass indicates specific amino acid substitutions. Most substitutions result from codon-anticodon mispairing. Errors occur at sites that evolve rapidly and that minimally affect energetic stability, indicating selection for high translation fidelity. Ribosome density data show that errors occur at sites where ribosome velocity is higher, demonstrating a trade-off between speed and accuracy. Treating bacteria with an aminoglycoside antibiotic or deprivation of specific amino acids resulted in particular patterns of errors. These results reveal a mechanistic and evolutionary basis for translation fidelity.


Assuntos
Substituição de Aminoácidos/genética , Biossíntese de Proteínas , Proteoma/genética , Seleção Genética , Aminoácidos/genética , Anticódon/genética , Códon/genética , Escherichia coli/genética , RNA de Transferência/genética , Ribossomos/genética , Saccharomyces cerevisiae/genética
9.
Molecules ; 24(12)2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31226791

RESUMO

Stapled α-helical peptides represent an emerging superclass of macrocyclic molecules with drug-like properties, including high-affinity target binding, protease resistance, and membrane permeability. As a model system for probing the chemical space available for optimizing these properties, we focused on dual Mdm2/MdmX antagonist stapled peptides related to the p53 N-terminus. Specifically, we first generated a library of ATSP-7041 (Chang et al., 2013) analogs iteratively modified by L-Ala and D-amino acids. Single L-Ala substitutions beyond the Mdm2/(X) binding interfacial residues (i.e., Phe3, Trp7, and Cba10) had minimal effects on target binding, α-helical content, and cellular activity. Similar binding affinities and cellular activities were noted at non-interfacial positions when the template residues were substituted with their d-amino acid counterparts, despite the fact that d-amino acid residues typically 'break' right-handed α-helices. d-amino acid substitutions at the interfacial residues Phe3 and Cba10 resulted in the expected decreases in binding affinity and cellular activity. Surprisingly, substitution at the remaining interfacial position with its d-amino acid equivalent (i.e., Trp7 to d-Trp7) was fully tolerated, both in terms of its binding affinity and cellular activity. An X-ray structure of the d-Trp7-modified peptide was determined and revealed that the indole side chain was able to interact optimally with its Mdm2 binding site by a slight global re-orientation of the stapled peptide. To further investigate the comparative effects of d-amino acid substitutions we used linear analogs of ATSP-7041, where we replaced the stapling amino acids by Aib (i.e., R84 to Aib4 and S511 to Aib11) to retain the helix-inducing properties of α-methylation. The resultant analog sequence Ac-Leu-Thr-Phe-Aib-Glu-Tyr-Trp-Gln-Leu-Cba-Aib-Ser-Ala-Ala-NH2 exhibited high-affinity target binding (Mdm2 Kd = 43 nM) and significant α-helicity in circular dichroism studies. Relative to this linear ATSP-7041 analog, several d-amino acid substitutions at Mdm2(X) non-binding residues (e.g., d-Glu5, d-Gln8, and d-Leu9) demonstrated decreased binding and α-helicity. Importantly, circular dichroism (CD) spectroscopy showed that although helicity was indeed disrupted by d-amino acids in linear versions of our template sequence, stapled molecules tolerated these residues well. Further studies on stapled peptides incorporating N-methylated amino acids, l-Pro, or Gly substitutions showed that despite some positional dependence, these helix-breaking residues were also generally tolerated in terms of secondary structure, binding affinity, and cellular activity. Overall, macrocyclization by hydrocarbon stapling appears to overcome the destabilization of α-helicity by helix breaking residues and, in the specific case of d-Trp7-modification, a highly potent ATSP-7041 analog (Mdm2 Kd = 30 nM; cellular EC50 = 600 nM) was identified. Our findings provide incentive for future studies to expand the chemical diversity of macrocyclic α-helical peptides (e.g., d-amino acid modifications) to explore their biophysical properties and cellular permeability. Indeed, using the library of 50 peptides generated in this study, a good correlation between cellular permeability and lipophilicity was observed.


Assuntos
Aminoácidos/química , Peptídeos Penetradores de Células/química , Fragmentos de Peptídeos/química , Conformação Proteica , Sequência de Aminoácidos/genética , Substituição de Aminoácidos/genética , Aminoácidos/síntese química , Peptídeos Penetradores de Células/síntese química , Peptídeos Penetradores de Células/genética , Peptídeos Penetradores de Células/farmacologia , Dicroísmo Circular , Dipeptídeos/química , Humanos , Oligopeptídeos/química , Peptídeos Cíclicos/farmacologia , Permeabilidade/efeitos dos fármacos , Estrutura Secundária de Proteína , Proteínas Proto-Oncogênicas c-mdm2/química , Proteínas Proto-Oncogênicas c-mdm2/genética
10.
Cancer Immunol Immunother ; 68(7): 1143-1155, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31177328

RESUMO

Enhancement of endogenous immunity to tumor-associated self-antigens and neoantigens is the goal of preventive vaccination. Toward this goal, we compared the efficacy of the following HER2 DNA vaccine constructs: vaccines encoding wild-type HER2, hybrid HER2 vaccines consisting of human HER2 and rat Neu, HER2 vaccines with single residue substitutions and a novel human HER2 DNA vaccine, ph(es)E2TM. ph(es)E2TM was designed to contain five evolution-selected substitutions: M198V, Q398R, F425L, H473R and A622T that occur frequently in 12 primate HER2 sequences. These ph(es)E2TM substitutions score 0 to 1 in blocks substitutions matrix (BLOSUM), indicating minimal biochemical alterations. h(es)E2TM recombinant protein is recognized by a panel of anti-HER2 mAbs, demonstrating the preservation of HER2 protein structure. Compared to native human HER2, electrovaccination of HER2 transgenic mice with ph(es)E2TM induced a threefold increase in HER2-binding antibody (Ab) and elevated levels of IFNγ-producing T cells. ph(es)E2TM, but not pE2TM immune serum, recognized HER2 peptide p95 355LPESFDGDPASNTAP369, suggesting a broadening of epitope recognition induced by the minimally modified HER2 vaccine. ph(es)E2TM vaccination reduced tumor growth more effectively than wild-type HER2 or HER2 vaccines with more extensive modifications. The elevation of tumor immunity by ph(es)E2TM vaccination would create a favorable tumor microenvironment for neoantigen priming, further enhancing the protective immunity. The fundamental principle of exploiting evolution-selected amino acid substitutions is novel, effective and applicable to vaccine development in general.


Assuntos
Antígenos de Neoplasias/imunologia , Vacinas Anticâncer/imunologia , Imunoterapia/métodos , Neoplasias Mamárias Experimentais/terapia , Receptor ErbB-2/imunologia , Substituição de Aminoácidos/genética , Substituição de Aminoácidos/imunologia , Animais , Antígenos de Neoplasias/genética , Vacinas Anticâncer/genética , Vacinas Anticâncer/uso terapêutico , Linhagem Celular Tumoral/transplante , Células Dendríticas/imunologia , Evolução Molecular , Feminino , Imunogenicidade da Vacina/genética , Neoplasias Mamárias Experimentais/genética , Neoplasias Mamárias Experimentais/imunologia , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Transgênicos , Receptor ErbB-2/genética , Proteínas Recombinantes/genética , Proteínas Recombinantes/imunologia , Tolerância a Antígenos Próprios/genética , Microambiente Tumoral/imunologia , Vacinas de DNA/genética , Vacinas de DNA/imunologia , Vacinas de DNA/uso terapêutico
11.
Arch Virol ; 164(8): 2023-2029, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31111259

RESUMO

We previously obtained mouse-adapted variants of H1N2 avian influenza virus that contained PB2-L134H, PB2-I647L, PB2-D701N, HA-G228S, and M1-D231N mutations. Here, we analyzed the effects of these mutations on viral pathogenicity in a mammalian model. By evaluating the virulence of mouse-adapted H1N2 variants at different generations, we found that the PB2-D701N and HA-G228S mutations both contribute to the virulence of this virus in mammals. Furthermore, we found that the PB2-D701N and HA-G228S mutations both enhance the ability of the virus to replicate in vivo and in vitro and that the PB2-D701N substitution results in an expansion of viral tissue tropism. These results suggest that the PB2-D701N mutation and the HA-G228S mutation are the major mammalian determinants of H1N2 virus. These results help us to understand more about the mechanisms by which influenza viruses adapt to mammals, and monitoring of these mutations can be used in continuous influenza surveillance to assess the pandemic potential of avian influenza virus variants.


Assuntos
Glicoproteínas de Hemaglutininação de Vírus da Influenza/genética , Vírus da Influenza A Subtipo H1N2/genética , Influenza Aviária/virologia , Mutação/genética , Proteínas Virais/genética , Virulência/genética , Adaptação Biológica/genética , Substituição de Aminoácidos/genética , Animais , Aves , Linhagem Celular , Cães , Feminino , Células Madin Darby de Rim Canino , Mamíferos/virologia , Camundongos , Camundongos Endogâmicos BALB C , Infecções por Orthomyxoviridae/virologia , Fenótipo , Replicação Viral/genética
12.
Arch Virol ; 164(8): 2137-2145, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31111260

RESUMO

The complete nucleotide sequence of the viral protein 2 (VP2) ORF was determined for 26 Vietnamese infectious bursal disease isolates collected from clinical outbreaks in vaccinated flocks from 1987 to 2018 and two commercial vaccine specimens. These sequences were compared for molecular classification with 42 reference strains representing all four main classes of serotype 1, including very virulent (vvIBDV), classical (cvIBDV), antigenic variant (avIBDV) and attenuated (atIBDV) strains, and serotype 2 strains. Amino acids at nine key positions in the VP2-HVR in 20 Vietnamese isolates, A222, I242, Q253, I256, D279, A284, I294, S299, A329, which are typical of the vvIBDV class, were found to be identical in all of the isolates. Eighteen of these isolates had a unique change at residue 212 (D212N) located in the PAB loop. Phylogenetic analysis revealed a distinct lineage/subclade with strong nodal support (96%) that included recent Chinese IBDV strains that were distinct from typical vvIBDVs. Six isolates contained the amino acid substitutions P222, V242, Q253, V256, D279, A284, I294, N299, A329, which are present in two vaccine strains derived from strain 2512 and these isolates were also closely related to the classical virulent STC strain. Data from this study show that there is considerable genetic diversity among vvIBDVs, which vary according to geographic region. Antigenic drift and differences in genetic characteristics between virulent strains and IBDV vaccine strains may be the cause of vaccine failure. Better antigenic matching of vaccines to the strains circulating in Vietnam is therefore required.


Assuntos
Infecções por Birnaviridae/virologia , Vírus da Doença Infecciosa da Bursa/genética , Vírus da Doença Infecciosa da Bursa/isolamento & purificação , Sequência de Aminoácidos , Substituição de Aminoácidos/genética , Animais , Variação Antigênica/genética , Infecções por Birnaviridae/epidemiologia , Infecções por Birnaviridae/veterinária , Galinhas/virologia , Surtos de Doenças , Genótipo , Filogenia , Doenças das Aves Domésticas/epidemiologia , Doenças das Aves Domésticas/virologia , Vietnã/epidemiologia , Proteínas Estruturais Virais/genética
13.
Molecules ; 24(10)2019 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-31117243

RESUMO

The human KRAS (Kirsten rat sarcoma) is an oncogene, involved in the regulation of cell growth and division. The mutations in the KRAS gene have the potential to cause normal cells to become cancerous in human lungs. In the present study, we focus on non-synonymous single nucleotide polymorphisms (nsSNPs), which are point mutations in the DNA sequence leading to the amino acid variants in the encoded protein. To begin with, we developed a pipeline to utilize a set of computational tools in order to obtain the most deleterious nsSNPs (Q22K, Q61P, and Q61R) associated with lung cancer in the human KRAS gene. Furthermore, molecular dynamics simulation and structural analyses of the 3D structures of native and mutant proteins confirmed the impact of these nsSNPs on the stability of the protein. Finally, the experimental results demonstrated that the structural stability of the mutant proteins was worse than that of the native protein. This study provides significant guidance for narrowing down the number of KRAS mutations to be screened as potential diagnostic biomarkers and to better understand the structural and functional mechanisms of the KRAS protein.


Assuntos
Biomarcadores Tumorais/genética , Neoplasias Pulmonares/diagnóstico , Proteínas Proto-Oncogênicas p21(ras)/genética , Substituição de Aminoácidos/genética , Biomarcadores Tumorais/química , Biologia Computacional , Humanos , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Conformação Molecular , Simulação de Dinâmica Molecular , Mutação/genética , Polimorfismo de Nucleotídeo Único/genética , Proteínas Proto-Oncogênicas p21(ras)/química , Relação Estrutura-Atividade
14.
BMC Evol Biol ; 19(1): 99, 2019 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-31068148

RESUMO

BACKGROUND: RNA interference (RNAi) related pathways provide defense against viruses and transposable elements, and have been implicated in the suppression of meiotic drive elements. Genes in these pathways often exhibit high levels of adaptive substitution, and over longer timescales show gene duplication and loss-most likely as a consequence of their role in mediating conflict with these parasites. This is particularly striking for Argonaute 2 (Ago2), which is ancestrally the key effector of antiviral RNAi in insects, but has repeatedly formed new testis-specific duplicates in the recent history of the obscura species-group of Drosophila. RESULTS: Here we take advantage of publicly available genomic and transcriptomic data to identify six further RNAi-pathway genes that have duplicated in this clade of Drosophila, and examine their evolutionary history. As seen for Ago2, we observe high levels of adaptive amino-acid substitution and changes in sex-biased expression in many of the paralogs. However, our phylogenetic analysis suggests that co-duplications of the RNAi machinery were not synchronous, and our expression analysis fails to identify consistent male-specific expression. CONCLUSIONS: These results confirm that RNAi genes, including genes of the antiviral and piRNA pathways, have undergone multiple independent duplications and that their history has been particularly labile within the obscura group. However, they also suggest that the selective pressures driving these changes have not been consistent, implying that more than one selective agent may be responsible.


Assuntos
Adaptação Fisiológica/genética , Drosophila/genética , Duplicação Gênica , Genes de Insetos , Interferência de RNA , Substituição de Aminoácidos/genética , Animais , Teorema de Bayes , Proteínas CLOCK/genética , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Evolução Molecular , Regulação da Expressão Gênica , Masculino , Filogenia
15.
Hum Immunol ; 80(9): 731-738, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31122742

RESUMO

Kawasaki disease (KD) is a pediatric vasculitis caused by an unknown trigger in genetically susceptible children. The incidence varies widely across genetically diverse populations. Several associations with HLA Class I alleles have been reported in single cohort studies. Using a genetic approach, from the nine single nucleotide variants (SNVs) associated with KD susceptibility in children of European descent, we identified SNVs near the HLA-C (rs6906846) and HLA-B genes (rs2254556) whose association was replicated in a Japanese descent cohort (rs6906846 p = 0.01, rs2254556 p = 0.005). The risk allele (A at rs6906846) was also associated with HLA-C*07:02 and HLA-C*04:01 in both US multi-ethnic and Japanese cohorts and HLA-C*12:02 only in the Japanese cohort. The risk A-allele was associated with eight non-conservative amino acid substitutions (amino acid positions); Asp or Ser (9), Arg (14), Ala (49), Ala (73), Ala (90), Arg (97), Phe or Ser (99), and Phe or Ser (116) in the HLA-C peptide binding groove that binds peptides for presentation to cytotoxic T cells (CTL). This raises the possibility of increased affinity to a "KD peptide" that contributes to the vasculitis of KD in genetically susceptible children.


Assuntos
Substituição de Aminoácidos/genética , Sítios de Ligação/genética , Predisposição Genética para Doença , Antígenos HLA-C/genética , Síndrome de Linfonodos Mucocutâneos/genética , Polimorfismo de Nucleotídeo Único/genética , Ligação Proteica/genética , Alelos , Sequência de Aminoácidos/genética , Apresentação do Antígeno/genética , Estudos de Coortes , Frequência do Gene/genética , Genótipo , Antígenos HLA-C/química , Teste de Histocompatibilidade , Humanos , Japão , Peptídeos/genética , Domínios Proteicos/genética , Linfócitos T Citotóxicos/imunologia
16.
Microb Drug Resist ; 25(7): 1072-1079, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31021305

RESUMO

Using direct-acting antiviral agents (DAAs) against hepatitis C virus (HCV) infection results in a high treatment response rate. However, several factors can significantly alter this outcome such as resistance-associated substitutions (RASs) in HCV NS5A gene. This study aimed to evaluate the prevalence of naturally occurring RASs of NS5A in HCV genotype 3 (HCV-3) sequences isolated from individuals with chronic HCV-3 infection. All the registered sequences in the GenBank under "NS5A" AND "Hepacivirus C" query were evaluated and screened, those which followed our inclusion criteria were enrolled in our pooled analysis. The retrieved sequences of included studies were evaluated for substitutions, RASs, and RASs conferring >100 resistance fold change (RASs >100 × ) in NS5A amino acid positions 24, 28, 30, 31, 62, 92, and 93. From 7 enrolled studies, a total of 370 HCV-3a isolates were retrieved and investigated. Forty-eight (13.0%, 95% CI = 9.9-16.8%) isolates harbored NS5A RASs. Moreover, Y93H was the only NS5A RAS >100 × observed in 13 (3.5%, 95% CI = 2.0-5.9%) retrieved sequences. The low frequency of naturally occurring NS5A RASs, especially those with clinical relevance (RASs >100 × ), among individuals with HCV-3 infection and the high rate of treatment response to DAAs suggest not to investigate every individual with HCV-3 infection for NS5A RASs before treatment.


Assuntos
Substituição de Aminoácidos/genética , Hepacivirus/genética , Hepatite C Crônica/virologia , Proteínas não Estruturais Virais/genética , Antivirais/farmacologia , Bases de Dados de Ácidos Nucleicos , Farmacorresistência Viral/efeitos dos fármacos , Farmacorresistência Viral/genética , Genótipo , Hepacivirus/efeitos dos fármacos , Hepatite C Crônica/tratamento farmacológico , Humanos , Prevalência , Análise de Sequência de DNA/métodos
17.
Ann Biol Clin (Paris) ; 77(3): 287-294, 2019 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-31021322

RESUMO

Biology flourished during the XXth century and was profoundly disrupted during the last decade because of the transition to the post-genomic era, the spread of high-throughput biology, and the advent of a relatively new discipline, namely bioinformatics. This latter, which encompasses the collection, organization and analysis of biological data using the computer tool, has quickly become inseparable from the studies related to the genome understanding. The consequences of the different mutations that may affect our genes are responsible for a change in the protein sequence and are likely to affect, for example, the stability of the protein, its intracellular targeting, its maturation, its assembly in a multimeric structure, the essential sites for its enzymatic activity or for the interaction with ligands. Thus, a number of bioinformatic developments have made it possible to set up in silico prediction tools of the structure of a protein that is aiming at predicting the impact of local mutations on the structure of proteins. Throughout our study, we have been interested in exploring, through in silico bioinformatic study, three analytical, prediction and modeling, software, choosing as exemple the G12D mutation that affects the proto-oncogene KRAS found in numerous algerian patients with bronchopulmonary cancers cells (NSCLC). This study allowed us to integrate these bioinformatic tools into our laboratory of developmental biology and LBDD differentiation at the University of Oran 1 Ahmed Benbella, in Algeria. Thus, we have been able to conclude, even if the found mutation is predicted to be tolerated and has no deleterious effect on the entire Ras protein, that the consequence of this missense mutation depends mainly on the position in the protein and the chemical properties of the amino acid involved in the substitution and which shows a strong affinity with the GTP molecule.


Assuntos
Carcinoma Pulmonar de Células não Pequenas/genética , Biologia Computacional/métodos , Neoplasias Pulmonares/genética , Mutação de Sentido Incorreto , Proteínas Proto-Oncogênicas p21(ras)/genética , Argélia , Substituição de Aminoácidos/genética , Ácido Aspártico/genética , Carcinoma Pulmonar de Células não Pequenas/patologia , Análise Mutacional de DNA/métodos , Bases de Dados Genéticas , Éxons , Estudos de Associação Genética/métodos , Glicina/genética , Humanos , Neoplasias Pulmonares/patologia , Modelos Moleculares , Proteínas Proto-Oncogênicas p21(ras)/química , Software
18.
Methods Mol Biol ; 1958: 173-185, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30945219

RESUMO

The ability to predict how mutations affect protein structure, folding, and flexibility can elucidate the molecular mechanisms leading to disruption of supersecondary structures, the emergence of phenotypes, as well guiding rational protein engineering. The advent of fast and accurate computational tools has enabled us to comprehensively explore the landscape of mutation effects on protein structures, prioritizing mutations for rational experimental validation.Here we describe the use of two complementary web-based in silico methods, DUET and DynaMut, developed to infer the effects of mutations on folding, stability, and flexibility and how they can be used to explore and interpret these effects on protein supersecondary structures.


Assuntos
Substituição de Aminoácidos/genética , Biologia Computacional/métodos , Engenharia de Proteínas/métodos , Proteínas/química , Motivos de Aminoácidos , Humanos , Mutação de Sentido Incorreto/genética , Dobramento de Proteína , Estabilidade Proteica , Proteínas/genética
19.
Nat Commun ; 10(1): 1849, 2019 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-31015395

RESUMO

The bacterial cell wall plays a crucial role in viability and is an important drug target. In Escherichia coli, the peptidoglycan crosslinking reaction to form the cell wall is primarily carried out by penicillin-binding proteins that catalyse D,D-transpeptidase activity. However, an alternate crosslinking mechanism involving the L,D-transpeptidase YcbB can lead to bypass of D,D-transpeptidation and beta-lactam resistance. Here, we show that the crystallographic structure of YcbB consists of a conserved L,D-transpeptidase catalytic domain decorated with a subdomain on the dynamic substrate capping loop, peptidoglycan-binding and large scaffolding domains. Meropenem acylation of YcbB gives insight into the mode of inhibition by carbapenems, the singular antibiotic class with significant activity against L,D-transpeptidases. We also report the structure of PBP5-meropenem to compare interactions mediating inhibition. Additionally, we probe the interaction network of this pathway and assay beta-lactam resistance in vivo. Our results provide structural insights into the mechanism of action and the inhibition of L,D-transpeptidation, and into YcbB-mediated antibiotic resistance.


Assuntos
Antibacterianos/farmacologia , Proteínas de Escherichia coli/metabolismo , Escherichia coli/fisiologia , Meropeném/farmacologia , Peptidil Transferases/metabolismo , Resistência beta-Lactâmica/fisiologia , Acilação/efeitos dos fármacos , Substituição de Aminoácidos/genética , Antibacterianos/química , Domínio Catalítico/fisiologia , Parede Celular/efeitos dos fármacos , Parede Celular/metabolismo , Cristalografia por Raios X , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/isolamento & purificação , Meropeném/química , Simulação de Dinâmica Molecular , Proteínas de Ligação às Penicilinas/metabolismo , Peptidoglicano/metabolismo , Peptidil Transferases/química , Peptidil Transferases/genética , Peptidil Transferases/isolamento & purificação , Mapas de Interação de Proteínas/fisiologia , Proteínas Recombinantes/química , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo
20.
Mutat Res ; 815: 1-9, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30974384

RESUMO

In this study we investigated nucleotide usage biases along the length of a gene encoding human epidermal growth factor receptor (EGFR) and found out that there had been mutational GC-pressure with stronger asymmetric C-pressure in that gene before the preferable direction of nucleotide mutations changed. Current preferable direction of germline mutations in EGFR gene has been estimated with the help of Ensembl data base of gene variations. Preferable direction of somatic mutations in EGFR gene from cancer cells has been estimated with the help of COSMIC data base. Both germline and somatic mutations in cancer cells have the same GC to AT preferable direction in EGFR gene. These data have been used with the aim to find fragments of EGFR gene that have lower probability of missense C to T and G to A transitions to occur. So, the less mutable parts of extracellular EGFR domain are: C-terminal part of the first beta barrel and the central part of the second beta barrel. The less mutable parts of tyrosine kinase EGFR domain are: ATP-binding site (partially), regulatory alpha helix, and fragments that change their secondary structure during the activation process. These parts of EGFR should be considered as the best targets for new types of therapy development. Such criterion as low mutability is especially important for the selection of targets for anti-tumor therapy, since we have detected positive selection of amino acid replacements during somatic mutagenesis of EGFR gene in cancer cells.


Assuntos
Células Germinativas/metabolismo , Mutagênese/genética , Mutação de Sentido Incorreto/genética , Seleção Genética/genética , Substituição de Aminoácidos/genética , Antineoplásicos/farmacologia , Receptores ErbB/genética , Humanos
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA