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1.
Cell Syst ; 12(8): 780-794.e7, 2021 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-34139154

RESUMO

COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.


Assuntos
Biomarcadores/análise , COVID-19/patologia , Progressão da Doença , Proteoma/fisiologia , Fatores Etários , Contagem de Células Sanguíneas , Gasometria , Ativação Enzimática , Humanos , Inflamação/patologia , Aprendizado de Máquina , Prognóstico , Proteômica , SARS-CoV-2/imunologia
2.
Arch Microbiol ; 203(6): 3269-3278, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-33846829

RESUMO

All bacteria can survive and adapt to different stresses, such as fluctuations in temperature, pH oxidative, and osmotic pressure occurring in their surrounding environments. This study aims to evaluate the effects of a variety of stress conditions on the growth, and proteome of Raoultella planticola PTCC 1598. R. planticola cells were exposed to different values of temperatures, sodium chloride, pH, and hydrogen peroxide stresses. Among the stress conditions, oxidative stress, upon exposure to hydrogen peroxide (H2O2) at 4000 ppm concentration was selected for proteomics analysis in detail. Approximately, 1400 spots were identified in two-dimensional gel electrophoresis (2-DE). Among the identified spots, 85 spots were repeatable using 2D-Platinum software and eye confirmation and, nine protein spots were differentially expressed. Among nine proteins, six proteins identified successfully with an MASCOT score greater than 40 (p < 0.05) were 2,3-dihydroxybenzoate-2,3-dehydrogenase (oxidoreductase family), hypothetical protein G787-04832, periplasmic D-galactose-binding protein, uridine phosphorylase (glycosyltransferases), a single peptide match to cysteine-binding periplasmic protein, and NADP(H) nitroreductase. All identified proteins showed decreased level expression. Based on the obtained results, we concluded that hydrogen peroxide as an antiseptic compound could affect cell growth and proteomics of R. planticola. Therefore, we recommend using an antiseptic solution containing H2O2 to prevent the spread of R. planticola as a new emerging pathogen.


Assuntos
Infecções por Enterobacteriaceae , Enterobacteriaceae , Proteoma , Estresse Fisiológico , Eletroforese em Gel Bidimensional , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/genética , Enterobacteriaceae/crescimento & desenvolvimento , Infecções por Enterobacteriaceae/microbiologia , Humanos , Peróxido de Hidrogênio/farmacologia , Proteoma/fisiologia
3.
NPJ Syst Biol Appl ; 7(1): 14, 2021 03 08.
Artigo em Inglês | MEDLINE | ID: mdl-33686098

RESUMO

Although the effect of temperature on microbial growth has been widely studied, the role of proteome allocation in bringing about temperature-induced changes remains elusive. To tackle this problem, we propose a coarse-grained model of microbial growth, including the processes of temperature-sensitive protein unfolding and chaperone-assisted (re)folding. We determine the proteome sector allocation that maximizes balanced growth rate as a function of nutrient limitation and temperature. Calibrated with quantitative proteomic data for Escherichia coli, the model allows us to clarify general principles of temperature-dependent proteome allocation and formulate generalized growth laws. The same activation energy for metabolic enzymes and ribosomes leads to an Arrhenius increase in growth rate at constant proteome composition over a large range of temperatures, whereas at extreme temperatures resources are diverted away from growth to chaperone-mediated stress responses. Our approach points at risks and possible remedies for the use of ribosome content to characterize complex ecosystems with temperature variation.


Assuntos
Bactérias/crescimento & desenvolvimento , Proteoma/metabolismo , Temperatura , Simulação por Computador , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Expressão Gênica/genética , Regulação Bacteriana da Expressão Gênica/genética , Modelos Biológicos , Modelos Teóricos , Nutrientes/metabolismo , Proteoma/fisiologia , Proteômica/métodos , Ribossomos , Biologia de Sistemas/métodos
4.
Arterioscler Thromb Vasc Biol ; 41(3): 999-1011, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33441027

RESUMO

Platelets rapidly undergo responsive transitions in form and function to repair vascular endothelium and mediate hemostasis. In contrast, heterogeneous platelet subpopulations with a range of primed or refractory phenotypes gradually arise in chronic inflammatory and other conditions in a manner that may indicate or support disease. Qualitatively distinguishable platelet phenotypes are increasingly associated with a variety of physiological and pathological circumstances; however, the origins and significance of platelet phenotypic variation remain unclear and conceptually vague. As changes in platelet function in disease exhibit many similarities to platelets following the activation of platelet agonist receptors, the intracellular responses of platelets common to hemostasis and inflammation may provide insights to the molecular basis of platelet phenotype. Here, we review concepts around how protein-level relations-from platelet receptors through intracellular signaling events-may help to define platelet phenotypes in inflammation, immune responses, aging, and other conditions. We further discuss how representing systems-wide platelet proteomics data profiles as circuit-like networks of causally related intracellular events, or, pathway maps, may inform molecular definitions of platelet phenotype. In addition to offering insights into platelets as druggable targets, maps of causally arranged intracellular relations underlying platelet function can also advance precision and interceptive medicine efforts by leveraging platelets as accessible, dynamic, endogenous, circulating biomarkers of vascular wellness and disease. Graphic Abstract: A graphic abstract is available for this article.


Assuntos
Plaquetas/fisiologia , Proteoma/fisiologia , Doenças Vasculares/sangue , Animais , Biomarcadores/sangue , Endotélio Vascular/fisiologia , Hemostasia/fisiologia , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/sangue , Peptídeos e Proteínas de Sinalização Intracelular/fisiologia , Modelos Cardiovasculares , Fenótipo , Proteômica , Transdução de Sinais , Doenças Vasculares/fisiopatologia
5.
Plant Physiol Biochem ; 160: 8-17, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33445043

RESUMO

Yellowhorn (Xanthoceras sorbifolium Bunge) is a woody oil species that is widely distributed in northwestern China. To investigate the molecular mechanisms underlying the drought and heat tolerance response of yellowhorn seedlings, changes in protein abundance were analyzed via comparative proteomics. Drought and heat treatment of seedlings was applied in growth chamber, and the leaves were harvested after 7 days of treatment. The total protein was extracted, and comparative proteomic analysis was performed via isobaric tag for relative and absolute quantitation (iTRAQ). The abundance of most of the proteins associated with oxidative phosphorylation, NADH dehydrogenase and superoxide dismutase (SOD) was reduced. The differential proteins associated with photosynthesis enzymes indicated that stress had different effects on photosystem I (PSI) and photosystem II (PSII). After comprehensively analyzing the results, we speculated that drought and heat stress could hinder the synthesis of riboflavin, reducing NADH dehydrogenase content, which might further have an impact on energy utilization. Yellowhorn seedlings relied on Fe-Mn SOD enzymes rather than Cu/Zn SOD enzymes to remove reactive oxygen species (ROS). In addition, heat-shock proteins (HSPs) had significant increase and played a key role in stress response, which could be divided into two categories according to their transcription and translation efficiency. Over all, the results can provide a basis for understanding the molecular mechanism underlying resistance to drought and heat stress in yellowhorn and for subsequent research of posttranslational modification-related omics of key proteins.


Assuntos
Secas , Resposta ao Choque Térmico , Proteoma/fisiologia , Sapindaceae/fisiologia , Temperatura Alta , Plântula/fisiologia , Estresse Fisiológico
6.
Plant J ; 105(1): 223-244, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33118270

RESUMO

Photosynthetic acclimation, the ability to adjust the composition of the thylakoid membrane to optimise the efficiency of electron transfer to the prevailing light conditions, is crucial to plant fitness in the field. While much is known about photosynthetic acclimation in Arabidopsis, to date there has been no study that combines both quantitative label-free proteomics and photosynthetic analysis by gas exchange, chlorophyll fluorescence and P700 absorption spectroscopy. Using these methods we investigated how the levels of 402 thylakoid proteins, including many regulatory proteins not previously quantified, varied upon long-term (weeks) acclimation of Arabidopsis to low (LL), moderate (ML) and high (HL) growth light intensity and correlated these with key photosynthetic parameters. We show that changes in the relative abundance of cytb6 f, ATP synthase, FNR2, TIC62 and PGR6 positively correlate with changes in estimated PSII electron transfer rate and CO2 assimilation. Improved photosynthetic capacity in HL grown plants is paralleled by increased cyclic electron transport, which positively correlated with NDH, PGRL1, FNR1, FNR2 and TIC62, although not PGR5 abundance. The photoprotective acclimation strategy was also contrasting, with LL plants favouring slowly reversible non-photochemical quenching (qI), which positively correlated with LCNP, while HL plants favoured rapidly reversible quenching (qE), which positively correlated with PSBS. The long-term adjustment of thylakoid membrane grana diameter positively correlated with LHCII levels, while grana stacking negatively correlated with CURT1 and RIQ protein abundance. The data provide insights into how Arabidopsis tunes photosynthetic electron transfer and its regulation during developmental acclimation to light intensity.


Assuntos
Aclimatação , Arabidopsis/efeitos da radiação , Proteoma/efeitos da radiação , Tilacoides/efeitos da radiação , Arabidopsis/metabolismo , Arabidopsis/fisiologia , Dióxido de Carbono/metabolismo , Clorofila/metabolismo , Transporte de Elétrons , Luz/efeitos adversos , Espectrometria de Massas , Fotossíntese/efeitos da radiação , Complexo de Proteína do Fotossistema II/metabolismo , Proteoma/metabolismo , Proteoma/fisiologia , Tilacoides/metabolismo , Tilacoides/fisiologia
7.
Nutrients ; 13(1)2020 Dec 25.
Artigo em Inglês | MEDLINE | ID: mdl-33375592

RESUMO

Dietary fiber intake during pregnancy may improve offspring intestinal development. The aim of this study was to evaluate the effect of maternal high fiber intake during late gestation on intestinal morphology, microbiota, and intestinal proteome of newborn piglets. Sixteen sows were randomly allocated into two groups receiving the control diet (CD) and high-fiber diet (HFD) from day 90 of gestation to farrowing. Newborn piglets were selected from each litter, named as CON and Fiber group, respectively. Maternal high fiber intake did not markedly improve the birth weight, but increased the body length, the ileal crypt depth and colonic acetate level. In addition, maternal high fiber intake increased the -diversity indices (Observed species, Simpson, and ACE), and the abundance of Acidobacteria and Bacteroidetes at phylum level, significantly increased the abundance of Bradyrhizobium and Phyllobacterium at genus level in the colon of newborn piglets. Moreover, maternal high fiber intake markedly altered the ileal proteome, increasing the abundances of proteins associated with oxidative status, energy metabolism, and immune and inflammatory responses, and decreasing abundances of proteins related to cellular apoptosis, cell structure, and motility. These findings indicated that maternal high fiber intake could alter intestinal morphology, along with the altered intestinal microbiota composition and proteome of offspring.


Assuntos
Animais Recém-Nascidos/anatomia & histologia , Animais Recém-Nascidos/fisiologia , Fibras na Dieta/administração & dosagem , Microbioma Gastrointestinal/fisiologia , Intestinos/embriologia , Proteoma/fisiologia , Actinobacteria , Animais , Animais Recém-Nascidos/microbiologia , Bactérias/classificação , Bacteroidetes , Colo/química , Colo/microbiologia , Ácidos Graxos Voláteis/análise , Feminino , Íleo/metabolismo , Íleo/ultraestrutura , Intestinos/fisiologia , Fenômenos Fisiológicos da Nutrição Materna/fisiologia , Modelos Animais , Gravidez , Proteobactérias , Sus scrofa
8.
PLoS Comput Biol ; 16(9): e1008245, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32986690

RESUMO

Universal observations in Biology are sometimes described as "laws". In E. coli, experimental studies performed over the past six decades have revealed major growth laws relating ribosomal mass fraction and cell size to the growth rate. Because they formalize complex emerging principles in biology, growth laws have been instrumental in shaping our understanding of bacterial physiology. Here, we discovered a novel size law that connects cell size to the inverse of the metabolic proteome mass fraction and the active fraction of ribosomes. We used a simple whole-cell coarse-grained model of cell physiology that combines the proteome allocation theory and the structural model of cell division. This integrated model captures all available experimental data connecting the cell proteome composition, ribosome activity, division size and growth rate in response to nutrient quality, antibiotic treatment and increased protein burden. Finally, a stochastic extension of the model explains non-trivial correlations observed in single cell experiments including the adder principle. This work provides a simple and robust theoretical framework for studying the fundamental principles of cell size determination in unicellular organisms.


Assuntos
Fenômenos Fisiológicos Bacterianos , Escherichia coli , Modelos Biológicos , Modelos Moleculares , Antibacterianos/farmacologia , Meios de Cultura/farmacologia , Escherichia coli/citologia , Escherichia coli/efeitos dos fármacos , Escherichia coli/fisiologia , Proteoma/fisiologia , Ribossomos/fisiologia , Biologia de Sistemas
9.
BMC Plant Biol ; 20(1): 431, 2020 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-32938390

RESUMO

BACKGROUND: High-temperature stress (HTS) is one of the main environmental stresses that limit plant growth and crop production in agricultural systems. Maca (Lepidium meyenii) is an important high-altitude herbaceous plant adapted to a wide range of environmental stimuli such as cold, strong wind and UV-B exposure. However, it is an extremely HTS-sensitive plant species. Thus far, there is limited information about gene/protein regulation and signaling pathways related to the heat stress responses in maca. In this study, proteome profiles of maca seedlings exposed to HTS for 12 h were investigated using a tandem mass tag (TMT)-based proteomic approach. RESULTS: In total, 6966 proteins were identified, of which 300 showed significant alterations in expression following HTS. Bioinformatics analyses indicated that protein processing in endoplasmic reticulum was the most significantly up-regulated metabolic pathway following HTS. Quantitative RT-PCR (qRT-PCR) analysis showed that the expression levels of 19 genes encoding proteins mapped to this pathway were significantly up-regulated under HTS. These results show that protein processing in the endoplasmic reticulum may play a crucial role in the responses of maca to HTS. CONCLUSIONS: Our proteomic data can be a good resource for functional proteomics of maca and our results may provide useful insights into the molecular response mechanisms underlying herbal plants to HTS.


Assuntos
Lepidium/fisiologia , Proteoma/fisiologia , Clorofila/metabolismo , Regulação da Expressão Gênica de Plantas , Resposta ao Choque Térmico , Lepidium/genética , Lepidium/metabolismo , Redes e Vias Metabólicas , Proteínas de Plantas/metabolismo , Proteínas de Plantas/fisiologia , Proteoma/genética , Proteoma/metabolismo , Reação em Cadeia da Polimerase em Tempo Real , Plântula/metabolismo , Plântula/fisiologia
10.
Int J Mol Sci ; 21(19)2020 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-32987815

RESUMO

ROP (Rho-like GTPases from plants) GTPases are polarly localized key regulators of polar growth in pollen tubes and other cells in plants. However, how ROP GTPases are regulated and how they control polar growth remains to be fully understood. To gain new insights into ROP-dependent mechanisms underlying polar cell growth, we characterized the interactome of ROP1 GTPase that controls Arabidopsis pollen tube (PT) tip growth, an extreme form of polar cell growth. We established an efficient method for culturing Arabidopsis pollen tubes in liquid medium, which was used for immunoprecipitation/mass spectrometry-based identification of ROP1-associated proteins. A total of 654 candidates were isolated from the ROP1 interactome in Arabidopsis pollen tubes, and GO (Gene Ontology) classification and pathway analysis revealed multiple uncharacterized ROP1-dependent processes including translation, cell wall modification, post transcriptional modification, and ion homeostasis, in addition to known ROP1-dependent pathways. The ROP1-interactome data was further supported by the co-expression of the candidate interactors in highly mature pollen with PT germination and growth defects being discovered in 25% (8/32) of the candidate mutant genes. Taken together, our work uncovers valuable information for the identification and functional elucidation of ROP-associated proteins in the regulation of polar growth, and provides a reliable reference to identify critical regulators of polar cell growth in the future.


Assuntos
Proteínas de Arabidopsis/fisiologia , Arabidopsis/fisiologia , Proteínas de Ligação ao GTP/fisiologia , Tubo Polínico/fisiologia , Regulação da Expressão Gênica de Plantas , Germinação , Proteoma/fisiologia , Transdução de Sinais , Técnicas de Cultura de Tecidos
11.
Cell ; 183(1): 269-283.e19, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-32916130

RESUMO

Determining protein levels in each tissue and how they compare with RNA levels is important for understanding human biology and disease as well as regulatory processes that control protein levels. We quantified the relative protein levels from over 12,000 genes across 32 normal human tissues. Tissue-specific or tissue-enriched proteins were identified and compared to transcriptome data. Many ubiquitous transcripts are found to encode tissue-specific proteins. Discordance of RNA and protein enrichment revealed potential sites of synthesis and action of secreted proteins. The tissue-specific distribution of proteins also provides an in-depth view of complex biological events that require the interplay of multiple tissues. Most importantly, our study demonstrated that protein tissue-enrichment information can explain phenotypes of genetic diseases, which cannot be obtained by transcript information alone. Overall, our results demonstrate how understanding protein levels can provide insights into regulation, secretome, metabolism, and human diseases.


Assuntos
Proteoma/genética , Proteômica/métodos , Transcriptoma/genética , Expressão Gênica/genética , Perfilação da Expressão Gênica/métodos , Humanos , Proteoma/fisiologia , RNA/genética , RNA Mensageiro/metabolismo , Transcriptoma/fisiologia
12.
Medicine (Baltimore) ; 99(39): e22172, 2020 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-32991410

RESUMO

Osteoporosis is a severe chronic skeletal disorder that increases the risks of disability and mortality; however, the mechanism of this disease and the protein markers for prognosis of osteoporosis have not been well characterized. This study aims to characterize the imbalanced serum proteostasis, the disturbed pathways, and potential serum markers in osteoporosis by using a set of bioinformatic analyses. In the present study, the large-scale proteomics datasets (PXD006464) were adopted from the Proteome Xchange database and processed with MaxQuant. The differentially expressed serum proteins were identified. The biological process and molecular function were analyzed. The protein-protein interactions and subnetwork modules were constructed. The signaling pathways were enriched. We identified 209 upregulated and 230 downregulated serum proteins. The bioinformatic analyses revealed a highly overlapped functional protein classification and the gene ontology terms between the upregulated and downregulated protein groups. Protein-protein interactions and pathway analyses showed a high enrichment in protein synthesis, inflammation, and immune response in the upregulated proteins, and cell adhesion and cytoskeleton regulation in the downregulated proteins. Our findings greatly expand the current view of the roles of serum proteins in osteoporosis and shed light on the understanding of its underlying mechanisms and the discovery of serum proteins as potential markers for the prognosis of osteoporosis.


Assuntos
Mineração de Dados/métodos , Osteoporose/sangue , Proteoma/fisiologia , Biomarcadores , Adesão Celular/fisiologia , Biologia Computacional , Citoesqueleto/metabolismo , Regulação para Baixo , Humanos , Mediadores da Inflamação/metabolismo , Mapas de Interação de Proteínas/fisiologia , Proteômica , Regulação para Cima
13.
Sci Rep ; 10(1): 11213, 2020 07 08.
Artigo em Inglês | MEDLINE | ID: mdl-32641697

RESUMO

The Tibetan chicken is a unique breed that has adapted to the high-altitude hypoxic conditions of the Tibetan plateau. A number of positively selected genes have been reported in these chickens; however, the mechanisms of gene expression for hypoxia adaptation are not fully understood. In the present study, eggs from Tibetan and Chahua chickens were incubated under hypoxic and normoxic conditions, and vascularization in the chorioallantoic membrane (CAM) of embryos was observed. We found that the vessel density index in the CAM of Tibetan chickens was lower than in Chahua chickens under hypoxia conditions. Transcriptomic and proteomic analyses of CAM tissues were performed in Tibetan and Chahua chicken embryos under hypoxic incubation using RNA-Seq and iTRAQ. We obtained 160 differentially expressed genes and 387 differentially expressed proteins that were mainly enriched in angiogenesis, vasculature development, blood vessel morphogenesis, blood circulation, renin-angiotensin system, and HIF-1 and VEGF signaling pathways. Twenty-six genes involved in angiogenesis and blood circulation, two genes involved in ion transport, and six genes that regulated energy metabolism were identified as candidate functional genes in regulating hypoxic adaptation of chicken embryos. This research provided insights into the molecular mechanism of hypoxia adaptation in Tibetan chickens.


Assuntos
Aclimatação/genética , Altitude , Galinhas/fisiologia , Hipóxia/fisiopatologia , Animais , Circulação Sanguínea/genética , Embrião de Galinha , Membrana Corioalantoide/irrigação sanguínea , Regulação da Expressão Gênica no Desenvolvimento , Neovascularização Fisiológica/genética , Proteoma/fisiologia , Proteômica , RNA-Seq , Tibet , Transcriptoma/fisiologia
14.
Methods Mol Biol ; 2175: 181-196, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32681491

RESUMO

Intrinsically disordered proteins (IDPs) play crucial roles in cell functioning, although they do not possess defined three-dimensional architecture. They are highly abundant in the cell nucleus, and the vast majority of transcription factors (TFs) contain extended regions of intrinsic disorder. IDPs do not respond to denaturing conditions in a standard manner, and this can be used for their separation from structured proteins. Here we describe a protocol for the isolation and characterization of nuclear IDPs in which heat treatment is used for enrichment of IDPs in samples. The whole workflow comprises the following steps: nuclei isolation from HEK293 (human embryonic kidney) cells, protein extraction, enrichment of IDPs, sample preparation for mass spectrometric analysis, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, in silico assessment of protein disorder, and Gene Ontology analysis.


Assuntos
Núcleo Celular/fisiologia , Proteínas Intrinsicamente Desordenadas/isolamento & purificação , Espectrometria de Massas/métodos , Proteoma/fisiologia , Proteômica/métodos , Fatores de Transcrição/fisiologia , Cromatografia Líquida , Biologia Computacional/métodos , Ontologia Genética , Células HEK293 , Humanos , Proteínas Intrinsicamente Desordenadas/química , Conformação Proteica
15.
Proc Natl Acad Sci U S A ; 117(29): 17094-17103, 2020 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-32611817

RESUMO

Declining ejaculate performance with male age is taxonomically widespread and has broad fitness consequences. Ejaculate success requires fully functional germline (sperm) and soma (seminal fluid) components. However, some aging theories predict that resources should be preferentially diverted to the germline at the expense of the soma, suggesting differential impacts of aging on sperm and seminal fluid and trade-offs between them or, more broadly, between reproduction and lifespan. While harmful effects of male age on sperm are well known, we do not know how much seminal fluid deteriorates in comparison. Moreover, given the predicted trade-offs, it remains unclear whether systemic lifespan-extending interventions could ameliorate the declining performance of the ejaculate as a whole. Here, we address these problems using Drosophila melanogaster. We demonstrate that seminal fluid deterioration contributes to male reproductive decline via mating-dependent mechanisms that include posttranslational modifications to seminal proteins and altered seminal proteome composition and transfer. Additionally, we find that sperm production declines chronologically with age, invariant to mating activity such that older multiply mated males become infertile principally via reduced sperm transfer and viability. Our data, therefore, support the idea that both germline and soma components of the ejaculate contribute to male reproductive aging but reveal a mismatch in their aging patterns. Our data do not generally support the idea that the germline is prioritized over soma, at least, within the ejaculate. Moreover, we find that lifespan-extending systemic down-regulation of insulin signaling results in improved late-life ejaculate performance, indicating simultaneous amelioration of both somatic and reproductive aging.


Assuntos
Envelhecimento , Drosophila melanogaster , Proteínas de Plasma Seminal , Espermatozoides , Envelhecimento/genética , Envelhecimento/fisiologia , Animais , Drosophila melanogaster/genética , Drosophila melanogaster/fisiologia , Feminino , Fertilidade/genética , Fertilidade/fisiologia , Infertilidade Masculina/genética , Infertilidade Masculina/fisiopatologia , Masculino , Proteoma/análise , Proteoma/genética , Proteoma/fisiologia , Proteínas de Plasma Seminal/análise , Proteínas de Plasma Seminal/fisiologia , Comportamento Sexual Animal/fisiologia , Espermatozoides/química , Espermatozoides/fisiologia
16.
Mol Cell Proteomics ; 19(9): 1418-1435, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32518069

RESUMO

Synaptic transmission leading to release of neurotransmitters in the nervous system is a fast and highly dynamic process. Previously, protein interaction and phosphorylation have been thought to be the main regulators of synaptic transmission. Here we show that sialylation of N-linked glycosylation is a novel potential modulator of neurotransmitter release mechanisms by investigating depolarization-dependent changes of formerly sialylated N-linked glycopeptides. We suggest that negatively charged sialic acids can be modulated, similarly to phosphorylation, by the action of sialyltransferases and sialidases thereby changing local structure and function of membrane glycoproteins. We characterized site-specific alteration in sialylation on N-linked glycoproteins in isolated rat nerve terminals after brief depolarization using quantitative sialiomics. We identified 1965 formerly sialylated N-linked glycosites in synaptic proteins and found that the abundances of 430 glycosites changed after 5 s depolarization. We observed changes on essential synaptic proteins such as synaptic vesicle proteins, ion channels and transporters, neurotransmitter receptors and cell adhesion molecules. This study is to our knowledge the first to describe ultra-fast site-specific modulation of the sialiome after brief stimulation of a biological system.


Assuntos
Glicoproteínas de Membrana/metabolismo , Neurotransmissores/metabolismo , Nervos Periféricos/metabolismo , Proteoma/metabolismo , Ácidos Siálicos/metabolismo , Sinapses/metabolismo , Membranas Sinápticas/metabolismo , Animais , Cloratos/farmacologia , Cromatografia Líquida , Glicosídeos/metabolismo , Glicosilação , Masculino , Glicoproteínas de Membrana/química , Nervos Periféricos/enzimologia , Nervos Periféricos/fisiologia , Proteoma/química , Proteoma/efeitos dos fármacos , Proteoma/fisiologia , Proteômica , Ratos , Ratos Sprague-Dawley , Receptores de N-Metil-D-Aspartato/química , Ácidos Siálicos/química , Transdução de Sinais/efeitos dos fármacos , Transdução de Sinais/fisiologia , Sinapses/química , Sinapses/efeitos dos fármacos , Sinapses/fisiologia , Membranas Sinápticas/efeitos dos fármacos , Membranas Sinápticas/enzimologia , Espectrometria de Massas em Tandem
17.
Integr Comp Biol ; 60(2): 304-317, 2020 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-32458981

RESUMO

The gill proteome of threespine sticklebacks (Gasterosteus aculeatus) differs greatly in populations that inhabit diverse environments characterized by different temperature, salinity, food availability, parasites, and other parameters. To assess the contribution of a specific environmental parameter to such differences it is necessary to isolate its effects from those of other parameters. In this study the effect of environmental salinity on the gill proteome of G. aculeatus was isolated in controlled mesocosm experiments. Salinity-dependent changes in the gill proteome were analyzed by Liquid chromatography/Tandem mass spectrometry data-independent acquisition (DIA) and Skyline. Relative abundances of 1691 proteins representing the molecular phenotype of stickleback gills were quantified using previously developed MSMS spectral and assay libraries in combination with DIA quantitative proteomics. Non-directional stress responses were distinguished from osmoregulatory protein abundance changes by their consistent occurrence during both hypo- and hyper-osmotic salinity stress in six separate mesocosm experiments. If the abundance of a protein was consistently regulated in opposite directions by hyper- versus hypo-osmotic salinity stress, then it was considered an osmoregulatory protein. In contrast, if protein abundance was consistently increased irrespective of whether salinity was increased or decreased, then it was considered a non-directional response protein. KEGG pathway analysis revealed that the salivary secretion, inositol phosphate metabolism, valine, leucine, and isoleucine degradation, citrate cycle, oxidative phosphorylation, and corresponding endocrine and extracellular signaling pathways contain most of the osmoregulatory gill proteins whose abundance is directly proportional to environmental salinity. Most proteins that were inversely correlated with salinity map to KEGG pathways that represent proteostasis, immunity, and related intracellular signaling processes. Non-directional stress response proteins represent fatty and amino acid degradation, purine metabolism, focal adhesion, mRNA surveillance, phagosome, endocytosis, and associated intracellular signaling KEGG pathways. These results demonstrate that G. aculeatus responds to salinity changes by adjusting osmoregulatory mechanisms that are distinct from transient non-directional stress responses to control compatible osmolyte synthesis, transepithelial ion transport, and oxidative energy metabolism. Furthermore, this study establishes salinity as a key factor for causing the regulation of numerous proteins and KEGG pathways with established functions in proteostasis, immunity, and tissue remodeling. We conclude that the corresponding osmoregulatory gill proteins and KEGG pathways represent molecular phenotypes that promote transepithelial ion transport, cellular osmoregulation, and gill epithelial remodeling to adjust gill function to environmental salinity.


Assuntos
Proteínas de Peixes/fisiologia , Brânquias/fisiologia , Osmorregulação , Proteoma/fisiologia , Smegmamorpha/fisiologia , Animais , Proteômica
18.
Dev Neurobiol ; 80(3-4): 98-110, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32267608

RESUMO

Muller glia are the predominant glial cell type in the retina, and they structurally and metabolically support retinal neurons. Wnt/ß-catenin signaling pathways play essential roles in the central nervous system, including glial and neuronal differentiation, axonal growth, and neuronal regeneration. We previously demonstrated that Wnt signaling activation in retinal ganglion cells (RGC) induces axonal regeneration after injury. However, whether Wnt signaling within the adjacent Muller glia plays an axongenic role is not known. In this study, we characterized the effect of Wnt signaling in Muller glia on RGC neurite growth. Primary Muller glia and RGC cells were grown in transwell co-cultures and adenoviral constructs driving Wnt regulatory genes were used to activate and inhibit Wnt signaling specifically in primary Muller glia. Our results demonstrated that activation of Wnt signaling in Muller glia significantly increased RGC average neurite length and branch site number. In addition, the secretome of Muller glia after induction or inhibition of Wnt signaling was characterized using protein profiling of conditioned media by Q Exactive mass spectrometry. The Muller glia secretome after activation of Wnt signaling had distinct and more numerous proteins involved in regulation of axon extension, axon projection and cell adhesion. Furthermore, we showed highly redundant expression of Wnt signaling ligands in Muller glia and Frizzled receptors in RGCs and Muller glia. Therefore, this study provides new information about potential neurite growth promoting molecules in the Muller glia secretome, and identified Wnt-dependent target proteins that may mediate the axonal growth.


Assuntos
Neuritos/fisiologia , Neuroglia/fisiologia , Proteoma/fisiologia , Células Ganglionares da Retina/fisiologia , Proteínas Wnt/metabolismo , Via de Sinalização Wnt/fisiologia , Animais , Feminino , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Neuritos/metabolismo , Neuroglia/metabolismo , Proteoma/metabolismo , Células Ganglionares da Retina/metabolismo
19.
Exp Cell Res ; 392(1): 111997, 2020 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-32302626

RESUMO

Recent findings have revealed that many genomic regions previously annotated as non-protein coding actually contain small open reading frames, smaller that 300 bp, that are transcribed and translated into evolutionary conserved microproteins. To date, only a small subset of them have been functionally characterized, but they play key functions in fundamental processes such as DNA repair, RNA processing and metabolism regulation. This emergent field seems to hide a new category of molecular regulators with clinical potential. In this review, we focus on its relevance for cancer. Following Hanahan and Weinberg's classification of the hallmarks of cancer, we provide an overview of those microproteins known to be implicated in cancer or those that, based on their function, are likely to play a role in cancer. The resulting picture is that while we are at the very early times of this field, it holds the promise to provide crucial information to understand cancer biology.


Assuntos
Proteínas de Neoplasias/fisiologia , Neoplasias/metabolismo , Fragmentos de Peptídeos/fisiologia , Proteoma/fisiologia , Sequência de Aminoácidos , Transformação Celular Neoplásica/genética , Transformação Celular Neoplásica/metabolismo , Genômica/métodos , Genômica/tendências , Humanos , Oncologia/métodos , Oncologia/tendências , Proteínas de Neoplasias/química , Neoplasias/genética , Fases de Leitura Aberta , Fragmentos de Peptídeos/química , Processamento de Proteína Pós-Traducional/fisiologia , Proteoma/análise
20.
Science ; 367(6479): 800-806, 2020 02 14.
Artigo em Inglês | MEDLINE | ID: mdl-32054765

RESUMO

Circadian (~24 hour) clocks have a fundamental role in regulating daily physiology. The transcription factor BMAL1 is a principal driver of a molecular clock in mammals. Bmal1 deletion abolishes 24-hour activity patterning, one measure of clock output. We determined whether Bmal1 function is necessary for daily molecular oscillations in skin fibroblasts and liver slices. Unexpectedly, in Bmal1 knockout mice, both tissues exhibited 24-hour oscillations of the transcriptome, proteome, and phosphoproteome over 2 to 3 days in the absence of any exogenous drivers such as daily light or temperature cycles. This demonstrates a competent 24-hour molecular pacemaker in Bmal1 knockouts. We suggest that such oscillations might be underpinned by transcriptional regulation by the recruitment of ETS family transcription factors, and nontranscriptionally by co-opting redox oscillations.


Assuntos
Fatores de Transcrição ARNTL/genética , Fatores de Transcrição ARNTL/fisiologia , Relógios Circadianos/genética , Ritmo Circadiano/genética , Fígado/fisiologia , Fenômenos Fisiológicos da Pele , Animais , Fibroblastos/metabolismo , Fibroblastos/fisiologia , Deleção de Genes , Regulação da Expressão Gênica , Fígado/metabolismo , Camundongos , Camundongos Knockout , Fosfoproteínas/metabolismo , Proteoma/metabolismo , Proteoma/fisiologia , Transcrição Genética , Transcriptoma/fisiologia
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