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We report the sequencing and detection of 36 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples containing lineage-defining mutations specific to viruses belonging to the B.1.1.7 lineage in the Philippines.
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The cellular concentration of Bcl-xL is among the most important determinants of treatment response and overall prognosis in a broad range of tumors as well as an important determinant of the cellular response to several forms of tissue injury. We and others have previously shown that human Bcl-xL undergoes deamidation at two asparaginyl residues and that DNA-damaging antineoplastic agents as well as other stimuli can increase the rate of deamidation. Deamidation results in the replacement of asparginyl residues with aspartyl or isoaspartyl residues. Thus deamidation, like phosphorylation, introduces a negative charge into proteins. Here we show that the level of human Bcl-xL is constantly modulated by deamidation because deamidation, like phosphorylation in other proteins, activates a conditional PEST sequence to target Bcl-xL for degradation. Additionally, we show that degradation of deamidated Bcl-xL is mediated at least in part by calpain. Notably, we present sequence and biochemical data that suggest that deamidation has been conserved from the simplest extant metazoans through the human form of Bcl-xL, underscoring its importance in Bcl-xL regulation. Our findings strongly suggest that deamidation-regulated Bcl-xL degradation is an important component of the cellular rheostat that determines susceptibility to DNA-damaging agents and other death stimuli.
Assuntos
Amidas/metabolismo , Proteólise , Proteína bcl-X/metabolismo , Sequência de Aminoácidos , Animais , Calpaína/metabolismo , Linhagem Celular , Sequência Conservada , Dano ao DNA , Humanos , Concentração de Íons de Hidrogênio , Camundongos , Dados de Sequência Molecular , Estrutura Terciária de Proteína , Proteína bcl-X/químicaRESUMO
In a screen for genes expressed specifically in gastric mucous neck cells, we identified GKN3, the recently discovered third member of the gastrokine family. We present confirmatory mouse data and novel porcine data showing that mouse GKN3 expression is confined to mucous cells of the corpus neck and antrum base and is prominently expressed in metaplastic lesions. GKN3 was proposed originally to be expressed in some human populations and a pseudogene in others. To investigate that hypothesis, we studied human GKN3 evolution in the context of its paralogous genomic neighbors, GKN1 and GKN2. Haplotype analysis revealed that GKN3 mimics GKN2 in patterns of exonic SNP allocation, whereas GKN1 appeared to be more stringently selected. GKN3 showed signatures of both directional selection and population based selective sweeps in humans. One such selective sweep includes SNP rs10187256, originally identified as an ancestral tryptophan to premature STOP codon mutation. The derived (nonancestral) allele went to fixation in Asia. We show that another SNP, rs75578132, identified 5 bp downstream of rs10187256, exhibits a second selective sweep in almost all Europeans, some Latinos, and some Africans, possibly resulting from a reintroduction of European genes during African colonization. Finally, we identify a mutation that would destroy the splice donor site in the putative exon3-intron3 boundary, which occurs in all human genomes examined to date. Our results highlight a stomach-specific human genetic locus, which has undergone various selective sweeps across European, Asian, and African populations and thus reflects geographic and ethnic patterns in genome evolution.
Assuntos
Proteínas de Transporte/genética , Evolução Molecular , Loci Gênicos/genética , Proteínas de Membrana/genética , Pseudogenes/genética , Grupos Raciais/genética , Seleção Genética/genética , Animais , Proteínas de Transporte/metabolismo , Biologia Computacional , Primers do DNA/genética , Imunofluorescência , Mucosa Gástrica/metabolismo , Genética Populacional , Genótipo , Haplótipos/genética , Humanos , Funções Verossimilhança , Macaca mulatta/genética , Proteínas de Membrana/metabolismo , Camundongos , Camundongos Endogâmicos C57BL/genética , Análise em Microsséries , Microscopia Confocal , Modelos Genéticos , Mutação/genética , Filogenia , Polimorfismo de Nucleotídeo Único/genética , Especificidade da Espécie , Sus scrofa/genéticaRESUMO
BACKGROUND: It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an increase or decrease in affinity, or a predisposition towards misfolding. Here, we describe a tool where such mutations are efficiently identified, categorized and visualized. To categorize the mutations, amino acids in a mutation matrix are arranged according to one of three sets of physicochemical characteristics, namely hydrophilicity, size and polarizability, and charge and polarity. The magnitude and frequencies of mutations for an alignment are subsequently described using color information and scaling factors. RESULTS: To illustrate the capabilities of our approach, the technique is used to visualize and to compare mutation patterns in evolving sequences with diametrically opposite characteristics. Results show the emergence of distinct patterns not immediately discernible from the raw matrices. CONCLUSION: Our technique enables effective categorization and visualization of mutations by using specifically-arranged mutation matrices. This tool has a number of possible applications in protein engineering, notably in simplifying the identification of mutations and/or mutation trends that are associated with specific engineered protein characteristics and behavior.
