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1.
Nat Commun ; 12(1): 5004, 2021 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-34408154

RESUMO

The endoplasmic reticulum (ER) Hsp70 chaperone BiP is regulated by AMPylation, a reversible inactivating post-translational modification. Both BiP AMPylation and deAMPylation are catalysed by a single ER-localised enzyme, FICD. Here we present crystallographic and solution structures of a deAMPylation Michaelis complex formed between mammalian AMPylated BiP and FICD. The latter, via its tetratricopeptide repeat domain, binds a surface that is specific to ATP-state Hsp70 chaperones, explaining the exquisite selectivity of FICD for BiP's ATP-bound conformation both when AMPylating and deAMPylating Thr518. The eukaryotic deAMPylation mechanism thus revealed, rationalises the role of the conserved Fic domain Glu234 as a gatekeeper residue that both inhibits AMPylation and facilitates hydrolytic deAMPylation catalysed by dimeric FICD. These findings point to a monomerisation-induced increase in Glu234 flexibility as the basis of an oligomeric state-dependent switch between FICD's antagonistic activities, despite a similar mode of engagement of its two substrates - unmodified and AMPylated BiP.


Assuntos
Monofosfato de Adenosina/metabolismo , Proteínas de Choque Térmico/química , Proteínas de Choque Térmico/metabolismo , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo , Nucleotidiltransferases/química , Nucleotidiltransferases/metabolismo , Monofosfato de Adenosina/química , Trifosfato de Adenosina/química , Trifosfato de Adenosina/metabolismo , Motivos de Aminoácidos , Biocatálise , Dimerização , Proteínas de Choque Térmico/genética , Humanos , Proteínas de Membrana/genética , Nucleotidiltransferases/genética , Processamento de Proteína Pós-Traducional
2.
J Microbiol ; 59(9): 848-853, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34449058

RESUMO

Rap small GTPases are involved in diverse signaling pathways associated with cell growth, proliferation, and cell migration. There are three Rap proteins in Dictyostelium, RapA, RapB, and RapC. RapA is a key regulator in the control of cell adhesion and migration. Recently RapA and RapC have been reported to have opposite functions in the regulation of cellular processes. In this study, we demonstrate that the C-terminus of RapC, which is not found in RapA, is essential for the opposite functions of RapC and is able to reverse the functions of RapA when fused to the tail of RapA. Cells lacking RapC displayed several defective phenotypes, including spread morphology, strong adhesion, and decreased cell migration compared to wild-type cells. These phenotypes were rescued by full-length RapC, but not by RapC missing the C-terminus. Furthermore, recombinant RapA fused with the C-terminus of RapC completely recovered the phenotypes of rapC null cells, indicating that the functions of RapA were modified to become similar to those of RapC by the C-terminus of RapC with respect to cell morphology, cell adhesion and migration, cytokinesis, and development. These results suggest that the C-terminal residues of RapC are able to suppress and change the functions of other Ras proteins in Ras oncogenic signaling pathways.


Assuntos
Dictyostelium/enzimologia , Proteínas de Protozoários/metabolismo , Proteínas ras/metabolismo , Motivos de Aminoácidos , Dictyostelium/química , Dictyostelium/genética , Regulação da Expressão Gênica , Ligação Proteica , Proteínas de Protozoários/química , Proteínas de Protozoários/genética , Proteínas ras/genética
3.
Int J Mol Sci ; 22(16)2021 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-34445319

RESUMO

Anticancer peptides (ACPs) could potentially offer many advantages over other cancer therapies. ACPs often target cell membranes, where their surface mechanism is coupled to a conformational change into helical structures. However, details on their binding are still unclear, which would be crucial to reach progress in connecting structural aspects to ACP action and to therapeutic developments. Here we investigated natural helical ACPs, Lasioglossin LL-III, Macropin 1, Temporin-La, FK-16, and LL-37, on model liposomes, and also on extracellular vesicles (EVs), with an outer leaflet composition similar to cancer cells. The combined simulations and experiments identified three distinct binding modes to the membranes. Firstly, a highly helical structure, lying mainly on the membrane surface; secondly, a similar, yet only partially helical structure with disordered regions; and thirdly, a helical monomeric form with a non-inserted perpendicular orientation relative to the membrane surface. The latter allows large swings of the helix while the N-terminal is anchored to the headgroup region. These results indicate that subtle differences in sequence and charge can result in altered binding modes. The first two modes could be part of the well-known carpet model mechanism, whereas the newly identified third mode could be an intermediate state, existing prior to membrane insertion.


Assuntos
Peptídeos Catiônicos Antimicrobianos/química , Antineoplásicos/química , Venenos de Abelha/química , Membrana Celular/metabolismo , Motivos de Aminoácidos , Peptídeos Catiônicos Antimicrobianos/metabolismo , Antineoplásicos/metabolismo , Venenos de Abelha/metabolismo , Vesículas Extracelulares/metabolismo , Humanos , Ligação Proteica , Domínios Proteicos
4.
Acta Crystallogr D Struct Biol ; 77(Pt 8): 1040-1049, 2021 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-34342277

RESUMO

The ß-link is a composite protein motif consisting of a G1ß ß-bulge and a type II ß-turn, and is generally found at the end of two adjacent strands of antiparallel ß-sheet. The 1,2-positions of the ß-bulge are also the 3,4-positions of the ß-turn, with the result that the N-terminal portion of the polypeptide chain is orientated at right angles to the ß-sheet. Here, it is reported that the ß-link is frequently found in certain protein folds of the SCOPe structural classification at specific locations where it connects a ß-sheet to another area of a protein. It is found at locations where it connects one ß-sheet to another in the ß-sandwich and related structures, and in small (four-, five- or six-stranded) ß-barrels, where it connects two ß-strands through the polypeptide chain that crosses an open end of the barrel. It is not found in larger (eight-stranded or more) ß-barrels that are straightforward ß-meanders. In some cases it initiates a connection between a single ß-sheet and an α-helix. The ß-link also provides a framework for catalysis in serine proteases, where the catalytic serine is part of a conserved ß-link, and in cysteine proteases, including Mpro of human SARS-CoV-2, in which two residues of the active site are located in a conserved ß-link.


Assuntos
Estrutura Secundária de Proteína , Serina Proteases/química , Motivos de Aminoácidos , Animais , Domínio Catalítico , Proteases 3C de Coronavírus/química , Proteases 3C de Coronavírus/metabolismo , Cisteína Proteases/química , Cisteína Proteases/metabolismo , Bases de Dados de Proteínas , Humanos , Ligação de Hidrogênio , Modelos Moleculares , SARS-CoV-2/química , SARS-CoV-2/enzimologia , Serina Proteases/metabolismo , Homologia Estrutural de Proteína
5.
Nature ; 596(7870): 138-142, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34290405

RESUMO

In early mitosis, the duplicated chromosomes are held together by the ring-shaped cohesin complex1. Separation of chromosomes during anaphase is triggered by separase-a large cysteine endopeptidase that cleaves the cohesin subunit SCC1 (also known as RAD212-4). Separase is activated by degradation of its inhibitors, securin5 and cyclin B6, but the molecular mechanisms of separase regulation are not clear. Here we used cryogenic electron microscopy to determine the structures of human separase in complex with either securin or CDK1-cyclin B1-CKS1. In both complexes, separase is inhibited by pseudosubstrate motifs that block substrate binding at the catalytic site and at nearby docking sites. As in Caenorhabditis elegans7 and yeast8, human securin contains its own pseudosubstrate motifs. By contrast, CDK1-cyclin B1 inhibits separase by deploying pseudosubstrate motifs from intrinsically disordered loops in separase itself. One autoinhibitory loop is oriented by CDK1-cyclin B1 to block the catalytic sites of both separase and CDK19,10. Another autoinhibitory loop blocks substrate docking in a cleft adjacent to the separase catalytic site. A third separase loop contains a phosphoserine6 that promotes complex assembly by binding to a conserved phosphate-binding pocket in cyclin B1. Our study reveals the diverse array of mechanisms by which securin and CDK1-cyclin B1 bind and inhibit separase, providing the molecular basis for the robust control of chromosome segregation.


Assuntos
Proteína Quinase CDC2/química , Proteína Quinase CDC2/metabolismo , Ciclina B1/química , Ciclina B1/metabolismo , Securina/química , Securina/metabolismo , Separase/química , Separase/metabolismo , Motivos de Aminoácidos , Proteína Quinase CDC2/antagonistas & inibidores , Proteína Quinase CDC2/ultraestrutura , Quinases relacionadas a CDC2 e CDC28/química , Quinases relacionadas a CDC2 e CDC28/metabolismo , Quinases relacionadas a CDC2 e CDC28/ultraestrutura , Proteínas de Ciclo Celular/metabolismo , Segregação de Cromossomos , Microscopia Crioeletrônica , Ciclina B1/ultraestrutura , Proteínas de Ligação a DNA/metabolismo , Humanos , Modelos Moleculares , Fosfosserina/metabolismo , Ligação Proteica , Domínios Proteicos , Securina/ultraestrutura , Separase/antagonistas & inibidores , Separase/ultraestrutura , Especificidade por Substrato
6.
Arch Virol ; 166(10): 2859-2863, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34291341

RESUMO

Sclerotinia sclerotiorum ourmiavirus 17 (SsOV17) was isolated from the hypovirulent strain GF3 of Sclerotinia sclerotiorum. The genome of SsOV17 is 2,802 nt in length and contains a single long open reading frame (ORF) flanked by a short structured 5'-untranslated region (5'-UTR) (28 nt) and a long 3'-UTR (788 nt), respectively. The ORF encodes a protein with 663 amino acids and a predicted molecular mass of 75.0 kDa. A BLASTp search indicated that the protein encoded by SsOV17 is closely related to the putative RNA-dependent RNA polymerase (RdRp) of Sclerotinia sclerotiorum ourmiavirus 13 (71% identity). A multiple sequence alignment indicated that eight conserved amino acid motifs were present in the RdRp conserved region of SsOV17. Phylogenetic analysis demonstrated that SsOV17 clustered with members of the genus Botoulivirus.


Assuntos
Ascomicetos/virologia , Micovírus/classificação , Doenças das Plantas/microbiologia , Vírus de RNA/classificação , Motivos de Aminoácidos , Ascomicetos/patogenicidade , Brassica napus/microbiologia , Micovírus/genética , Micovírus/isolamento & purificação , Genoma Viral/genética , Fases de Leitura Aberta/genética , Filogenia , Vírus de RNA/genética , Vírus de RNA/isolamento & purificação , RNA Viral/genética , RNA Polimerase Dependente de RNA/genética , Regiões não Traduzidas/genética
7.
J Chem Theory Comput ; 17(8): 5276-5286, 2021 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-34261315

RESUMO

Membrane curvature plays an essential role in the organization and trafficking of membrane associated proteins. Comparison or prediction of the experimentally resolved protein concentrations adopted at different membrane curvatures requires direct quantification of the relative partitioning free energy. Here, we present a highly efficient and simple to implement a free-energy calculation method which is able to directly resolve the relative partitioning free energy of proteins as a direct function of membrane curvature, i.e., a curvature sensing profile, within (coarse-grained) molecular dynamics simulations. We demonstrate its utility by resolving these profiles for two known curvature sensing peptides, namely ALPS and α-synuclein, for a membrane curvature ranging from -1/6.5 to +1/6.5 nm-1. We illustrate that the difference in relative partitioning (binding) free energy between these two extrema is only about 13 kBT for both peptides, illustrating that the driving force of curvature sensing is subtle. Furthermore, we illustrate that ALPS and α-synuclein sense curvature via a contrasting mechanism, which is differentially affected by membrane composition. In addition, we demonstrate that the intrinsic spontaneous curvature of both of these peptides lies beyond the range of membrane curvature accessible in micropipette aspiration experiments, being about 1/7 nm -1. Our approach offers an efficient and simple to implement in silico tool for exploring and screening the membrane curvature sensing mechanisms of proteins.


Assuntos
alfa-Sinucleína/química , Motivos de Aminoácidos , Cinética , Simulação de Dinâmica Molecular , alfa-Sinucleína/metabolismo
8.
Nat Commun ; 12(1): 4322, 2021 07 14.
Artigo em Inglês | MEDLINE | ID: mdl-34262048

RESUMO

Successful cell division relies on the timely removal of key cell cycle proteins such as securin. Securin inhibits separase, which cleaves the cohesin rings holding chromosomes together. Securin must be depleted before anaphase to ensure chromosome segregation occurs with anaphase. Here we find that in meiosis I, mouse oocytes contain an excess of securin over separase. We reveal a mechanism that promotes excess securin destruction in prometaphase I. Importantly, this mechanism relies on two phenylalanine residues within the separase-interacting segment (SIS) of securin that are only exposed when securin is not bound to separase. We suggest that these residues facilitate the removal of non-separase-bound securin ahead of metaphase, as inhibiting this period of destruction by mutating both residues causes the majority of oocytes to arrest in meiosis I. We further propose that cellular securin levels exceed the amount an oocyte is capable of removing in metaphase alone, such that the prometaphase destruction mechanism identified here is essential for correct meiotic progression in mouse oocytes.


Assuntos
Meiose , Oócitos/citologia , Securina/metabolismo , Motivos de Aminoácidos , Animais , Segregação de Cromossomos , Camundongos , Mutação , Oócitos/metabolismo , Fenilalanina/genética , Fenilalanina/metabolismo , Prometáfase , Ligação Proteica , Securina/química , Securina/genética , Separase/metabolismo
9.
Int J Mol Sci ; 22(12)2021 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-34203933

RESUMO

Natural resistance-associated macrophage proteins (Nramps) are specific metal transporters in plants with different functions among various species. The evolutionary and functional information of the Nramp gene family in Spirodela polyrhiza has not been previously reported in detail. To identify the Nramp genes in S. polyrhiza, we performed genome-wide identification, characterization, classification, and cis-elements analysis among 22 species with 138 amino acid sequences. We also conducted chromosomal localization and analyzed the synteny relationship, promoter, subcellular localization, and expression patterns in S. polyrhiza. ß-Glucuronidase staining indicated that SpNramp1 and SpNramp3 mainly accumulated in the root and joint between mother and daughter frond. Moreover, SpNramp1 was also widely displayed in the frond. SpNramp2 was intensively distributed in the root and frond. Quantitative real-time PCR results proved that the SpNramp gene expression level was influenced by Cd stress, especially in response to Fe or Mn deficiency. The study provides detailed information on the SpNramp gene family and their distribution and expression, laying a beneficial foundation for functional research.


Assuntos
Araceae/genética , Cádmio/toxicidade , Proteínas de Transporte de Cátions/genética , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Família Multigênica , Proteínas de Plantas/genética , Estresse Fisiológico/genética , Motivos de Aminoácidos , Sequência de Aminoácidos , Araceae/efeitos dos fármacos , Proteínas de Transporte de Cátions/química , Proteínas de Transporte de Cátions/metabolismo , Cromossomos de Plantas/genética , Sequência Conservada , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Genes de Plantas , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Regiões Promotoras Genéticas/genética , Estresse Fisiológico/efeitos dos fármacos , Sintenia/genética
10.
Methods Mol Biol ; 2328: 47-65, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34251619

RESUMO

Gene expression data analysis and the prediction of causal relationships within gene regulatory networks (GRNs) have guided the identification of key regulatory factors and unraveled the dynamic properties of biological systems. However, drawing accurate and unbiased conclusions requires a comprehensive understanding of relevant tools, computational methods, and their workflows. The topics covered in this chapter encompass the entire workflow for GRN inference including: (1) experimental design; (2) RNA sequencing data processing; (3) differentially expressed gene (DEG) selection; (4) clustering prior to inference; (5) network inference techniques; and (6) network visualization and analysis. Moreover, this chapter aims to present a workflow feasible and accessible for plant biologists without a bioinformatics or computer science background. To address this need, TuxNet, a user-friendly graphical user interface that integrates RNA sequencing data analysis with GRN inference, is chosen for the purpose of providing a detailed tutorial.


Assuntos
Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica/genética , Redes Reguladoras de Genes/genética , Algoritmos , Motivos de Aminoácidos/genética , Análise por Conglomerados , Família Multigênica , RNA-Seq/métodos , Software , Análise Espaço-Temporal , Fluxo de Trabalho
11.
Methods Mol Biol ; 2328: 171-182, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34251625

RESUMO

With the advent of recent next-generation sequencing (NGS) technologies in genomics, transcriptomics, and epigenomics, profiling single-cell sequencing became possible. The single-cell RNA sequencing (scRNA-seq) is widely used to characterize diverse cell populations and ascertain cell type-specific regulatory mechanisms. The gene regulatory network (GRN) mainly consists of genes and their regulators-transcription factors (TF). Here, we describe the lightning-fast Python implementation of the SCENIC (Single-Cell reEgulatory Network Inference and Clustering) pipeline called pySCENIC. Using single-cell RNA-seq data, it maps TFs onto gene regulatory networks and integrates various cell types to infer cell-specific GRNs. There are two fast and efficient GRN inference algorithms, GRNBoost2 and GENIE3, optionally available with pySCENIC. The pipeline has three steps: (1) identification of potential TF targets based on co-expression; (2) TF-motif enrichment analysis to identify the direct targets (regulons); and (3) scoring the activity of regulons (or other gene sets) on single cell types.


Assuntos
Redes Reguladoras de Genes/genética , RNA-Seq/métodos , Análise de Célula Única/métodos , Fatores de Transcrição/metabolismo , Algoritmos , Motivos de Aminoácidos/genética , Análise por Conglomerados , Linguagens de Programação , Fatores de Transcrição/genética
12.
Int J Mol Sci ; 22(12)2021 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-34200573

RESUMO

In recent years, cyclic guanosine 3',5'-cyclic monophosphate (cGMP) and guanylyl cyclases (GCs), which catalyze the formation of cGMP, were implicated in a growing number of plant processes, including plant growth and development and the responses to various stresses. To identify novel GCs in plants, an amino acid sequence of a catalytic motif with a conserved core was designed through bioinformatic analysis. In this report, we describe the performed analyses and consider the changes caused by the introduced modification within the GC catalytic motif, which eventually led to the description of a plasma membrane receptor of peptide signaling molecules-BdPepR2 in Brachypodium distachyon. Both in vitro GC activity studies and structural and docking analyses demonstrated that the protein could act as a GC and contains a highly conserved 14-aa GC catalytic center. However, we observed that in the case of BdPepR2, this catalytic center is altered where a methionine instead of the conserved lysine or arginine residues at position 14 of the motif, conferring higher catalytic activity than arginine and alanine, as confirmed through mutagenesis studies. This leads us to propose the expansion of the GC motif to cater for the identification of GCs in monocots. Additionally, we show that BdPepR2 also has in vitro kinase activity, which is modulated by cGMP.


Assuntos
Brachypodium/enzimologia , GMP Cíclico/metabolismo , Guanilato Ciclase/metabolismo , Mutação , Proteínas de Plantas/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Domínio Catalítico , Guanilato Ciclase/química , Guanilato Ciclase/genética , Técnicas In Vitro , Mutagênese Sítio-Dirigida , Fosforilação , Proteínas de Plantas/química , Proteínas de Plantas/genética , Ligação Proteica , Conformação Proteica , Homologia de Sequência , Transdução de Sinais
13.
J Gen Virol ; 102(7)2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34292864

RESUMO

Hepatitis B virus surface antigen (HBsAg) encoded by the S gene is highly expressed during the replication cycle of hepatitis B virus (HBV). However, the frequent usage of tryptophan in HBsAg, which leads to a high cost of biosynthesis, is inconsistent with the high expression level of this protein. Tryptophan-truncated mutation of HBsAg, that is, a tryptophan to stop codon mutation resulting in truncated HBsAg, might help to maintain its high expression with lower biosynthetic cost. We aimed to investigate the prevalence of tryptophan-truncated S quasispecies in treatment-naïve patients with chronic hepatitis B (CHB) by applying CirSeq as well as a site-by-site algorithm developed by us to identify variants at extremely low frequencies in the carboxyl terminus of HBsAg. A total of 730 mutations were identified in 27 patients with CHB, varying from seven to 56 mutations per sample. The number of synonymous mutations was much higher than that of nonsynonymous mutations in the reverse transcriptase (RT) coding region and vice versa in the S coding region, implying that the evolutionary constraints on the RT and S genes might be different. We showed that 25 (92.6 %) of 27 patients had at least one S-truncated mutation, most of which were derived from tryptophan, indicating a high prevalence of tryptophan-truncated S mutations in treatment-naïve patients with CHB. In terms of the RT gene, 21 (77.8 %) patients had pre-existing drug-resistant mutations, while no truncated mutations were detected. Our findings that tryptophan-truncated S quasispecies and drug-resistant RT mutants were highly prevalent in treatment-naïve patients with CHB provide new insights into the composition of the HBV population, which might help optimize the treatment and management of patients with CHB.


Assuntos
Antígenos de Superfície da Hepatite B/genética , Vírus da Hepatite B/genética , Hepatite B Crônica/virologia , Mutação , Triptofano/genética , Adolescente , Adulto , Algoritmos , Motivos de Aminoácidos , Antivirais/farmacologia , Antivirais/uso terapêutico , Códon , Farmacorresistência Viral , Evolução Molecular , Feminino , Genes Virais , Antígenos de Superfície da Hepatite B/química , Vírus da Hepatite B/química , Vírus da Hepatite B/efeitos dos fármacos , Hepatite B Crônica/tratamento farmacológico , Humanos , Masculino , Pessoa de Meia-Idade , Quase-Espécies , DNA Polimerase Dirigida por RNA/genética , Análise de Sequência de DNA , Adulto Jovem
14.
Nat Commun ; 12(1): 4466, 2021 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-34294725

RESUMO

Macrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are known to interrupt translation at specific sequence motifs, with ketolides predominantly stalling at Arg/Lys-X-Arg/Lys motifs and macrolides displaying a broader specificity, a structural basis for their context-specific action has been lacking. Here, we present structures of ribosomes arrested during the synthesis of an Arg-Leu-Arg sequence by the macrolide erythromycin (ERY) and the ketolide telithromycin (TEL). Together with deep mutagenesis and molecular dynamics simulations, the structures reveal how ERY and TEL interplay with the Arg-Leu-Arg motif to induce translational arrest and illuminate the basis for the less stringent sequence-specific action of ERY over TEL. Because programmed stalling at the Arg/Lys-X-Arg/Lys motifs is used to activate expression of antibiotic resistance genes, our study also provides important insights for future development of improved macrolide antibiotics.


Assuntos
Antibacterianos/farmacologia , Cetolídeos/farmacologia , Macrolídeos/farmacologia , Inibidores da Síntese de Proteínas/farmacologia , Motivos de Aminoácidos , Sequência de Aminoácidos , Antibacterianos/química , Bacillus subtilis/efeitos dos fármacos , Bacillus subtilis/enzimologia , Bacillus subtilis/genética , Sítios de Ligação/genética , Microscopia Crioeletrônica , Resistência Microbiana a Medicamentos/genética , Eritromicina/química , Eritromicina/farmacologia , Genes Bacterianos , Cetolídeos/química , Cetolídeos/farmacocinética , Macrolídeos/química , Metiltransferases/química , Metiltransferases/genética , Metiltransferases/metabolismo , Simulação de Dinâmica Molecular , Mutagênese Insercional , Biossíntese de Proteínas/efeitos dos fármacos , Inibidores da Síntese de Proteínas/química , Ribossomos/efeitos dos fármacos
15.
Nat Commun ; 12(1): 4536, 2021 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-34315872

RESUMO

Despite the substantial impact of post-translational modifications on programmed cell death 1 ligand 1 (PD-L1), its importance in therapeutic resistance in pancreatic cancer remains poorly defined. Here, we demonstrate that never in mitosis gene A-related kinase 2 (NEK2) phosphorylates PD-L1 to maintain its stability, causing PD-L1-targeted pancreatic cancer immunotherapy to have poor efficacy. We identify NEK2 as a prognostic factor in immunologically "hot" pancreatic cancer, involved in the onset and development of pancreatic tumors in an immune-dependent manner. NEK2 deficiency results in the suppression of PD-L1 expression and enhancement of lymphocyte infiltration. A NEK binding motif (F/LXXS/T) is identified in the glycosylation-rich region of PD-L1. NEK2 interacts with PD-L1, phosphorylating the T194/T210 residues and preventing ubiquitin-proteasome pathway-mediated degradation of PD-L1 in ER lumen. NEK2 inhibition thereby sensitizes PD-L1 blockade, synergically enhancing the anti-pancreatic cancer immune response. Together, the present study proposes a promising strategy for improving the effectiveness of pancreatic cancer immunotherapy.


Assuntos
Antígeno B7-H1/metabolismo , Imunidade , Quinases Relacionadas a NIMA/antagonistas & inibidores , Neoplasias Pancreáticas/imunologia , Adenocarcinoma/genética , Adenocarcinoma/imunologia , Adenocarcinoma/patologia , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Carcinoma Ductal Pancreático/genética , Carcinoma Ductal Pancreático/imunologia , Carcinoma Ductal Pancreático/patologia , Linhagem Celular Tumoral , Feminino , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Humanos , Masculino , Camundongos Nus , Pessoa de Meia-Idade , Modelos Biológicos , Quinases Relacionadas a NIMA/deficiência , Quinases Relacionadas a NIMA/genética , Quinases Relacionadas a NIMA/metabolismo , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/patologia , Fosforilação , Fosfosserina/metabolismo , Prognóstico , Complexo de Endopeptidases do Proteassoma/metabolismo , Ligação Proteica , Estabilidade Proteica , Proteólise , Ubiquitinação
16.
Nat Commun ; 12(1): 4349, 2021 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-34272394

RESUMO

Bacterial extracellular polysaccharides (EPSs) play critical roles in virulence. Many bacteria assemble EPSs via a multi-protein "Wzx-Wzy" system, involving glycan polymerization at the outer face of the cytoplasmic/inner membrane. Gram-negative species couple polymerization with translocation across the periplasm and outer membrane and the master regulator of the system is the tyrosine autokinase, Wzc. This near atomic cryo-EM structure of dephosphorylated Wzc from E. coli shows an octameric assembly with a large central cavity formed by transmembrane helices. The tyrosine autokinase domain forms the cytoplasm region, while the periplasmic region contains small folded motifs and helical bundles. The helical bundles are essential for function, most likely through interaction with the outer membrane translocon, Wza. Autophosphorylation of the tyrosine-rich C-terminus of Wzc results in disassembly of the octamer into multiply phosphorylated monomers. We propose that the cycling between phosphorylated monomer and dephosphorylated octamer regulates glycan polymerization and translocation.


Assuntos
Cápsulas Bacterianas/química , Cápsulas Bacterianas/metabolismo , Proteínas de Escherichia coli/química , Escherichia coli/metabolismo , Proteínas de Membrana/química , Periplasma/metabolismo , Polissacarídeos Bacterianos/metabolismo , Proteínas Tirosina Quinases/química , Motivos de Aminoácidos , Domínio Catalítico , Microscopia Crioeletrônica , Citoplasma/metabolismo , Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Espectrometria de Massas , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Modelos Moleculares , Periplasma/química , Fosforilação , Conformação Proteica em alfa-Hélice , Proteínas Tirosina Quinases/genética , Proteínas Tirosina Quinases/metabolismo , Tirosina/química , Tirosina/metabolismo
17.
BMC Plant Biol ; 21(1): 333, 2021 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-34256694

RESUMO

BACKGROUND: Canavalia rosea (Sw.) DC. (bay bean) is an extremophile halophyte that is widely distributed in coastal areas of the tropics and subtropics. Seawater and drought tolerance in this species may be facilitated by aquaporins (AQPs), channel proteins that transport water and small molecules across cell membranes and thereby maintain cellular water homeostasis in the face of abiotic stress. In C. rosea, AQP diversity, protein features, and their biological functions are still largely unknown. RESULTS: We describe the action of AQPs in C. rosea using evolutionary analyses coupled with promoter and expression analyses. A total of 37 AQPs were identified in the C. rosea genome and classified into five subgroups: 11 plasma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, 11 Nod26-like intrinsic proteins, 4 small and basic intrinsic proteins, and 1 X-intrinsic protein. Analysis of RNA-Seq data and targeted qPCR revealed organ-specific expression of aquaporin genes and the involvement of some AQP members in adaptation of C. rosea to extreme coral reef environments. We also analyzed C. rosea sequences for phylogeny reconstruction, protein modeling, cellular localizations, and promoter analysis. Furthermore, one of PIP1 gene, CrPIP1;5, was identified as functional using a yeast expression system and transgenic overexpression in Arabidopsis. CONCLUSIONS: Our results indicate that AQPs play an important role in C. rosea responses to saline-alkaline soils and drought stress. These findings not only increase our understanding of the role AQPs play in mediating C. rosea adaptation to extreme environments, but also improve our knowledge of plant aquaporin evolution more generally.


Assuntos
Aquaporinas/genética , Canavalia/genética , Secas , Solo/química , Adaptação Fisiológica , Motivos de Aminoácidos , Aquaporinas/fisiologia , Evolução Biológica , Canavalia/fisiologia , Mapeamento Cromossômico , Cromossomos de Plantas , Ecossistema , Genoma de Planta , Família Multigênica , Proteínas de Plantas/genética , Regiões Promotoras Genéticas , RNA-Seq , Estresse Fisiológico , Transcriptoma
18.
Viruses ; 13(7)2021 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-34202565

RESUMO

Arenaviruses and coronaviruses include several human pathogenic viruses, such as Lassa virus, Lymphocytic choriomeningitis virus (LCMV), SARS-CoV, MERS-CoV, and SARS-CoV-2. Although these viruses belong to different virus families, they possess a common motif, the DED/EDh motif, known as an exonuclease (ExoN) motif. In this study, proof-of-concept studies, in which the DED/EDh motif in these viral proteins, NP for arenaviruses, and nsp14 for coronaviruses, could be a drug target, were performed. Docking simulation studies between two structurally different chemical compounds, ATA and PV6R, and the DED/EDh motifs in these viral proteins indicated that these compounds target DED/EDh motifs. The concentration which exhibited modest cell toxicity was used with these compounds to treat LCMV and SARS-CoV-2 infections in two different cell lines, A549 and Vero 76 cells. Both ATA and PV6R inhibited the post-entry step of LCMV and SARS-CoV-2 infection. These studies strongly suggest that DED/EDh motifs in these viral proteins could be a drug target to combat two distinct viral families, arenaviruses and coronaviruses.


Assuntos
Antivirais/farmacologia , Exorribonucleases/antagonistas & inibidores , Vírus da Coriomeningite Linfocítica/efeitos dos fármacos , SARS-CoV-2/efeitos dos fármacos , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas Virais/antagonistas & inibidores , Replicação Viral/efeitos dos fármacos , Células A549 , Motivos de Aminoácidos , Animais , Chlorocebus aethiops , Descoberta de Drogas , Humanos , Simulação de Acoplamento Molecular , Células Vero
19.
Nat Microbiol ; 6(8): 1094-1101, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34163035

RESUMO

Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the reported cases. Phylogenetic analyses of these sequences revealed the emergence of lineage A.23.1 from lineage A.23. Lineage A.23.1 represented 88% of the genomes observed in December 2020, then 100% of the genomes observed in January 2021. The A.23.1 lineage was also reported in 26 other countries. Although the precise changes in A.23.1 differ from those reported in the first three SARS-CoV-2 variants of concern (VOCs), the A.23.1 spike-protein-coding region has changes similar to VOCs including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1 lineage has changes in non-spike proteins including nsp6, ORF8 and ORF9 that are also altered in other VOCs. The clinical impact of the A.23.1 variant is not yet clear and it has not been designated as a VOC. However, our findings of emergence and spread of this variant indicate that careful monitoring of this variant, together with assessment of the consequences of the spike protein changes for COVID-19 vaccine performance, are advisable.


Assuntos
COVID-19/epidemiologia , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/genética , Motivos de Aminoácidos , Proteínas do Nucleocapsídeo de Coronavírus/genética , Variação Genética/genética , Genoma Viral/genética , Humanos , Fosfoproteínas/genética , Filogenia , Uganda/epidemiologia , Proteínas Virais/genética
20.
Methods Mol Biol ; 2323: 221-232, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34086284

RESUMO

RNA-protein (RNP) complexes are promising biomaterials for the fields of nanotechnology and synthetic biology. Protein-responsive RNA sequences (RNP motifs) can be integrated into various RNAs, such as messenger RNA, short-hairpin RNA, and synthetic RNA nanoobjects for a variety of purposes. Direct observation of RNP interaction in solution at high resolution is important in the design and construction of RNP-mediated nanostructures. Here we describe a method to construct and visualize RNP nanostructures that precisely arrange a target protein on the RNA scaffold with nanometer scale. High-speed AFM (HS-AFM) images of RNP nanostructures show that the folding of RNP complexes of defined sizes can be directly visualized at single RNP resolution in solution.


Assuntos
Microscopia de Força Atômica/métodos , Nanoestruturas/química , Ribonucleoproteínas/química , Motivos de Aminoácidos , Ensaio de Desvio de Mobilidade Eletroforética/métodos , Motivos de Nucleotídeos , Dobramento de Proteína
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