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1.
Cell ; 186(12): 2656-2671.e18, 2023 06 08.
Artigo em Inglês | MEDLINE | ID: mdl-37295403

RESUMO

Plant roots encounter numerous pathogenic microbes that often cause devastating diseases. One such pathogen, Plasmodiophora brassicae (Pb), causes clubroot disease and severe yield losses on cruciferous crops worldwide. Here, we report the isolation and characterization of WeiTsing (WTS), a broad-spectrum clubroot resistance gene from Arabidopsis. WTS is transcriptionally activated in the pericycle upon Pb infection to prevent pathogen colonization in the stele. Brassica napus carrying the WTS transgene displayed strong resistance to Pb. WTS encodes a small protein localized in the endoplasmic reticulum (ER), and its expression in plants induces immune responses. The cryoelectron microscopy (cryo-EM) structure of WTS revealed a previously unknown pentameric architecture with a central pore. Electrophysiology analyses demonstrated that WTS is a calcium-permeable cation-selective channel. Structure-guided mutagenesis indicated that channel activity is strictly required for triggering defenses. The findings uncover an ion channel analogous to resistosomes that triggers immune signaling in the pericycle.


Assuntos
Brassica napus , Plasmodioforídeos , Microscopia Crioeletrônica , Chumbo , Brassica napus/genética , Plasmodioforídeos/fisiologia , Canais Iônicos , Doenças das Plantas
2.
Cell ; 185(16): 2961-2974.e19, 2022 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-35839760

RESUMO

Wheat crops are frequently devastated by pandemic stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). Here, we identify and characterize a wheat receptor-like cytoplasmic kinase gene, TaPsIPK1, that confers susceptibility to this pathogen. PsSpg1, a secreted fungal effector vital for Pst virulence, can bind TaPsIPK1, enhance its kinase activity, and promote its nuclear localization, where it phosphorylates the transcription factor TaCBF1d for gene regulation. The phosphorylation of TaCBF1d switches its transcriptional activity on the downstream genes. CRISPR-Cas9 inactivation of TaPsIPK1 in wheat confers broad-spectrum resistance against Pst without impacting important agronomic traits in two years of field tests. The disruption of TaPsIPK1 leads to immune priming without constitutive activation of defense responses. Taken together, TaPsIPK1 is a susceptibility gene known to be targeted by rust effectors, and it has great potential for developing durable resistance against rust by genetic modifications.


Assuntos
Basidiomycota , Triticum , Basidiomycota/genética , Basidiomycota/metabolismo , Doenças das Plantas , Proteínas Quinases/genética , Proteínas Quinases/metabolismo , Triticum/genética , Triticum/metabolismo , Triticum/microbiologia , Virulência/genética
3.
Cell ; 184(13): 3528-3541.e12, 2021 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-33984278

RESUMO

Nucleotide-binding, leucine-rich repeat receptors (NLRs) are major immune receptors in plants and animals. Upon activation, the Arabidopsis NLR protein ZAR1 forms a pentameric resistosome in vitro and triggers immune responses and cell death in plants. In this study, we employed single-molecule imaging to show that the activated ZAR1 protein can form pentameric complexes in the plasma membrane. The ZAR1 resistosome displayed ion channel activity in Xenopus oocytes in a manner dependent on a conserved acidic residue Glu11 situated in the channel pore. Pre-assembled ZAR1 resistosome was readily incorporated into planar lipid-bilayers and displayed calcium-permeable cation-selective channel activity. Furthermore, we show that activation of ZAR1 in the plant cell led to Glu11-dependent Ca2+ influx, perturbation of subcellular structures, production of reactive oxygen species, and cell death. The results thus support that the ZAR1 resistosome acts as a calcium-permeable cation channel to trigger immunity and cell death.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/imunologia , Arabidopsis/metabolismo , Cálcio/metabolismo , Proteínas de Transporte/metabolismo , Resistência à Doença/imunologia , Imunidade Vegetal , Transdução de Sinais , Animais , Morte Celular , Membrana Celular/metabolismo , Permeabilidade da Membrana Celular , Ácido Glutâmico/metabolismo , Bicamadas Lipídicas/metabolismo , Oócitos/metabolismo , Células Vegetais/metabolismo , Multimerização Proteica , Protoplastos/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Imagem Individual de Molécula , Vacúolos/metabolismo , Xenopus
4.
Cell ; 181(5): 978-989, 2020 05 28.
Artigo em Inglês | MEDLINE | ID: mdl-32442407

RESUMO

Plants employ numerous cell-surface and intracellular immune receptors to perceive a variety of immunogenic signals associated with pathogen infection and subsequently activate defenses. Immune signaling is potentiated by the major defense hormone salicylic acid (SA), which reprograms the transcriptome for defense. Here we highlight recent advances in understanding the mechanisms underlying activation of the main classes of immune receptors, summarize the current understanding of their signaling mechanisms, and discuss an updated model for SA perception and signaling. In addition, we discuss how different receptors are organized into networks and the implications of such networks in the integration of complex danger signals for appropriate defense outputs.


Assuntos
Imunidade Vegetal/genética , Imunidade Vegetal/imunologia , Imunidade Vegetal/fisiologia , Regulação da Expressão Gênica de Plantas/genética , Doenças das Plantas/imunologia , Reguladores de Crescimento de Plantas/genética , Reguladores de Crescimento de Plantas/metabolismo , Proteínas de Plantas/metabolismo , Transdução de Sinais/genética
5.
Am J Hum Genet ; 111(3): 456-472, 2024 Mar 07.
Artigo em Inglês | MEDLINE | ID: mdl-38367619

RESUMO

The impact of tobacco exposure on health varies by race and ethnicity and is closely tied to internal nicotine dose, a marker of carcinogen uptake. DNA methylation is strongly responsive to smoking status and may mediate health effects, but study of associations with internal dose is limited. We performed a blood leukocyte epigenome-wide association study (EWAS) of urinary total nicotine equivalents (TNEs; a measure of nicotine uptake) and DNA methylation measured using the MethylationEPIC v1.0 BeadChip (EPIC) in six racial and ethnic groups across three cohort studies. In the Multiethnic Cohort Study (discovery, n = 1994), TNEs were associated with differential methylation at 408 CpG sites across >250 genomic regions (p < 9 × 10-8). The top significant sites were annotated to AHRR, F2RL3, RARA, GPR15, PRSS23, and 2q37.1, all of which had decreasing methylation with increasing TNEs. We identified 45 novel CpG sites, of which 42 were unique to the EPIC array and eight annotated to genes not previously linked with smoking-related DNA methylation. The most significant signal in a novel gene was cg03748458 in MIR383;SGCZ. Fifty-one of the 408 discovery sites were validated in the Singapore Chinese Health Study (n = 340) and the Southern Community Cohort Study (n = 394) (Bonferroni corrected p < 1.23 × 10-4). Significant heterogeneity by race and ethnicity was detected for CpG sites in MYO1G and CYTH1. Furthermore, TNEs significantly mediated the association between cigarettes per day and DNA methylation at 15 sites (average 22.5%-44.3% proportion mediated). Our multiethnic study highlights the transethnic and ethnic-specific methylation associations with internal nicotine dose, a strong predictor of smoking-related morbidities.


Assuntos
MicroRNAs , Fumantes , Humanos , Nicotina , Epigênese Genética/genética , Epigenoma , Estudos de Coortes , Estudos Prospectivos , Estudo de Associação Genômica Ampla , Metilação de DNA/genética , Ilhas de CpG/genética , Receptores de Peptídeos/genética , Receptores Acoplados a Proteínas G/genética
6.
Nat Methods ; 2024 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-38907114

RESUMO

Advances in spatial omics technologies now allow multiple types of data to be acquired from the same tissue slice. To realize the full potential of such data, we need spatially informed methods for data integration. Here, we introduce SpatialGlue, a graph neural network model with a dual-attention mechanism that deciphers spatial domains by intra-omics integration of spatial location and omics measurement followed by cross-omics integration. We demonstrated SpatialGlue on data acquired from different tissue types using different technologies, including spatial epigenome-transcriptome and transcriptome-proteome modalities. Compared to other methods, SpatialGlue captured more anatomical details and more accurately resolved spatial domains such as the cortex layers of the brain. Our method also identified cell types like spleen macrophage subsets located at three different zones that were not available in the original data annotations. SpatialGlue scales well with data size and can be used to integrate three modalities. Our spatial multi-omics analysis tool combines the information from complementary omics modalities to obtain a holistic view of cellular and tissue properties.

7.
Cell ; 148(5): 873-85, 2012 Mar 02.
Artigo em Inglês | MEDLINE | ID: mdl-22385957

RESUMO

Tumor heterogeneity presents a challenge for inferring clonal evolution and driver gene identification. Here, we describe a method for analyzing the cancer genome at a single-cell nucleotide level. To perform our analyses, we first devised and validated a high-throughput whole-genome single-cell sequencing method using two lymphoblastoid cell line single cells. We then carried out whole-exome single-cell sequencing of 90 cells from a JAK2-negative myeloproliferative neoplasm patient. The sequencing data from 58 cells passed our quality control criteria, and these data indicated that this neoplasm represented a monoclonal evolution. We further identified essential thrombocythemia (ET)-related candidate mutations such as SESN2 and NTRK1, which may be involved in neoplasm progression. This pilot study allowed the initial characterization of the disease-related genetic architecture at the single-cell nucleotide level. Further, we established a single-cell sequencing method that opens the way for detailed analyses of a variety of tumor types, including those with high genetic complex between patients.


Assuntos
Evolução Clonal , Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Janus Quinase 2/genética , Transtornos Mieloproliferativos/genética , Transtornos Mieloproliferativos/patologia , Análise de Célula Única/métodos , Trombocitemia Essencial/genética , Exoma , Genoma Humano , Humanos , Masculino , Pessoa de Meia-Idade , Mutação
8.
Nature ; 592(7852): 105-109, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33692546

RESUMO

The plant immune system is fundamental for plant survival in natural ecosystems and for productivity in crop fields. Substantial evidence supports the prevailing notion that plants possess a two-tiered innate immune system, called pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI is triggered by microbial patterns via cell surface-localized pattern-recognition receptors (PRRs), whereas ETI is activated by pathogen effector proteins via predominantly intracellularly localized receptors called nucleotide-binding, leucine-rich repeat receptors (NLRs)1-4. PTI and ETI are initiated by distinct activation mechanisms and involve different early signalling cascades5,6. Here we show that Arabidopsis PRR and PRR co-receptor mutants-fls2 efr cerk1 and bak1 bkk1 cerk1 triple mutants-are markedly impaired in ETI responses when challenged with incompatible Pseudomonas syrinage bacteria. We further show that the production of reactive oxygen species by the NADPH oxidase RBOHD is a critical early signalling event connecting PRR- and NLR-mediated immunity, and that the receptor-like cytoplasmic kinase BIK1 is necessary for full activation of RBOHD, gene expression and bacterial resistance during ETI. Moreover, NLR signalling rapidly augments the transcript and/or protein levels of key PTI components. Our study supports a revised model in which potentiation of PTI is an indispensable component of ETI during bacterial infection. This revised model conceptually unites two major immune signalling cascades in plants and mechanistically explains some of the long-observed similarities in downstream defence outputs between PTI and ETI.


Assuntos
Arabidopsis/imunologia , Proteínas NLR/imunologia , Imunidade Vegetal/imunologia , Receptores de Reconhecimento de Padrão/imunologia , Arabidopsis/genética , Arabidopsis/microbiologia , Proteínas de Arabidopsis/metabolismo , NADPH Oxidases/metabolismo , Doenças das Plantas/genética , Doenças das Plantas/imunologia , Doenças das Plantas/microbiologia , Proteínas Serina-Treonina Quinases/metabolismo , Pseudomonas syringae/imunologia , Espécies Reativas de Oxigênio/metabolismo , Transdução de Sinais/imunologia
9.
Nature ; 598(7881): 495-499, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34497423

RESUMO

Plants deploy cell-surface and intracellular leucine rich-repeat domain (LRR) immune receptors to detect pathogens1. LRR receptor kinases and LRR receptor proteins at the plasma membrane recognize microorganism-derived molecules to elicit pattern-triggered immunity (PTI), whereas nucleotide-binding LRR proteins detect microbial effectors inside cells to confer effector-triggered immunity (ETI). Although PTI and ETI are initiated in different host cell compartments, they rely on the transcriptional activation of similar sets of genes2, suggesting pathway convergence upstream of nuclear events. Here we report that PTI triggered by the Arabidopsis LRR receptor protein RLP23 requires signalling-competent dimers of the lipase-like proteins EDS1 and PAD4, and of ADR1 family helper nucleotide-binding LRRs, which are all components of ETI. The cell-surface LRR receptor kinase SOBIR1 links RLP23 with EDS1, PAD4 and ADR1 proteins, suggesting the formation of supramolecular complexes containing PTI receptors and transducers at the inner side of the plasma membrane. We detected similar evolutionary patterns in LRR receptor protein and nucleotide-binding LRR genes across Arabidopsis accessions; overall higher levels of variation in LRR receptor proteins than in LRR receptor kinases are consistent with distinct roles of these two receptor families in plant immunity. We propose that the EDS1-PAD4-ADR1 node is a convergence point for defence signalling cascades, activated by both surface-resident and intracellular LRR receptors, in conferring pathogen immunity.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/imunologia , Hidrolases de Éster Carboxílico/metabolismo , Proteínas de Ligação a DNA/metabolismo , Imunidade Vegetal , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas de Arabidopsis/química , Hidrolases de Éster Carboxílico/química , Proteínas de Ligação a DNA/química , Domínios Proteicos , Proteínas Quinases/química , Proteínas Quinases/metabolismo , Multimerização Proteica , Proteínas Serina-Treonina Quinases/química , Receptores de Superfície Celular/química , Receptores de Superfície Celular/metabolismo
10.
Proc Natl Acad Sci U S A ; 121(25): e2312415121, 2024 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-38875149

RESUMO

Plants rely on immune receptor complexes at the cell surface to perceive microbial molecules and transduce these signals into the cell to regulate immunity. Various immune receptors and associated proteins are often dynamically distributed in specific nanodomains on the plasma membrane (PM). However, the exact molecular mechanism and functional relevance of this nanodomain targeting in plant immunity regulation remain largely unknown. By utilizing high spatiotemporal resolution imaging and single-particle tracking analysis, we show that myosin XIK interacts with remorin to recruit and stabilize PM-associated kinase BOTRYTIS-INDUCED KINASE 1 (BIK1) within immune receptor FLAGELLIN SENSING 2 (FLS2)-containing nanodomains. This recruitment facilitates FLS2/BIK1 complex formation, leading to the full activation of BIK1-dependent defense responses upon ligand perception. Collectively, our findings provide compelling evidence that myosin XI functions as a molecular scaffold to enable a spatially confined complex assembly within nanodomains. This ensures the presence of a sufficient quantity of preformed immune receptor complex for efficient signaling transduction from the cell surface.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Imunidade Inata , Miosinas , Imunidade Vegetal , Proteínas Serina-Treonina Quinases , Arabidopsis/imunologia , Arabidopsis/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Membrana Celular/metabolismo , Miosinas/metabolismo , Doenças das Plantas/imunologia , Doenças das Plantas/microbiologia , Proteínas Quinases/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Transdução de Sinais
11.
EMBO J ; 41(23): e107257, 2022 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-36314733

RESUMO

Plant immunity is tightly controlled by a complex and dynamic regulatory network, which ensures optimal activation upon detection of potential pathogens. Accordingly, each component of this network is a potential target for manipulation by pathogens. Here, we report that RipAC, a type III-secreted effector from the bacterial pathogen Ralstonia solanacearum, targets the plant E3 ubiquitin ligase PUB4 to inhibit pattern-triggered immunity (PTI). PUB4 plays a positive role in PTI by regulating the homeostasis of the central immune kinase BIK1. Before PAMP perception, PUB4 promotes the degradation of non-activated BIK1, while after PAMP perception, PUB4 contributes to the accumulation of activated BIK1. RipAC leads to BIK1 degradation, which correlates with its PTI-inhibitory activity. RipAC causes a reduction in pathogen-associated molecular pattern (PAMP)-induced PUB4 accumulation and phosphorylation. Our results shed light on the role played by PUB4 in immune regulation, and illustrate an indirect targeting of the immune signalling hub BIK1 by a bacterial effector.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Ubiquitina-Proteína Ligases/genética , Ubiquitina-Proteína Ligases/metabolismo , Moléculas com Motivos Associados a Patógenos/metabolismo , Imunidade Vegetal/genética , Doenças das Plantas , Proteínas Serina-Treonina Quinases/genética
12.
Plant Cell ; 35(6): 2413-2428, 2023 05 29.
Artigo em Inglês | MEDLINE | ID: mdl-36943771

RESUMO

Activation of mitogen-activated protein kinase (MAP kinase) cascades is essential for plant immunity. Upon activation by surface-localized immune receptors, receptor-like cytoplasmic kinases (RLCKs) in the cytoplasm phosphorylate MAP kinase kinase kinases (MAPKKKs) to initiate MAP kinase activation. Surprisingly, we found that both the phosphorylation of Arabidopsis (Arabidopsis thaliana) MAPKKKs and the subsequent activation of MAP kinase cascades require the λ and κ isoforms of 14-3-3 proteins, which directly interact with multiple RLCKs and MAPKKKs. The N- and C-termini of MAPKKK5 interact intramolecularly to inhibit the access to the C terminus by RLCKs, whereas the 14-3-3 proteins relieve this inhibition and facilitate the interaction of RLCKs with the C-terminus of MAPKKK5. This enables the phosphorylation of MAPKK5 at Ser599 and Ser682, thus promoting MAP kinase activation and enhancing plant disease resistance. Our study reveals a role of 14-3-3 proteins as scaffolds and activators in the regulation of the RLCK-MAPKKK5 module and provides insight into the mechanism of plant immune signaling.


Assuntos
Arabidopsis , Proteínas Quinases Ativadas por Mitógeno , Proteínas Quinases Ativadas por Mitógeno/genética , Proteínas Quinases Ativadas por Mitógeno/metabolismo , Proteínas 14-3-3/genética , Proteínas 14-3-3/metabolismo , Sistema de Sinalização das MAP Quinases , MAP Quinase Quinase Quinase 5/metabolismo , Fosforilação , Arabidopsis/metabolismo , Plantas/metabolismo
13.
Mol Cell ; 69(3): 493-504.e6, 2018 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-29358080

RESUMO

Plant pattern recognition receptors (PRRs) perceive microbial and endogenous molecular patterns to activate immune signaling. The cytoplasmic kinase BIK1 acts downstream of multiple PRRs as a rate-limiting component, whose phosphorylation and accumulation are central to immune signal propagation. Previous work identified the calcium-dependent protein kinase CPK28 and heterotrimeric G proteins as negative and positive regulators of BIK1 accumulation, respectively. However, mechanisms underlying this regulation remain unknown. Here we show that the plant U-box proteins PUB25 and PUB26 are homologous E3 ligases that mark BIK1 for degradation to negatively regulate immunity. We demonstrate that the heterotrimeric G proteins inhibit PUB25/26 activity to stabilize BIK1, whereas CPK28 specifically phosphorylates conserved residues in PUB25/26 to enhance their activity and promote BIK1 degradation. Interestingly, PUB25/26 specifically target non-activated BIK1, suggesting that activated BIK1 is maintained for immune signaling. Our findings reveal a multi-protein regulatory module that enables robust yet tightly regulated immune responses.


Assuntos
Proteínas de Arabidopsis/metabolismo , Proteínas Quinases/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Ubiquitina-Proteína Ligases/metabolismo , Arabidopsis/metabolismo , Citoplasma , Citosol , Regulação da Expressão Gênica de Plantas/genética , Homeostase , Fosforilação , Imunidade Vegetal/fisiologia , Proteínas de Plantas , Transdução de Sinais , Fatores de Transcrição
14.
Hepatology ; 80(1): 87-101, 2024 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-38381705

RESUMO

BACKGROUND AND AIMS: Despite the substantial impact of environmental factors, individuals with a family history of liver cancer have an increased risk for HCC. However, genetic factors have not been studied systematically by genome-wide approaches in large numbers of individuals from European descent populations (EDP). APPROACH AND RESULTS: We conducted a 2-stage genome-wide association study (GWAS) on HCC not affected by HBV infections. A total of 1872 HCC cases and 2907 controls were included in the discovery stage, and 1200 HCC cases and 1832 controls in the validation. We analyzed the discovery and validation samples separately and then conducted a meta-analysis. All analyses were conducted in the presence and absence of HCV. The liability-scale heritability was 24.4% for overall HCC. Five regions with significant ORs (95% CI) were identified for nonviral HCC: 3p22.1, MOBP , rs9842969, (0.51, [0.40-0.65]); 5p15.33, TERT , rs2242652, (0.70, (0.62-0.79]); 19q13.11, TM6SF2 , rs58542926, (1.49, [1.29-1.72]); 19p13.11 MAU2 , rs58489806, (1.53, (1.33-1.75]); and 22q13.31, PNPLA3 , rs738409, (1.66, [1.51-1.83]). One region was identified for HCV-induced HCC: 6p21.31, human leukocyte antigen DQ beta 1, rs9275224, (0.79, [0.74-0.84]). A combination of homozygous variants of PNPLA3 and TERT showing a 6.5-fold higher risk for nonviral-related HCC compared to individuals lacking these genotypes. This observation suggests that gene-gene interactions may identify individuals at elevated risk for developing HCC. CONCLUSIONS: Our GWAS highlights novel genetic susceptibility of nonviral HCC among European descent populations from North America with substantial heritability. Selected genetic influences were observed for HCV-positive HCC. Our findings indicate the importance of genetic susceptibility to HCC development.


Assuntos
Carcinoma Hepatocelular , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Neoplasias Hepáticas , Humanos , Neoplasias Hepáticas/genética , Carcinoma Hepatocelular/genética , Masculino , Feminino , Pessoa de Meia-Idade , América do Norte/epidemiologia , Estudos de Casos e Controles , Polimorfismo de Nucleotídeo Único , Idoso , Loci Gênicos , População Branca/genética
15.
Plant Cell ; 34(5): 1600-1620, 2022 04 26.
Artigo em Inglês | MEDLINE | ID: mdl-35166827

RESUMO

The nucleotide-binding, leucine-rich receptor (NLR) protein HOPZ-ACTIVATED RESISTANCE 1 (ZAR1), an immune receptor, interacts with HOPZ-ETI-DEFICIENT 1 (ZED1)-related kinases (ZRKs) and AVRPPHB SUSCEPTIBLE 1-like proteins to form a pentameric resistosome, triggering immune responses. Here, we show that ZAR1 emerged through gene duplication and that ZRKs were derived from the cell surface immune receptors wall-associated protein kinases (WAKs) through the loss of the extracellular domain before the split of eudicots and monocots during the Jurassic period. Many angiosperm ZAR1 orthologs, but not ZAR1 paralogs, are capable of oligomerization in the presence of AtZRKs and triggering cell death, suggesting that the functional ZAR1 resistosome might have originated during the early evolution of angiosperms. Surprisingly, inter-specific pairing of ZAR1 and AtZRKs sometimes results in the formation of a resistosome in the absence of pathogen stimulation, suggesting within-species compatibility between ZAR1 and ZRKs as a result of co-evolution. Numerous concerted losses of ZAR1 and ZRKs occurred in angiosperms, further supporting the ancient co-evolution between ZAR1 and ZRKs. Our findings provide insights into the origin of new plant immune surveillance networks.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Proteínas de Transporte/metabolismo , Proteínas NLR/metabolismo , Fosfotransferases/metabolismo , Imunidade Vegetal/fisiologia
16.
Hum Genomics ; 18(1): 21, 2024 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-38414044

RESUMO

BACKGROUND: Single-nucleotide variants (SNVs) within gene coding sequences can significantly impact pre-mRNA splicing, bearing profound implications for pathogenic mechanisms and precision medicine. In this study, we aim to harness the well-established full-length gene splicing assay (FLGSA) in conjunction with SpliceAI to prospectively interpret the splicing effects of all potential coding SNVs within the four-exon SPINK1 gene, a gene associated with chronic pancreatitis. RESULTS: Our study began with a retrospective analysis of 27 SPINK1 coding SNVs previously assessed using FLGSA, proceeded with a prospective analysis of 35 new FLGSA-tested SPINK1 coding SNVs, followed by data extrapolation, and ended with further validation. In total, we analyzed 67 SPINK1 coding SNVs, which account for 9.3% of the 720 possible coding SNVs. Among these 67 FLGSA-analyzed SNVs, 12 were found to impact splicing. Through detailed comparison of FLGSA results and SpliceAI predictions, we inferred that the remaining 653 untested coding SNVs in the SPINK1 gene are unlikely to significantly affect splicing. Of the 12 splice-altering events, nine produced both normally spliced and aberrantly spliced transcripts, while the remaining three only generated aberrantly spliced transcripts. These splice-impacting SNVs were found solely in exons 1 and 2, notably at the first and/or last coding nucleotides of these exons. Among the 12 splice-altering events, 11 were missense variants (2.17% of 506 potential missense variants), and one was synonymous (0.61% of 164 potential synonymous variants). Notably, adjusting the SpliceAI cut-off to 0.30 instead of the conventional 0.20 would improve specificity without reducing sensitivity. CONCLUSIONS: By integrating FLGSA with SpliceAI, we have determined that less than 2% (1.67%) of all possible coding SNVs in SPINK1 significantly influence splicing outcomes. Our findings emphasize the critical importance of conducting splicing analysis within the broader genomic sequence context of the study gene and highlight the inherent uncertainties associated with intermediate SpliceAI scores (0.20 to 0.80). This study contributes to the field by being the first to prospectively interpret all potential coding SNVs in a disease-associated gene with a high degree of accuracy, representing a meaningful attempt at shifting from retrospective to prospective variant analysis in the era of exome and genome sequencing.


Assuntos
Splicing de RNA , Inibidor da Tripsina Pancreática de Kazal , Humanos , Inibidor da Tripsina Pancreática de Kazal/genética , Estudos Retrospectivos , Splicing de RNA/genética , Éxons/genética , Sequência de Bases , Processamento Alternativo/genética
17.
J Immunol ; 210(6): 699-707, 2023 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-36881905

RESUMO

C-reactive protein (CRP) is a highly conserved pentraxin with pattern recognition receptor-like activities. However, despite being used widely as a clinical marker of inflammation, the in vivo functions of CRP and its roles in health and disease remain largely unestablished. This is, to certain extent, due to the drastically different expression patterns of CRP in mice and rats, raising concerns about whether the functions of CRP are essential and conserved across species and how these model animals should be manipulated to examine the in vivo actions of human CRP. In this review, we discuss recent advances highlighting the essential and conserved functions of CRP across species, and propose that appropriately designed animal models can be used to understand the origin-, conformation-, and localization-dependent actions of human CRP in vivo. The improved model design will contribute to establishing the pathophysiological roles of CRP and facilitate the development of novel CRP-targeting strategies.


Assuntos
Proteína C-Reativa , Inflamação , Humanos , Animais , Camundongos , Ratos , Modelos Animais
18.
Mol Cell Proteomics ; 22(10): 100639, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37657519

RESUMO

Recent advances in methodology have made phosphopeptide analysis a tractable problem for many proteomics researchers. There are now a wide variety of robust and accessible enrichment strategies to generate phosphoproteomes while free or inexpensive software tools for quantitation and site localization have simplified phosphoproteome analysis workflow tremendously. As a research group under the Association for Biomolecular Resource Facilities umbrella, the Proteomics Standards Research Group has worked to develop a multipathway phosphopeptide standard based on a mixture of heavy-labeled phosphopeptides designed to enable researchers to rapidly develop assays. This mixture contains 131 mass spectrometry vetted phosphopeptides specifically chosen to cover as many known biologically interesting phosphosites as possible from seven different signaling networks: AMPK signaling, death and apoptosis signaling, ErbB signaling, insulin/insulin-like growth factor-1 signaling, mTOR signaling, PI3K/AKT signaling, and stress (p38/SAPK/JNK) signaling. Here, we describe a characterization of this mixture spiked into a HeLa tryptic digest stimulated with both epidermal growth factor and insulin-like growth factor-1 to activate the MAPK and PI3K/AKT/mTOR pathways. We further demonstrate a comparison of phosphoproteomic profiling of HeLa performed independently in five labs using this phosphopeptide mixture with data-independent acquisition. Despite different experimental and instrumentation processes, we found that labs could produce reproducible, harmonized datasets by reporting measurements as ratios to the standard, while intensity measurements showed lower consistency between labs even after normalization. Our results suggest that widely available, biologically relevant phosphopeptide standards can act as a quantitative "yardstick" across laboratories and sample preparations enabling experimental designs larger than a single laboratory can perform. Raw data files are publicly available in the MassIVE dataset MSV000090564.


Assuntos
Fosfopeptídeos , Proteínas Proto-Oncogênicas c-akt , Fosforilação , Fosfopeptídeos/metabolismo , Proteínas Proto-Oncogênicas c-akt/metabolismo , Fosfatidilinositol 3-Quinases/metabolismo , Serina-Treonina Quinases TOR/metabolismo , Fosfoproteínas/metabolismo
19.
Nano Lett ; 24(13): 3890-3897, 2024 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-38526426

RESUMO

Chemical reaction kinetics at the nanoscale are intertwined with heterogeneity in structure and composition. However, mapping such heterogeneity in a liquid environment is extremely challenging. Here we integrate graphene liquid cell (GLC) transmission electron microscopy and four-dimensional scanning transmission electron microscopy to image the etching dynamics of gold nanorods in the reaction media. Critical to our experiment is the small liquid thickness in a GLC that allows the collection of high-quality electron diffraction patterns at low dose conditions. Machine learning-based data-mining of the diffraction patterns maps the three-dimensional nanocrystal orientation, groups spatial domains of various species in the GLC, and identifies newly generated nanocrystallites during reaction, offering a comprehensive understanding on the reaction mechanism inside a nanoenvironment. This work opens opportunities in probing the interplay of structural properties such as phase and strain with solution-phase reaction dynamics, which is important for applications in catalysis, energy storage, and self-assembly.

20.
Gut ; 73(7): 1142-1155, 2024 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-38553043

RESUMO

OBJECTIVE: Currently, there is no cure for chronic pancreatitis (CP). Germline loss-of-function variants in SPINK1 (encoding trypsin inhibitor) are common in patients with CP and are associated with acute attacks and progression of the disease. This preclinical study was conducted to explore the potential of adeno-associated virus type 8 (AAV8)-mediated overexpression of human SPINK1 (hSPINK1) for pancreatitis therapy in mice. DESIGN: A capsid-optimised AAV8-mediated hSPINK1 expression vector (AAV8-hSPINK1) to target the pancreas was constructed. Mice were treated with AAV8-hSPINK1 by intraperitoneal injection. Pancreatic transduction efficiency and safety of AAV8-hSPINK1 were dynamically evaluated in infected mice. The effectiveness of AAV8-hSPINK1 on pancreatitis prevention and treatment was studied in three mouse models (caerulein-induced pancreatitis, pancreatic duct ligation and Spink1 c.194+2T>C mouse models). RESULTS: The constructed AAV8-hSPINK1 vector specifically and safely targeted the pancreas, had low organ tropism for the heart, lungs, spleen, liver and kidneys and had a high transduction efficiency (the optimal expression dose was 2×1011 vg/animal). The expression and efficacy of hSPINK1 peaked at 4 weeks after injection and remained at significant level for up to at least 8 weeks. In all three mouse models, a single dose of AAV8-hSPINK1 before disease onset significantly alleviated the severity of pancreatitis, reduced the progression of fibrosis, decreased the levels of apoptosis and autophagy in the pancreas and accelerated the pancreatitis recovery process. CONCLUSION: One-time injection of AAV8-hSPINK1 safely targets the pancreas with high transduction efficiency and effectively ameliorates pancreatitis phenotypes in mice. This approach is promising for the prevention and treatment of CP.


Assuntos
Dependovirus , Modelos Animais de Doenças , Terapia Genética , Vetores Genéticos , Animais , Camundongos , Terapia Genética/métodos , Dependovirus/genética , Inibidor da Tripsina Pancreática de Kazal/genética , Pâncreas/patologia , Pâncreas/metabolismo , Humanos , Pancreatite Crônica/genética , Pancreatite Crônica/terapia , Masculino , Pancreatite/terapia , Pancreatite/prevenção & controle , Pancreatite/genética
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