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1.
Cell ; 159(5): 1056-1069, 2014 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-25416945

RESUMO

Cdc42 is a highly conserved master regulator of cell polarity. Here, we investigated the mechanism by which yeast cells never re-establish polarity at cortical sites (cytokinesis remnants [CRMs]) that have previously supported Cdc42-mediated growth as a paradigm to mechanistically understand how Cdc42-inhibitory polarity cues are established. We revealed a two-step mechanism of loading the Cdc42 antagonist Nba1 into CRMs to mark these compartments as refractory for a second round of Cdc42 activation. Our data indicate that Nba1 together with a cortically tethered adaptor protein confers memory of previous polarization events to translate this spatial legacy into a biochemical signal that ensures the local singularity of Cdc42 activation. "Memory loss" mutants that repeatedly use the same polarity site over multiple generations display nuclear segregation defects and a shorter lifespan. Our work thus established CRMs as negative polarity cues that prevent Cdc42 reactivation to sustain the fitness of replicating cells.


Assuntos
Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/citologia , Saccharomyces cerevisiae/metabolismo , Proteína cdc42 de Saccharomyces cerevisiae de Ligação ao GTP/metabolismo , Divisão Celular Assimétrica , Proteínas de Ciclo Celular/metabolismo , Polaridade Celular , Fatores de Troca do Nucleotídeo Guanina/metabolismo , Proteínas de Membrana/metabolismo
2.
Mol Cell ; 81(11): 2460-2476.e11, 2021 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-33974913

RESUMO

Selective protein degradation by the ubiquitin-proteasome system (UPS) is involved in all cellular processes. However, the substrates and specificity of most UPS components are not well understood. Here we systematically characterized the UPS in Saccharomyces cerevisiae. Using fluorescent timers, we determined how loss of individual UPS components affects yeast proteome turnover, detecting phenotypes for 76% of E2, E3, and deubiquitinating enzymes. We exploit this dataset to gain insights into N-degron pathways, which target proteins carrying N-terminal degradation signals. We implicate Ubr1, an E3 of the Arg/N-degron pathway, in targeting mitochondrial proteins processed by the mitochondrial inner membrane protease. Moreover, we identify Ylr149c/Gid11 as a substrate receptor of the glucose-induced degradation-deficient (GID) complex, an E3 of the Pro/N-degron pathway. Our results suggest that Gid11 recognizes proteins with N-terminal threonines, expanding the specificity of the GID complex. This resource of potential substrates and relationships between UPS components enables exploring functions of selective protein degradation.


Assuntos
Proteínas Mitocondriais/genética , Complexo de Endopeptidases do Proteassoma/metabolismo , Processamento de Proteína Pós-Traducional , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Ubiquitina-Proteína Ligases/genética , Perfilação da Expressão Gênica , Regulação Fúngica da Expressão Gênica , Genes Reporter , Proteínas de Fluorescência Verde/genética , Proteínas de Fluorescência Verde/metabolismo , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Proteínas Mitocondriais/classificação , Proteínas Mitocondriais/metabolismo , Transporte Proteico , Proteólise , Proteômica/métodos , Saccharomyces cerevisiae/enzimologia , Proteínas de Saccharomyces cerevisiae/metabolismo , Treonina/metabolismo , Ubiquitina/genética , Ubiquitina/metabolismo , Ubiquitina-Proteína Ligases/classificação , Ubiquitina-Proteína Ligases/metabolismo , Ubiquitinação , Proteína Vermelha Fluorescente
3.
Mol Cell ; 70(3): 488-501.e5, 2018 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-29727619

RESUMO

Most eukaryotic proteins are N-terminally acetylated. This modification can be recognized as a signal for selective protein degradation (degron) by the N-end rule pathways. However, the prevalence and specificity of such degrons in the proteome are unclear. Here, by systematically examining how protein turnover is affected by N-terminal sequences, we perform a comprehensive survey of degrons in the yeast N-terminome. We find that approximately 26% of nascent protein N termini encode cryptic degrons. These degrons exhibit high hydrophobicity and are frequently recognized by the E3 ubiquitin ligase Doa10, suggesting a role in protein quality control. In contrast, N-terminal acetylation rarely functions as a degron. Surprisingly, we identify two pathways where N-terminal acetylation has the opposite function and blocks protein degradation through the E3 ubiquitin ligase Ubr1. Our analysis highlights the complexity of N-terminal degrons and argues that hydrophobicity, not N-terminal acetylation, is the predominant feature of N-terminal degrons in nascent proteins.


Assuntos
Células Eucarióticas/metabolismo , Proteínas Fúngicas/metabolismo , Acetilação , Sequência de Aminoácidos , Proteólise , Proteoma/metabolismo , Ubiquitina-Proteína Ligases/metabolismo , Leveduras/metabolismo
4.
Proc Natl Acad Sci U S A ; 120(48): e2314043120, 2023 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-37991942

RESUMO

Hydrogen peroxide (H2O2) sensing and signaling involves the reversible oxidation of particular thiols on particular proteins to modulate protein function in a dynamic manner. H2O2 can be generated from various intracellular sources, but their identities and relative contributions are often unknown. To identify endogenous "hotspots" of H2O2 generation on the scale of individual proteins and protein complexes, we generated a yeast library in which the H2O2 sensor HyPer7 was fused to the C-terminus of all protein-coding open reading frames (ORFs). We also generated a control library in which a redox-insensitive mutant of HyPer7 (SypHer7) was fused to all ORFs. Both libraries were screened side-by-side to identify proteins located within H2O2-generating environments. Screening under a variety of different metabolic conditions revealed dynamic changes in H2O2 availability highly specific to individual proteins and protein complexes. These findings suggest that intracellular H2O2 generation is much more localized and functionally differentiated than previously recognized.


Assuntos
Técnicas Biossensoriais , Peróxido de Hidrogênio , Peróxido de Hidrogênio/metabolismo , Proteoma/metabolismo , Proteínas de Fluorescência Verde/metabolismo , Oxirredução
5.
EMBO Rep ; 24(5): e57162, 2023 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-36951170

RESUMO

Throughout the SARS-CoV-2 pandemic, limited diagnostic capacities prevented sentinel testing, demonstrating the need for novel testing infrastructures. Here, we describe the setup of a cost-effective platform that can be employed in a high-throughput manner, which allows surveillance testing as an acute pandemic control and preparedness tool, exemplified by SARS-CoV-2 diagnostics in an academic environment. The strategy involves self-sampling based on gargling saline, pseudonymized sample handling, automated RNA extraction, and viral RNA detection using a semiquantitative multiplexed colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay with an analytical sensitivity comparable with RT-qPCR. We provide standard operating procedures and an integrated software solution for all workflows, including sample logistics, analysis by colorimetry or sequencing, and communication of results. We evaluated factors affecting the viral load and the stability of gargling samples as well as the diagnostic sensitivity of the RT-LAMP assay. In parallel, we estimated the economic costs of setting up and running the test station. We performed > 35,000 tests, with an average turnover time of < 6 h from sample arrival to result announcement. Altogether, our work provides a blueprint for fast, sensitive, scalable, cost- and labor-efficient RT-LAMP diagnostics, which is independent of potentially limiting clinical diagnostics supply chains.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/diagnóstico , COVID-19/epidemiologia , Teste para COVID-19 , Técnicas de Laboratório Clínico/métodos , Pandemias/prevenção & controle , Sensibilidade e Especificidade , RNA Viral/genética
6.
EMBO J ; 39(2): e102586, 2020 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-31802527

RESUMO

ER-phagy, the selective autophagy of endoplasmic reticulum (ER), safeguards organelle homeostasis by eliminating misfolded proteins and regulating ER size. ER-phagy can occur by macroautophagic and microautophagic mechanisms. While dedicated machinery for macro-ER-phagy has been discovered, the molecules and mechanisms mediating micro-ER-phagy remain unknown. Here, we first show that micro-ER-phagy in yeast involves the conversion of stacked cisternal ER into multilamellar ER whorls during microautophagic uptake into lysosomes. Second, we identify the conserved Nem1-Spo7 phosphatase complex and the ESCRT machinery as key components for micro-ER-phagy. Third, we demonstrate that macro- and micro-ER-phagy are parallel pathways with distinct molecular requirements. Finally, we provide evidence that the ESCRT machinery directly functions in scission of the lysosomal membrane to complete the microautophagic uptake of ER. These findings establish a framework for a mechanistic understanding of micro-ER-phagy and, thus, a comprehensive appreciation of the role of autophagy in ER homeostasis.


Assuntos
Estresse do Retículo Endoplasmático/fisiologia , Retículo Endoplasmático/fisiologia , Complexos Endossomais de Distribuição Requeridos para Transporte , Membranas Intracelulares/metabolismo , Microautofagia , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/crescimento & desenvolvimento , Homeostase , Proteínas de Membrana/metabolismo , Proteínas Nucleares/metabolismo , Saccharomyces cerevisiae/metabolismo
7.
J Adv Nurs ; 2024 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-38558440

RESUMO

AIM: This study seeks to review how the use of digital technologies in clinical nursing affects nurses' professional identity and the relations of power within clinical environments. DESIGN: Literature review. DATA SOURCES: PubMed and CINAHL databases were searched in April 2023. METHODS: We screened 874 studies in English and German, of which 15 were included in our final synthesis reflecting the scientific discourse from 1992 until 2023. RESULTS: Our review revealed relevant effects of digital technologies on nurses' professional identity and power relations. Few studies cover outcomes relating to identity, such as moral agency or nurses' autonomy. Most studies describe negative impacts of technology on professional identity, for example, creating a barrier between nurses and patients leading to decreased empathetic interaction. Regarding power relations, technologically skilled nurses can yield power over colleagues and patients, while depending on technology. The investigation of these effects is underrepresented. CONCLUSION: Our review presents insights into the relation between technology and nurses' professional identity and prevalent power relations. For future studies, dedicated and critical investigations of digital technologies' impact on the formation of professional identity in nursing are required. IMPLICATIONS FOR THE PROFESSION: Nurses' professional identity may be altered by digital technologies used in clinical care. Nurses, who are aware of the potential effects of digitized work environments, can reflect on the relationship of technology and the nursing profession. IMPACT: The use of digital technology might lead to a decrease in nurses' moral agency and competence to shape patient-centred care. Digital technologies seem to become an essential measure for nurses to wield power over patients and colleagues, whilst being a control mechanism. Our work encourages nurses to actively shape digital care. REPORTING METHOD: We adhere to the JBI Manual for Evidence Synthesis where applicable. EQUATOR reporting guidelines were not applicable for this type of review. PATIENT OR PUBLIC CONTRIBUTION: No patient or public contribution.

8.
Infection ; 50(5): 1281-1293, 2022 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-35397099

RESUMO

PURPOSE: The objective of this study was to develop a scalable approach for direct comparison of the analytical sensitivities of commercially available SARS-CoV-2 antigen point-of-care tests (AgPOCTs) to rapidly identify poor-performing products. METHODS: We present a methodology for quick assessment of the sensitivity of SARS-CoV-2 AgPOCTs suitable for quality evaluation of many different products. We established reference samples with high, medium, and low SARS-CoV-2 viral loads along with a SARS-CoV-2 negative control sample. Test samples were used to semi-quantitatively assess the analytical sensitivities of 32 different commercial AgPOCTs in a head-to-head comparison. RESULTS: Among 32 SARS-CoV-2 AgPOCTs tested, we observe sensitivity differences across a broad range of viral loads (9.8 × 108 to 1.8 × 105 SARS-CoV-2 genome copies per ml). 23 AgPOCTs detected the Ct25 test sample (1.6 × 106 copies/ml), while only five tests detected the Ct28 test sample (1.8 × 105 copies/ml). In the low-range of analytical sensitivity, we found three saliva spit tests only delivering positive results for the Ct21 sample (2.7 × 107 copies/ml). Comparison with published data supports our AgPOCT ranking. Importantly, we identified an AgPOCT widely offered, which did not reliably recognize the sample with the highest viral load (Ct16 test sample with 9.8 × 108 copies/ml) leading to serious doubts about its usefulness in SARS-CoV-2 diagnostics. CONCLUSION: The results show that the rapid sensitivity assessment procedure presented here provides useful estimations on the analytical sensitivities of 32 AgPOCTs and identified a widely-spread AgPOCT with concerningly low sensitivity.


Assuntos
COVID-19 , SARS-CoV-2 , COVID-19/diagnóstico , Teste para COVID-19 , Técnicas de Laboratório Clínico/métodos , Humanos , Sistemas Automatizados de Assistência Junto ao Leito , Testes Imediatos , Sensibilidade e Especificidade
9.
BMC Biol ; 19(1): 169, 2021 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-34429100

RESUMO

BACKGROUND: Asexual fungi include important pathogens of plants and other organisms, and their effective management requires understanding of their evolutionary dynamics. Genetic recombination is critical for adaptability and could be achieved via heterokaryosis - the co-existence of genetically different nuclei in a cell resulting from fusion of non-self spores or hyphae - and the parasexual cycle in the absence of sexual reproduction. Fusion between different strains and establishment of viable heterokaryons are believed to be rare due to non-self recognition systems. Here, we investigate the extent and mechanisms of cell fusion and heterokaryosis in the important asexual plant pathogen Verticillium dahliae. RESULTS: We used live-cell imaging and genetic complementation assays of tagged V. dahliae strains to analyze the extent of non-self vegetative fusion, heterokaryotic cell fate, and nuclear behavior. An efficient CRISPR/Cas9-mediated system was developed to investigate the involvement of autophagy in heterokaryosis. Under starvation, non-self fusion of germinating spores occurs frequently regardless of the previously assessed vegetative compatibility of the partners. Supposedly "incompatible" fusions often establish viable heterokaryotic cells and mosaic mycelia, where nuclei can engage in fusion or transfer of genetic material. The molecular machinery of autophagy has a protective function against the destruction of "incompatible" heterokaryons. CONCLUSIONS: We demonstrate an imperfect function of somatic incompatibility systems in V. dahliae. These systems frequently tolerate the establishment of heterokaryons and potentially the initiation of the parasexual cycle even between strains that were previously regarded as "incompatible."


Assuntos
Núcleo Celular , Hifas , Fusão Celular , Fungos
10.
Curr Genet ; 67(3): 471-485, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33582843

RESUMO

Cell-to-cell fusion is a fundamental biological process across the tree of life. In filamentous fungi, somatic fusion (or anastomosis) is required for the normal development of their syncytial hyphal networks, and it can initiate non-sexual genetic exchange processes, such as horizontal genetic transfer and the parasexual cycle. Although these could be important drivers of the evolution of asexual fungi, this remains a largely unexplored possibility due to the lack of suitable resources for their study in these puzzling organisms. We thus aimed at the characterization of cell fusion in the important asexual fungus Verticillium dahliae via Conidial Anastomosis Tubes (CATs), which can be useful for the analysis of parasexuality. We optimized appropriate procedures for their highly reproducible quantification and live-cell imaging, which were used to characterize their physiology and cell biology, and to start elucidating their underlying genetic machinery. Formation of CATs was shown to depend on growth conditions and require functional Fus3 and Slt2 MAP kinases, as well as the NADPH oxidase NoxA, whereas the GPCR Ste2 and the mating-type protein MAT1-2-1 were dispensable. We show that nuclei and other organelles can migrate through CATs, which often leads to the formation of transient dikaryons. Their nuclei have possible windows of opportunity for genetic interaction before degradation of one by a presumably homeostatic mechanism. We establish here CAT-mediated fusion in V. dahliae as an experimentally convenient system for the cytological analysis of fungal non-sexual genetic interactions. We expect that it will facilitate the dissection of sexual alternatives in asexual fungi.


Assuntos
Acremonium/genética , Proteínas Fúngicas/genética , Reprodução Assexuada/genética , Esporos Fúngicos/genética , Acremonium/patogenicidade , Ascomicetos/genética , Ascomicetos/patogenicidade , Núcleo Celular/genética , Transferência Genética Horizontal/genética , Genes Fúngicos Tipo Acasalamento/genética , Hifas/genética , Hifas/crescimento & desenvolvimento , Proteínas Quinases Ativadas por Mitógeno/genética , NADPH Oxidases/genética , Proteínas de Saccharomyces cerevisiae/genética , Esporos Fúngicos/crescimento & desenvolvimento
11.
Nat Methods ; 15(8): 598-600, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29988096

RESUMO

Here we describe a C-SWAT library for high-throughput tagging of Saccharomyces cerevisiae open reading frames (ORFs). In 5,661 strains, we inserted an acceptor module after each ORF that can be efficiently replaced with tags or regulatory elements. We validated the library with targeted sequencing and tagged the proteome with bright fluorescent proteins to quantify the effect of heterologous transcription terminators on protein expression and to localize previously undetected proteins.


Assuntos
Genoma Fúngico , Biblioteca Genômica , Saccharomyces cerevisiae/genética , DNA Fúngico/genética , Sequenciamento de Nucleotídeos em Larga Escala , Fases de Leitura Aberta , Proteoma/genética , Proteômica , Proteínas de Saccharomyces cerevisiae/genética , Análise de Sequência de DNA , Sitios de Sequências Rotuladas
12.
Nucleic Acids Res ; 47(D1): D1245-D1249, 2019 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-30357397

RESUMO

The ability to measure the abundance and visualize the localization of proteins across the yeast proteome has stimulated hypotheses on gene function and fueled discoveries. While the classic C' tagged GFP yeast library has been the only resource for over a decade, the recent development of the SWAT technology has led to the creation of multiple novel yeast libraries where new-generation fluorescent reporters are fused at the N' and C' of open reading frames. Efficient access to these data requires a user interface to visualize and compare protein abundance, localization and co-localization across cells, strains, and libraries. YeastRGB (www.yeastRGB.org) was designed to address such a need, through a user-friendly interface that maximizes informative content. It employs a compact display where cells are cropped and tiled together into a 'cell-grid.' This representation enables viewing dozens of cells for a particular strain within a display unit, and up to 30 display units can be arrayed on a standard high-definition screen. Additionally, the display unit allows users to control zoom-level and overlay of images acquired using different color channels. Thus, YeastRGB makes comparing abundance and localization efficient, across thousands of cells from different strains and libraries.


Assuntos
Biologia Computacional/métodos , Bases de Dados de Proteínas , Biblioteca Gênica , Proteoma/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Armazenamento e Recuperação da Informação/métodos , Internet , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Microscopia de Fluorescência , Fases de Leitura Aberta/genética , Proteoma/genética , Saccharomyces cerevisiae/classificação , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Interface Usuário-Computador
13.
J Med Internet Res ; 23(8): e28151, 2021 08 26.
Artigo em Inglês | MEDLINE | ID: mdl-34435959

RESUMO

BACKGROUND: Owing to the shortage of medical professionals, as well as demographic and structural challenges, new care models have emerged to find innovative solutions to counter medical undersupply. Team-based primary care using medical delegation appears to be a promising approach to address these challenges; however, it demands efficient communication structures and mechanisms to reinsure patients and caregivers receive a delegated, treatment-related task. Digital health care technologies hold the potential to render these novel processes effective and demand driven. OBJECTIVE: The goal of this study is to recreate the daily work routines of general practitioners (GPs) and medical assistants (MAs) to explore promising approaches for the digital moderation of delegation processes and to deepen the understanding of subjective and perceptual factors that influence their technology assessment and use. METHODS: We conducted a combination of 19 individual and group interviews with 12 GPs and 14 MAs, seeking to identify relevant technologies for delegation purposes as well as stakeholders' perceptions of their effectiveness. Furthermore, a web-based survey was conducted asking the interviewees to order identified technologies based on their assessed applicability in multi-actor patient care. Interview data were analyzed using a three-fold inductive coding procedure. Multidimensional scaling was applied to analyze and visualize the survey data, leading to a triangulation of the results. RESULTS: Our results suggest that digital mediation of delegation underlies complex, reciprocal processes and biases that need to be identified and analyzed to improve the development and distribution of innovative technologies and to improve our understanding of technology use in team-based primary care. Nevertheless, medical delegation enhanced by digital technologies, such as video consultations, portable electrocardiograms, or telemedical stethoscopes, can counteract current challenges in primary care because of its unique ability to ensure both personal, patient-centered care for patients and create efficient and needs-based treatment processes. CONCLUSIONS: Technology-mediated delegation appears to be a promising approach to implement innovative, case-sensitive, and cost-effective ways to treat patients within the paradigm of primary care. The relevance of such innovative approaches increases with the tremendous need for differentiated and effective care, such as during the ongoing COVID-19 pandemic. For the successful and sustainable adoption of innovative technologies, MAs represent essential team members. In their role as mediators between GPs and patients, MAs are potentially able to counteract patients' resistance toward using innovative technology and compensate for patients' limited access to technology and care facilities.


Assuntos
COVID-19 , Telemedicina , Humanos , Pandemias , Atenção Primária à Saúde , SARS-CoV-2
14.
Genes Dev ; 27(3): 335-49, 2013 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-23388829

RESUMO

Nuclear migration during yeast karyogamy, termed nuclear congression, is required to initiate nuclear fusion. Congression involves a specific regulation of the microtubule minus end-directed kinesin-14 motor Kar3 and a rearrangement of the cytoplasmic microtubule attachment sites at the spindle pole bodies (SPBs). However, how these elements interact to produce the forces necessary for nuclear migration is less clear. We used electron tomography, molecular genetics, quantitative imaging, and first principles modeling to investigate how cytoplasmic microtubules are organized during nuclear congression. We found that Kar3, with the help of its light chain, Cik1, is anchored during mating to the SPB component Spc72 that also serves as a nucleator and anchor for microtubules via their minus ends. Moreover, we show that no direct microtubule-microtubule interactions are required for nuclear migration. Instead, SPB-anchored Kar3 exerts the necessary pulling forces laterally on microtubules emanating from the SPB of the mating partner nucleus. Therefore, a twofold symmetrical application of the core principle that drives nuclear migration in higher cells is used in yeast to drive nuclei toward each other before nuclear fusion.


Assuntos
Núcleo Celular/metabolismo , Proteínas Associadas aos Microtúbulos/metabolismo , Microtúbulos/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/fisiologia , Fuso Acromático/metabolismo , Núcleo Celular/ultraestrutura , Simulação por Computador , Proteínas Nucleares/metabolismo , Ligação Proteica , Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/ultraestrutura
15.
Biophys J ; 119(7): 1359-1370, 2020 10 06.
Artigo em Inglês | MEDLINE | ID: mdl-32919495

RESUMO

The ability to quantify protein concentrations and to measure protein interactions in vivo is key information needed for the understanding of complex processes inside cells, but the acquisition of such information from living cells is still demanding. Fluorescence-based methods like two-color fluorescence cross-correlation spectroscopy can provide this information, but measurement precision is hampered by various sources of errors caused by instrumental or optical limitations such as imperfect overlap of detection volumes or detector cross talk. Furthermore, the nature and properties of used fluorescent proteins or fluorescent dyes, such as labeling efficiency, fluorescent protein maturation, photostability, bleaching, and fluorescence brightness can have an impact. Here, we take advantage of previously published fluorescence lifetime correlation spectroscopy which relies on lifetime differences as a mean to discriminate fluorescent proteins with similar spectral properties and to use them for single-color fluorescence lifetime cross-correlation spectroscopy (sc-FLCCS). By using only one excitation and one detection wavelength, this setup avoids all sources of errors resulting from chromatic aberrations and detector cross talk. To establish sc-FLCCS, we first engineered and tested multiple green fluorescent protein (GFP)-like fluorescent proteins for their suitability. This identified a novel, to our knowledge, GFP variant termed short-lifetime monomeric GFP with the so-far shortest lifetime. Monte-Carlo simulations were employed to explore the suitability of different combinations of GFP variants. Two GFPs, Envy and short-lifetime monomeric GFP, were predicted to constitute the best performing couple for sc-FLCCS measurements. We demonstrated application of this GFP pair for measuring protein interactions between the proteasome and interacting proteins and for measuring protein interactions between three partners when combined with a red florescent protein. Together, our findings establish sc-FLCCS as a valid alternative for conventional dual-color fluorescence cross-correlation spectroscopy measurements.


Assuntos
Corantes Fluorescentes , Fluorescência , Proteínas de Fluorescência Verde/genética , Proteínas Luminescentes/genética , Espectrometria de Fluorescência
16.
Nature ; 516(7531): 410-3, 2014 Dec 18.
Artigo em Inglês | MEDLINE | ID: mdl-25519137

RESUMO

The nuclear envelope is a double membrane that separates the nucleus from the cytoplasm. The inner nuclear membrane (INM) functions in essential nuclear processes including chromatin organization and regulation of gene expression. The outer nuclear membrane is continuous with the endoplasmic reticulum and is the site of membrane protein synthesis. Protein homeostasis in this compartment is ensured by endoplasmic-reticulum-associated protein degradation (ERAD) pathways that in yeast involve the integral membrane E3 ubiquitin ligases Hrd1 and Doa10 operating with the E2 ubiquitin-conjugating enzymes Ubc6 and Ubc7 (refs 2, 3). However, little is known about protein quality control at the INM. Here we describe a protein degradation pathway at the INM in yeast (Saccharomyces cerevisiae) mediated by the Asi complex consisting of the RING domain proteins Asi1 and Asi3 (ref. 4). We report that the Asi complex functions together with the ubiquitin-conjugating enzymes Ubc6 and Ubc7 to degrade soluble and integral membrane proteins. Genetic evidence suggests that the Asi ubiquitin ligase defines a pathway distinct from, but complementary to, ERAD. Using unbiased screening with a novel genome-wide yeast library based on a tandem fluorescent protein timer, we identify more than 50 substrates of the Asi, Hrd1 and Doa10 E3 ubiquitin ligases. We show that the Asi ubiquitin ligase is involved in degradation of mislocalized integral membrane proteins, thus acting to maintain and safeguard the identity of the INM.


Assuntos
Membrana Nuclear/enzimologia , Saccharomyces cerevisiae/enzimologia , Degradação Associada com o Retículo Endoplasmático/fisiologia , Proteínas de Membrana/metabolismo , Membrana Nuclear/metabolismo , Transporte Proteico/fisiologia , Proteólise , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Enzimas de Conjugação de Ubiquitina/metabolismo
17.
Proc Natl Acad Sci U S A ; 114(22): E4442-E4451, 2017 05 30.
Artigo em Inglês | MEDLINE | ID: mdl-28416670

RESUMO

Eukaryotic DNA replication fidelity relies on the concerted action of DNA polymerase nucleotide selectivity, proofreading activity, and DNA mismatch repair (MMR). Nucleotide selectivity and proofreading are affected by the balance and concentration of deoxyribonucleotide (dNTP) pools, which are strictly regulated by ribonucleotide reductase (RNR). Mutations preventing DNA polymerase proofreading activity or MMR function cause mutator phenotypes and consequently increased cancer susceptibility. To identify genes not previously linked to high-fidelity DNA replication, we conducted a genome-wide screen in Saccharomyces cerevisiae using DNA polymerase active-site mutants as a "sensitized mutator background." Among the genes identified in our screen, three metabolism-related genes (GLN3, URA7, and SHM2) have not been previously associated to the suppression of mutations. Loss of either the transcription factor Gln3 or inactivation of the CTP synthetase Ura7 both resulted in the activation of the DNA damage response and imbalanced dNTP pools. Importantly, these dNTP imbalances are strongly mutagenic in genetic backgrounds where DNA polymerase function or MMR activity is partially compromised. Previous reports have shown that dNTP pool imbalances can be caused by mutations altering the allosteric regulation of enzymes involved in dNTP biosynthesis (e.g., RNR or dCMP deaminase). Here, we provide evidence that mutations affecting genes involved in RNR substrate production can cause dNTP imbalances, which cannot be compensated by RNR or other enzymatic activities. Moreover, Gln3 inactivation links nutrient deprivation to increased mutagenesis. Our results suggest that similar genetic interactions could drive mutator phenotypes in cancer cells.


Assuntos
Reparo de Erro de Pareamento de DNA/genética , Replicação do DNA/genética , Mutagênese/genética , Proteínas de Saccharomyces cerevisiae/genética , Fatores de Transcrição/genética , Carbono-Nitrogênio Ligases/genética , Carbono-Nitrogênio Ligases/metabolismo , Dano ao DNA/genética , Fosfatos de Dinucleosídeos/genética , Fosfatos de Dinucleosídeos/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo
18.
Nat Methods ; 13(4): 371-378, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26928762

RESUMO

The yeast Saccharomyces cerevisiae is ideal for systematic studies relying on collections of modified strains (libraries). Despite the significance of yeast libraries and the immense variety of available tags and regulatory elements, only a few such libraries exist, as their construction is extremely expensive and laborious. To overcome these limitations, we developed a SWAp-Tag (SWAT) method that enables one parental library to be modified easily and efficiently to give rise to an endless variety of libraries of choice. To showcase the versatility of the SWAT approach, we constructed and investigated a library of ∼1,800 strains carrying SWAT-GFP modules at the amino termini of endomembrane proteins and then used it to create two new libraries (mCherry and seamless GFP). Our work demonstrates how the SWAT method allows fast and effortless creation of yeast libraries, opening the door to new ways of systematically studying cell biology.


Assuntos
Biblioteca Gênica , Proteínas de Fluorescência Verde/metabolismo , Processamento de Imagem Assistida por Computador/métodos , Proteínas de Membrana/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Western Blotting , Biologia Celular , Proteínas de Fluorescência Verde/genética , Proteínas de Membrana/genética , Microscopia de Fluorescência , Peroxissomos/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crescimento & desenvolvimento , Proteínas de Saccharomyces cerevisiae/genética , Frações Subcelulares
19.
Mol Syst Biol ; 14(9): e8355, 2018 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-30181144

RESUMO

Embryogenesis relies on instructions provided by spatially organized signaling molecules known as morphogens. Understanding the principles behind morphogen distribution and how cells interpret locally this information remains a major challenge in developmental biology. Here, we introduce morphogen-age measurements as a novel approach to test models of morphogen gradient formation. Using a tandem fluorescent timer as a protein age sensor, we find a gradient of increasing age of Bicoid along the anterior-posterior axis in the early Drosophila embryo. Quantitative analysis of the protein age distribution across the embryo reveals that the synthesis-diffusion-degradation model is the most likely model underlying Bicoid gradient formation, and rules out other hypotheses for gradient formation. Moreover, we show that the timer can detect transitions in the dynamics associated with syncytial cellularization. Our results provide new insight into Bicoid gradient formation and demonstrate how morphogen-age information can complement knowledge about movement, abundance, and distribution, which should be widely applicable to other systems.


Assuntos
Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Embrião não Mamífero/metabolismo , Imunofluorescência/métodos , Regulação da Expressão Gênica no Desenvolvimento , Proteínas de Homeodomínio/genética , Imagem Óptica/métodos , Transativadores/genética , Animais , Padronização Corporal/genética , Proteínas de Drosophila/biossíntese , Drosophila melanogaster/crescimento & desenvolvimento , Drosophila melanogaster/metabolismo , Embrião não Mamífero/citologia , Embrião não Mamífero/diagnóstico por imagem , Genes Reporter , Proteínas de Fluorescência Verde/genética , Proteínas de Fluorescência Verde/metabolismo , Proteínas de Homeodomínio/biossíntese , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Estabilidade Proteica , Transporte Proteico , Proteólise , Transdução de Sinais , Transativadores/biossíntese , Proteína Vermelha Fluorescente
20.
Nature ; 503(7475): 285-9, 2013 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-24067609

RESUMO

The directed migration of cell collectives is a driving force of embryogenesis. The predominant view in the field is that cells in embryos navigate along pre-patterned chemoattractant gradients. One hypothetical way to free migrating collectives from the requirement of long-range gradients would be through the self-generation of local gradients that travel with them, a strategy that potentially allows self-determined directionality. However, a lack of tools for the visualization of endogenous guidance cues has prevented the demonstration of such self-generated gradients in vivo. Here we define the in vivo dynamics of one key guidance molecule, the chemokine Cxcl12a, by applying a fluorescent timer approach to measure ligand-triggered receptor turnover in living animals. Using the zebrafish lateral line primordium as a model, we show that migrating cell collectives can self-generate gradients of chemokine activity across their length via polarized receptor-mediated internalization. Finally, by engineering an external source of the atypical receptor Cxcr7 that moves with the primordium, we show that a self-generated gradient mechanism is sufficient to direct robust collective migration. This study thus provides, to our knowledge, the first in vivo proof for self-directed tissue migration through local shaping of an extracellular cue and provides a framework for investigating self-directed migration in many other contexts including cancer invasion.


Assuntos
Movimento Celular/fisiologia , Fatores Quimiotáticos/metabolismo , Peixe-Zebra/fisiologia , Animais , Quimiocina CXCL12/genética , Quimiocina CXCL12/metabolismo , Fatores Quimiotáticos/genética , Embrião não Mamífero , Regulação da Expressão Gênica no Desenvolvimento , Receptores CXCR/genética , Receptores CXCR/metabolismo , Peixe-Zebra/genética , Proteínas de Peixe-Zebra/genética , Proteínas de Peixe-Zebra/metabolismo
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