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1.
Nat Commun ; 12(1): 874, 2021 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-33558533

RESUMO

Base-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we use high-throughput sequencing and quantitative super-resolution imaging to probe the mutants of bacterial small RNA, SgrS, and their regulation of ptsG mRNA target. Mutations that disrupt binding of a chaperone protein, Hfq, and are distal to the mRNA annealing region still decrease the rate of target association, kon, and increase the dissociation rate, koff, showing that Hfq directly facilitates sRNA-mRNA annealing in vivo. Single base-pair mismatches in the annealing region reduce kon by 24-31% and increase koff by 14-25%, extending the time it takes to find and destroy the target by about a third. The effects of disrupting contiguous base-pairing are much more modest than that expected from thermodynamics, suggesting that Hfq buffers base-pair disruptions.


Assuntos
Pareamento de Bases/genética , Estabilidade de RNA , RNA Bacteriano/genética , Sequência de Bases , Escherichia coli/genética , Dosagem de Genes , Genes Reporter , Imageamento Tridimensional , Cinética , Mutação/genética , Nucleotídeos/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Fatores de Tempo
2.
Nat Commun ; 12(1): 611, 2021 01 27.
Artigo em Inglês | MEDLINE | ID: mdl-33504776

RESUMO

Genome sequences have been determined for many model organisms; however, repetitive regions such as centromeres, telomeres, and subtelomeres have not yet been sequenced completely. Here, we report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe. We overcame technical difficulties to obtain subtelomeric repetitive sequences by constructing strains that possess single SH regions of a standard laboratory strain. In addition, some natural isolates of S. pombe were analyzed using previous sequencing data. Whole sequences of SH regions revealed that each SH region consists of two distinct parts with mosaics of multiple common segments or blocks showing high variation among subtelomeres and strains. Subtelomere regions show relatively high frequency of nucleotide variations among strains compared with the other chromosomal regions. Furthermore, we identified subtelomeric RecQ-type helicase genes, tlh3 and tlh4, which add to the already known tlh1 and tlh2, and found that the tlh1-4 genes show high sequence variation with missense mutations, insertions, and deletions but no severe effects on their RNA expression. Our results indicate that SH sequences are highly polymorphic and hot spots for genome variation. These features of subtelomeres may have contributed to genome diversity and, conversely, various diseases.


Assuntos
Variação Genética , Genoma Fúngico , Schizosaccharomyces/genética , Telômero/genética , Sequência de Bases , Mutação INDEL/genética , Mosaicismo , Família Multigênica , Nucleotídeos/genética , Filogenia , RNA Fúngico/genética , RecQ Helicases/genética , Schizosaccharomyces/isolamento & purificação
3.
Arch Virol ; 166(2): 655-658, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33394170

RESUMO

RNA was extracted from 'Hugh Dickson' rose leaves displaying virus-like symptoms in Maryland, USA. Using high-throughput sequencing, we identified a new virus, tentatively named "rose virus R". This virus has a negative-sense, single-stranded RNA genome and exhibits genomic features of a rhabdovirus, including a genome organization of 3'-N-P-P3-M-G-P6-L-5' and a gene junction region consensus sequence 3'-AUUUAUUUUGACUCUA-5'. Rose virus R is phylogenetically related to cytorhabdoviruses, and the nucleotide and amino acid sequences of rose virus R and related cytorhabdoviruses have diverged considerably, suggesting that rose virus R should be classified as a member of a novel species in the genus Cytorhabdovirus.


Assuntos
Doenças das Plantas/virologia , Rosa/virologia , Vírus não Classificados/genética , Sequência de Aminoácidos , Genoma Viral/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Nucleotídeos/genética , Filogenia , RNA Viral/genética , Rhabdoviridae/genética , Proteínas Virais/genética , Sequenciamento Completo do Genoma/métodos
4.
Arch Virol ; 166(2): 665-669, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33409550

RESUMO

A putative mycovirus belonging to the proposed family "Fusariviridae" was discovered in Setosphaeria turcica by sequencing a double-stranded RNA extracted from this phytopathogenic fungus. The virus was tentatively named "Setosphaeria turcica fusarivirus 1" (StFV1). StFV1 has a genome comprising 6685 nucleotides. The genome contains three open reading frames (ORF). The largest ORF, ORF1, is preceded by an untranslated region (UTR) of 16 nucleotides and separated from ORF2 by an intergenic region of 63 nucleotides. The smallest ORF, ORF3, overlaps ORF2 by 16 nucleotides and is followed by a 3'-UTR of 82 nucleotides. The protein encoded by ORF1 is 71.8%, 67.4% and 68.1% identical to the RNA-dependent RNA polymerases (RdRps) of Pleospora typhicola fusarivirus 1 (PtFV1), Plasmopara viticola lesion-associated fusarivirus 1 (PvlaFV1), and Plasmopara viticola lesion-associated fusarivirus 3 (PvlaFV3), respectively, but has less than 47% amino acid sequence identity to the RdRps of other fusariviruses. To our knowledge, this is the first fusarivirus discovered in S. turcica and the first virus to be identified in this fungus using conventional cloning methods.


Assuntos
Ascomicetos/virologia , Vírus de RNA/genética , Regiões 3' não Traduzidas/genética , Sequência de Aminoácidos , Genoma Viral/genética , Nucleotídeos/genética , Fases de Leitura Aberta/genética , Filogenia , RNA de Cadeia Dupla/genética , RNA Viral/genética , /genética
5.
Nat Commun ; 12(1): 548, 2021 01 22.
Artigo em Inglês | MEDLINE | ID: mdl-33483497

RESUMO

Actin polymerization provides force for vital processes of the eukaryotic cell, but our understanding of actin dynamics and energetics remains limited due to the lack of high-quality probes. Most current probes affect dynamics of actin or its interactions with actin-binding proteins (ABPs), and cannot track the bound nucleotide. Here, we identify a family of highly sensitive fluorescent nucleotide analogues structurally compatible with actin. We demonstrate that these fluorescent nucleotides bind to actin, maintain functional interactions with a number of essential ABPs, are hydrolyzed within actin filaments, and provide energy to power actin-based processes. These probes also enable monitoring actin assembly and nucleotide exchange with single-molecule microscopy and fluorescence anisotropy kinetics, therefore providing robust and highly versatile tools to study actin dynamics and functions of ABPs.


Assuntos
Citoesqueleto de Actina/metabolismo , Actinas/metabolismo , Proteínas dos Microfilamentos/metabolismo , Proteínas Musculares/metabolismo , Nucleotídeos/metabolismo , Actinas/química , Algoritmos , Animais , Polarização de Fluorescência , Corantes Fluorescentes/química , Hidrólise , Cinética , Modelos Teóricos , Proteínas Musculares/química , Nucleotídeos/química , Ligação Proteica , Coelhos , Termodinâmica
6.
Nat Commun ; 12(1): 279, 2021 01 12.
Artigo em Inglês | MEDLINE | ID: mdl-33436624

RESUMO

Remdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analog and inhibits the RNA-dependent RNA polymerase (RdRp) of coronaviruses including SARS-CoV-2. Remdesivir is incorporated by the RdRp into the growing RNA product and allows for addition of three more nucleotides before RNA synthesis stalls. Here we use synthetic RNA chemistry, biochemistry and cryo-electron microscopy to establish the molecular mechanism of remdesivir-induced RdRp stalling. We show that addition of the fourth nucleotide following remdesivir incorporation into the RNA product is impaired by a barrier to further RNA translocation. This translocation barrier causes retention of the RNA 3'-nucleotide in the substrate-binding site of the RdRp and interferes with entry of the next nucleoside triphosphate, thereby stalling RdRp. In the structure of the remdesivir-stalled state, the 3'-nucleotide of the RNA product is matched and located with the template base in the active center, and this may impair proofreading by the viral 3'-exonuclease. These mechanistic insights should facilitate the quest for improved antivirals that target coronavirus replication.


Assuntos
Monofosfato de Adenosina/análogos & derivados , Monofosfato de Adenosina/farmacologia , Alanina/análogos & derivados , Alanina/farmacologia , /efeitos dos fármacos , Antivirais/farmacologia , Aptâmeros de Nucleotídeos , /efeitos dos fármacos , Nucleotídeos , RNA Viral , /enzimologia , Replicação Viral/efeitos dos fármacos
7.
Food Chem ; 336: 127672, 2021 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-32771899

RESUMO

Endophytic bacteria are always related to the host different traits, including the secondary metabolites production. However, the effect and mechanism of endophytic bacteria in the mushrooms fruit body on mycelia are still not clear. In this study, we investigated the effect of endophytic bacterial metabolites on the quality of Lyophyllum decastes mycelia. Soluble sugars, starch, protein, free amino acids, 5'-Nucleotides, EUC, and organic acids contents of mycelia were analyzed. We found that endophytic bacterial metabolites significantly increased the contents of soluble sugars, starch, protein, free amino acids, organic acids, and EUC. The present study thus suggests that endophytic bacteria could promote the quality of Lyophyllum decastes by improving non-volatile taste components of mycelia.


Assuntos
Agaricales/química , Bactérias/metabolismo , Endófitos/fisiologia , Micélio/química , Paladar , Agaricales/fisiologia , Aminoácidos/análise , Bactérias/isolamento & purificação , Microbiologia de Alimentos , Qualidade dos Alimentos , Proteínas Fúngicas/análise , Micélio/fisiologia , Nucleotídeos/análise , Compostos Orgânicos Voláteis
8.
Gene ; 766: 145096, 2021 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-32919006

RESUMO

The phylogenetic analysis based on sequence similarity targeted to real biological taxa is one of the major challenging tasks. In this paper, we propose a novel alignment-free method, CoFASA (Codon Feature based Amino acid Sequence Analyser), for similarity analysis of nucleotide sequences. At first, we assign numerical weights to the four nucleotides. We then calculate a score of each codon based on the numerical value of the constituent nucleotides, termed as degree of codons. Accordingly, we obtain the degree of each amino acid based on the degree of codons targeted towards a specific amino acid. Utilizing the degree of twenty amino acids and their relative abundance within a given sequence, we generate 20-dimensional features for every coding DNA sequence or protein sequence. We use the features for performing phylogenetic analysis of the set of candidate sequences. We use multiple protein sequences derived from Beta-globin (BG), NADH dehydrogenase subunit 5 (ND5), Transferrins (TFs), Xylanases, low identity (<40%) and high identity (⩾40%) protein sequences (encompassing 533 and 1064 protein families) for experimental assessments. We compare our results with sixteen (16) well-known methods, including both alignment-based and alignment-free methods. Various assessment indices are used, such as the Pearson correlation coefficient, RF (Robinson-Foulds) distance and ROC score for performance analysis. While comparing the performance of CoFASA with alignment-based methods (ClustalW, ClustalΩ, MAFFT, and MUSCLE), it shows very similar results. Further, CoFASA shows better performance in comparison to well-known alignment-free methods, including LZW-Kernal, jD2Stat, FFP, spaced, and AFKS-D2s in predicting taxonomic relationship among candidate taxa. Overall, we observe that the features derived by CoFASA are very much useful in isolating the sequences according to their taxonomic labels. While our method is cost-effective, at the same time, produces consistent and satisfactory outcomes.


Assuntos
Sequência de Aminoácidos/genética , Aminoácidos/genética , Códon/genética , Alinhamento de Sequência/métodos , Análise de Sequência de Proteína/métodos , Algoritmos , Animais , Humanos , Nucleotídeos/genética , Filogenia , Proteínas/genética
9.
J Formos Med Assoc ; 120(1 Pt 2): 303-310, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33109431

RESUMO

BACKGROUND: The biochemical response is a crucial indicator of prognosis in chronic hepatitis B (CHB) patients treated with nucleotide/nucleoside analogues (NAs). The impact of hepatitis D virus (HDV) infection on alanine aminotransferase normalization is elusive. METHODS: The longitudinal study recruited 1185 CHB patients who received NAs. These patients were tested for anti-HDV antibody and HDV RNA at the initiation of anti-hepatitis B virus (HBV) therapy and annually for patients who were HDV-seropositive. ALT levels were examined at the first and second year of anti-HBV therapy. ALT abnormality was defined as ALT levels above 40 IU/mL in both male and female, and the risk factors associated with ALT abnormality were analysed. RESULTS: Rates of seropositivity for anti-HDV and HDV RNA were 2.0% and 0.8% among 1185 NA-treated CHB patients, respectively. The strongest factor associated with ALT abnormality (>40 IU/mL) after first year treatment with NAs was HDV RNA seropositivity at year 1 (odds ratio [OR]/95% confidence interval [CI]: 31.44/3.49-283.56, P = 0.002), followed by liver cirrhosis (2.18/1.51-3.15, P < 0.001), detectable HBV DNA at year 1 (OR/CI: 1.99/1.36-2.92, P < 0.001), diabetes (OR/CI: 1.75/1.10-2.78, P = 0.02), body mass index (BMI) (OR/CI: 1.13/1.09-1.18, P < 0.001) and age (OR/CI: 0.97/0.96-0.98, P < 0.001). Among patients who were seronegative for HBV DNA at year 1, the strongest factor associated with ALT abnormality was HDV RNA seropositivity at year 1 (OR/CI: 30.00/3.28-274.05, P = 0.003), followed by liver cirrhosis (OR/CI: 1.83/1.21-2.75, P = 0.004), BMI (OR/CI: 1.16/1.11-1.21, P < 0.001) and age (OR/CI: 0.97/0.96-0.99, P < 0.001). Similarly, the impact of HDV RNA seropositivity on ALT abnormality was noted in patients without detectable HBV DNA but not in those with hepatitis B viremia at treatment year 2 (OR/CI: 10.16/1.33-77.74, P = 0.03). CONCLUSION: HDV infection played an important role in ALT abnormality in CHB patients receiving 1-year and 2-year NAs. The impact was particularly noted in patients who had successfully suppressed HBV DNA.


Assuntos
Hepatite B Crônica , Vírus Delta da Hepatite , Nucleosídeos/uso terapêutico , Nucleotídeos/uso terapêutico , Alanina Transaminase , DNA Viral , Feminino , Vírus da Hepatite B/genética , Hepatite B Crônica/tratamento farmacológico , Hepatite D , Vírus Delta da Hepatite/genética , Humanos , Estudos Longitudinais , Masculino
10.
Mol Phylogenet Evol ; 154: 106961, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-32956799

RESUMO

Heliamphora is a genus of carnivorous pitcher plants endemic to the Guiana Highlands with fragmented distributions. We present a well resolved, time-calibrated, and comprehensive Heliamphora phylogeny estimated using Bayesian inference and maximum likelihood based on nuclear genes (26S, ITS, and PHYC) and secondary calibration. We used stochastic mapping to infer ancestral states of morphological characters and ecological traits. Our ancestral state estimations revealed that the pitcher drainage structures characteristic of the genus transformed from a hole to a slit in single clade, while other features (scape pubescence and hammock-like growth) have been gained and lost multiple times. Habitat was similarly labile in Heliamphora, with multiple transitions from the ancestral highland habitats into the lowlands. Using a Mantel test, we found closely related species tend to be geographically closely distributed. Placing our phylogeny in a historical context, major clades likely emerged through both vicariance and dispersal during the Miocene with more recent diversification driven by vertical displacement during the Pleistocene glacial-interglacial thermal oscillations. Despite the dynamic climatic history experienced by Heliamphora, the temperature changes brought by global warming pose a significant threat, particularly for those species at the highest elevations.


Assuntos
Filogenia , Filogeografia , Sarraceniaceae/classificação , Áreas Alagadas , Teorema de Bayes , Funções Verossimilhança , Modelos Biológicos , Nucleotídeos/genética , Fenótipo , América do Sul
11.
Mol Phylogenet Evol ; 154: 106966, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-32971285

RESUMO

Although numerous studies have demonstrated the theoretical and empirical importance of treating gaps as insertion/deletion (indel) events in phylogenetic analyses, the standard approach to maximum likelihood (ML) analysis employed in the vast majority of empirical studies codes gaps as nucleotides of unknown identity ("missing data"). Therefore, it is imperative to understand the empirical consequences of different numbers and distributions of gaps treated as missing data. We evaluated the effects of variation in the number and distribution of gaps (i.e., no base, coded as IUPAC "." or "-") treated as missing data (i.e., any base, coded as "?" or IUPAC "N") in standard ML analysis. We obtained alignments with variable numbers and arrangements of gaps by aligning seven diverse empirical datasets under different gap opening costs using MAFFT. We selected the optimal substitution model for each alignment using the corrected Akaike Information Criterion in jModelTest2 and searched for optimal trees using GARLI. We also employed a Monte Carlo approach to randomly replace nucleotides with gaps (treated as missing data) in an empirical dataset to understand more precisely the effects of varying their number and distribution. To compare alignments, we developed four new indices and used several existing measures to quantify the number and distribution of gaps in all alignments. Our most important finding is that ML scores correlate negatively with gap opening costs and the amount of missing data. However, this negative relationship is not due to the increase in missing data per se-which increases ML scores-but instead to the effect of gaps on nucleotide homology. These variables also cause significant but largely unpredictable effects on tree topology.


Assuntos
Filogenia , Bases de Dados Genéticas , Funções Verossimilhança , Método de Monte Carlo , Nucleotídeos/genética , Padrões de Referência , Alinhamento de Sequência
12.
J Med Chem ; 64(1): 782-796, 2021 01 14.
Artigo em Inglês | MEDLINE | ID: mdl-33356231

RESUMO

Nucleotide analogues are used for treating viral infections such as HIV, hepatitis B, hepatitis C, influenza, and SARS-CoV-2. To become polymerase substrates, a nucleotide analogue must be phosphorylated by cellular kinases which is rate-limiting. The goal of this study is to develop dNTP/NTP analogues directly from nucleotides. Tenofovir (TFV) analogues were synthesized by conjugating with amino acids. We demonstrate that some conjugates act as dNTP analogues and HIV-1 reverse transcriptase (RT) catalytically incorporates the TFV part as the chain terminator. X-ray structures in complex with HIV-1 RT/dsDNA showed binding of the conjugates at the polymerase active site, however, in different modes in the presence of Mg2+ versus Mn2+ ions. The adaptability of the compounds is seemingly essential for catalytic incorporation of TFV by RT. 4d with a carboxyl sidechain demonstrated the highest incorporation. 4e showed weak incorporation and rather behaved as a dNTP-competitive inhibitor. This result advocates the feasibility of designing NTP/dNTP analogues by chemical substitutions to nucleotide analogues.


Assuntos
Aminoácidos/química , Nucleotídeos/química , Tenofovir/química , Viroses/tratamento farmacológico , Sítios de Ligação , /virologia , Domínio Catalítico , Desenho de Fármacos , Transcriptase Reversa do HIV/química , Transcriptase Reversa do HIV/metabolismo , Humanos , Magnésio/química , Simulação de Acoplamento Molecular , Nucleotídeos/metabolismo , Fosforilação , Especificidade por Substrato , Viroses/virologia
14.
Proc Natl Acad Sci U S A ; 117(52): 33530-33539, 2020 12 29.
Artigo em Inglês | MEDLINE | ID: mdl-33318202

RESUMO

Two-component systems (TCSs) in bacteria are molecular circuits that allow the perception of and response to diverse stimuli. These signaling circuits rely on phosphoryl-group transfers between transmitter and receiver domains of sensor kinase and response regulator proteins, and regulate several cellular processes in response to internal or external cues. Phosphorylation, and thereby activation, of response regulators has been demonstrated to occur by their cognate histidine kinases but also by low molecular weight phosphodonors such as acetyl phosphate and carbamoyl phosphate. Here, we present data indicating that the intermediates of the de novo syntheses of purines and histidine, 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (ZMP) and/or 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-triphosphate (ZTP), activate the response regulator UvrY, by promoting its autophosphorylation at the conserved aspartate at position 54. Moreover, these Z nucleotides are shown to also activate the nonrelated response regulators ArcA, CpxR, RcsB, and PhoQ. We propose that ZMP and/or ZTP act as alarmones for a wide range of response regulators in vivo, providing a novel mechanism by which they could impact gene expression in response to metabolic cues.


Assuntos
Escherichia coli/metabolismo , Nucleotídeos/farmacologia , Transdução de Sinais , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Regulação Bacteriana da Expressão Gênica/efeitos dos fármacos , Genes Bacterianos , Mutação/genética , Fosfatos/farmacologia , Fosforilação/efeitos dos fármacos , Transdução de Sinais/efeitos dos fármacos
15.
PLoS Biol ; 18(12): e3001015, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33332391

RESUMO

Reverse transcription, an essential event in the HIV-1 life cycle, requires deoxynucleotide triphosphates (dNTPs) to fuel DNA synthesis, thus requiring penetration of dNTPs into the viral capsid. The central cavity of the capsid protein (CA) hexamer reveals itself as a plausible channel that allows the passage of dNTPs into assembled capsids. Nevertheless, the molecular mechanism of nucleotide import into the capsid remains unknown. Employing all-atom molecular dynamics (MD) simulations, we established that cooperative binding between nucleotides inside a CA hexamer cavity results in energetically favorable conditions for passive translocation of dNTPs into the HIV-1 capsid. Furthermore, binding of the host cell metabolite inositol hexakisphosphate (IP6) enhances dNTP import, while binding of synthesized molecules like benzenehexacarboxylic acid (BHC) inhibits it. The enhancing effect on reverse transcription by IP6 and the consequences of interactions between CA and nucleotides were corroborated using atomic force microscopy, transmission electron microscopy, and virological assays. Collectively, our results provide an atomistic description of the permeability of the HIV-1 capsid to small molecules and reveal a novel mechanism for the involvement of metabolites in HIV-1 capsid stabilization, nucleotide import, and reverse transcription.


Assuntos
Capsídeo/metabolismo , HIV-1/metabolismo , Replicação Viral/fisiologia , Capsídeo/química , Capsídeo/fisiologia , Proteínas do Capsídeo/genética , Replicação do DNA/fisiologia , DNA Viral/metabolismo , Células HEK293 , HIV-1/genética , Interações Hospedeiro-Patógeno/fisiologia , Humanos , Simulação de Dinâmica Molecular , Nucleotídeos/metabolismo , Permeabilidade , Ácido Fítico/análise , Ácido Fítico/metabolismo , Vírion/genética , Montagem de Vírus/fisiologia , Replicação Viral/genética
16.
Mem Inst Oswaldo Cruz ; 115: e200303, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33146255

RESUMO

Giardiasis is an infectious disease caused by Giardia duodenalis. The pro-drug metronidazole (MTZ) is the first-line treatment for giardiasis. Parasite's proteins as pyruvate:ferredoxin oxidoreductase (PFOR), ferredoxin (Fd), nitroreductase-1 (NR-1) and thioredoxin reductase (TrxR) participate in MTZ activation. Here, we showed Giardia trophozoites long-term exposed to MTZ presented higher IC50 than controls, showing the drug influenced the parasite survival. That reduction in MTZ's susceptibility does not seem to be related to mutations in the genes pfor, fd, nr-1 or trxr. It points that different mechanism as alterations in other metabolic pathways can account for Giardia resistance to MTZ therapy.


Assuntos
Antiprotozoários , Resistência a Medicamentos/genética , Giardia lamblia , Metronidazol/farmacologia , Pró-Fármacos , Ativação Metabólica , Antiprotozoários/farmacologia , Giardia lamblia/efeitos dos fármacos , Giardia lamblia/genética , Nucleotídeos
17.
J Phys Chem Lett ; 11(21): 9408-9414, 2020 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-33104327

RESUMO

Chemical similarity-based approaches employed to repurpose or develop new treatments for emerging diseases, such as COVID-19, correlates molecular structure-based descriptors of drugs with those of a physiological counterpart or clinical phenotype. We propose novel descriptors based on a COSMO-RS (short for conductor-like screening model for real solvents) σ-profiles for enhanced drug screening enabled by machine learning (ML). The descriptors' performance is hereby illustrated for nucleotide analogue drugs that inhibit the ribonucleic acid-dependent ribonucleic acid polymerase, key to viral transcription and genome replication. The COSMO-RS-based descriptors account for both chemical reactivity and structure, and are more effective for ML-based screening than fingerprints based on molecular structure and simple physical/chemical properties. The descriptors are evaluated using principal component analysis, an unsupervised ML technique. Our results correlate with the active monophosphate forms of the leading drug remdesivir and the prospective drug EIDD-2801 with nucleotides, followed by other promising drugs, and are superior to those from molecular structure-based descriptors and molecular docking. The COSMO-RS-based descriptors could help accelerate drug discovery for the treatment of emerging diseases.


Assuntos
Aprendizado de Máquina , Nucleotídeos/química , Betacoronavirus/isolamento & purificação , Betacoronavirus/metabolismo , Sítios de Ligação , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/patologia , Infecções por Coronavirus/virologia , Avaliação Pré-Clínica de Medicamentos/métodos , Humanos , Simulação de Acoplamento Molecular , Nucleotídeos/metabolismo , Nucleotídeos/uso terapêutico , Pandemias , Pneumonia Viral/tratamento farmacológico , Pneumonia Viral/patologia , Pneumonia Viral/virologia , Análise de Componente Principal , Teoria Quântica , RNA Viral/química , RNA Viral/metabolismo , /genética , /metabolismo
18.
Nat Commun ; 11(1): 5388, 2020 10 23.
Artigo em Inglês | MEDLINE | ID: mdl-33097692

RESUMO

The alarmone nucleotides guanosine tetraphosphate and pentaphosphate, commonly referred to as (p)ppGpp, regulate bacterial responses to nutritional and other stresses. There is evidence for potential existence of a third alarmone, guanosine-5'-monophosphate-3'-diphosphate (pGpp), with less-clear functions. Here, we demonstrate the presence of pGpp in bacterial cells, and perform a comprehensive screening to identify proteins that interact respectively with pGpp, ppGpp and pppGpp in Bacillus species. Both ppGpp and pppGpp interact with proteins involved in inhibition of purine nucleotide biosynthesis and with GTPases that control ribosome assembly or activity. By contrast, pGpp interacts with purine biosynthesis proteins but not with the GTPases. In addition, we show that hydrolase NahA (also known as YvcI) efficiently produces pGpp by hydrolyzing (p)ppGpp, thus modulating alarmone composition and function. Deletion of nahA leads to reduction of pGpp levels, increased (p)ppGpp levels, slower growth recovery from nutrient downshift, and loss of competitive fitness. Our results support the existence and physiological relevance of pGpp as a third alarmone, with functions that can be distinct from those of (p)ppGpp.


Assuntos
Bacillus/metabolismo , Proteínas de Bactérias/metabolismo , Nucleotídeos de Guanina/metabolismo , Nucleotídeos/metabolismo , Bacillus/genética , Bacillus anthracis/metabolismo , Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Guanosina Tetrafosfato/metabolismo , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Ligação Proteica , Biossíntese de Proteínas
19.
Wei Sheng Yan Jiu ; 49(5): 716-723, 2020 Sep.
Artigo em Chinês | MEDLINE | ID: mdl-33070811

RESUMO

OBJECTIVE: To investigate the relationship between single nucleotides polymorphism of catalase(CAT) gene and susceptibility to noise-induced hearing loss(NIHL) in occupational noise exposed population. METHODS: A case-control study of 1∶1 was conducted to select 286 workers with binaural high frequency average hearing threshold ≥40 dB(HL), from 2006 to 2015 in a cohort study of occupational noise exposure workers in Henan Province. According to the type of work, the age difference was not more than 5 years and the length of exposure to noise was not more than 2 years. The polymorphism of 8 single nucleotides in CAT gene was detected by medium SNPscanTM, and the relationship between 8 single nucleotides polymorphism of CAT gene and NIHL susceptibility was analyzed by multivariate conditional logistic regression. RESULTS: Under the dominant model of rs208679 locus of CAT gene [(GA GG)/AA], the risk of NIHL in individuals carrying GA or GG genotype was 1. 431 times higher than that in individuals carrying AA genotype(95%CI 1. 020-2. 009), and P=0. 038. CONCLUSION: G, a mutant at rs208679 site of CAT gene, may be one of the risk factors for NIHL susceptibility.


Assuntos
Perda Auditiva Provocada por Ruído , Estudos de Casos e Controles , Catalase/genética , Estudos de Coortes , Predisposição Genética para Doença , Perda Auditiva Provocada por Ruído/epidemiologia , Perda Auditiva Provocada por Ruído/genética , Humanos , Nucleotídeos
20.
Mol Cell ; 80(1): 1-2, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-33007252

RESUMO

Wang et al. (2020) show that binding of the second messenger ppGpp to inosine-guanosine kinase (Gsk) in E. coli modulates the levels of the key metabolite phosphoribosyl pyrophosphate (pRpp), decreasing purine synthesis to favor amino acid synthesis during stress adaptation.


Assuntos
Escherichia coli , Nucleotídeos , Bactérias , Guanosina Pentafosfato , Guanosina Tetrafosfato
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