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1.
Nucleic Acids Res ; 52(D1): D67-D71, 2024 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-37971299

RESUMO

The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) provides database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), DDBJ accepts and distributes nucleotide sequence data as well as their study and sample information along with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute (EBI). Besides INSDC databases, the DDBJ Center provides databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank) and human genetic and phenotypic data (JGA: Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics (NIG) supercomputer, which is also open for domestic life science researchers to analyze large-scale sequence data. This paper reports recent updates on the archival databases and the services of the DDBJ Center, highlighting the newly redesigned MetaboBank. MetaboBank uses BioProject and BioSample in its metadata description making it suitable for multi-omics large studies. Its collaboration with MetaboLights at EBI brings synergy in locating and reusing public data.


Assuntos
Bases de Dados de Ácidos Nucleicos , Metabolômica , Metadados , Humanos , Biologia Computacional , Genômica , Internet , Japão , Multiômica/métodos
2.
FASEB J ; 38(1): e23391, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-38145327

RESUMO

Adipocytes play a key role in energy storage and homeostasis. Although the role of transcription factors in adipocyte differentiation is known, the effect of endogenous metabolites of low molecular weight remains unclear. Here, we analyzed time-dependent changes in the levels of these metabolites throughout adipocyte differentiation, using metabolome analysis, and demonstrated that there is a positive correlation between cyclic adenosine diphosphate ribose (cADPR) and Pparγ mRNA expression used as a marker of differentiation. We also found that the treatment of C3H10T1/2 adipocytes with cADPR increased the mRNA expression of those marker genes and the accumulation of triglycerides. Furthermore, inhibition of ryanodine receptors (RyR), which are activated by cADPR, caused a significant reduction in mRNA expression levels of the marker genes and triglyceride accumulation in adipocytes. Our findings show that cADPR accelerates adipocytic differentiation via RyR pathway.


Assuntos
Adipócitos , ADP-Ribose Cíclica , Camundongos , Animais , ADP-Ribose Cíclica/metabolismo , Adipócitos/metabolismo , Fatores de Transcrição/metabolismo , PPAR gama/metabolismo , Metaboloma , RNA Mensageiro/genética , Diferenciação Celular , Adenosina Difosfato Ribose/metabolismo , Adenosina Difosfato Ribose/farmacologia , Adipogenia/genética , Células 3T3-L1
3.
J Biol Chem ; 298(10): 102456, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-36063990

RESUMO

Adipocyte browning is one of the potential strategies for the prevention of obesity-related metabolic syndromes, but it is a complex process. Although previous studies make it increasingly clear that several transcription factors and enzymes are essential to induce browning, it is unclear what dynamic and metabolic changes occur in induction of browning. Here, we analyzed the effect of a beta-adrenergic receptor agonist (CL316243, accelerator of browning) on metabolic change in mice adipose tissue and plasma using metabolome analysis and speculated that browning is regulated partly by inosine 5'-monophosphate (IMP) metabolism. To test this hypothesis, we investigated whether Ucp-1, a functional marker of browning, mRNA expression is influenced by IMP metabolism using immortalized adipocytes. Our study showed that mycophenolic acid, an IMP dehydrogenase inhibitor, increases the mRNA expression of Ucp-1 in immortalized adipocytes. Furthermore, we performed a single administration of mycophenolate mofetil, a prodrug of mycophenolic acid, to mice and demonstrated that mycophenolate mofetil induces adipocyte browning and miniaturization of adipocyte size, leading to adipose tissue weight loss. These findings showed that IMP metabolism has a significant effect on adipocyte browning, suggesting that the regulator of IMP metabolism has the potential to prevent obesity.


Assuntos
Adipócitos , Inosina Monofosfato , Ácido Micofenólico , Animais , Camundongos , Adipócitos/efeitos dos fármacos , Adipócitos/metabolismo , Tecido Adiposo Marrom/metabolismo , Tecido Adiposo Branco/metabolismo , Inosina Monofosfato/metabolismo , Metabolômica , Camundongos Endogâmicos C57BL , Ácido Micofenólico/farmacologia , Ácido Micofenólico/metabolismo , Obesidade/metabolismo , RNA Mensageiro/metabolismo
4.
Biosci Biotechnol Biochem ; 85(5): 1194-1204, 2021 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-33704369

RESUMO

Papaya (Carica papaya L.) is widely cultivated in tropical and subtropical countries. While ripe fruit is a popular food item globally, the unripe fruit is only consumed in some Asian countries. To promote the utilization of unripe papaya based on the compositional changes of biological active metabolites, we performed liquid chromatography-Orbitrap-mass spectrometry-based analysis to reveal the comprehensive metabolite profile of the peel and pulp of unripe and ripe papaya fruits. The number of peaks annotated as phenolics and aminocarboxylic acids increased in the pulp and peel of ripe fruit, respectively. Putative carpaine derivatives, known alkaloids with cardiovascular effects, decreased, while carpamic acid derivatives increased in the peel of ripe fruit. Furthermore, the functionality of unripe fruit, the benzyl glucosinolate content, total polyphenol content, and proteolytic activity were detectable after heating and powder processing treatments, suggesting a potential utilization in powdered form as functional material.


Assuntos
Alcaloides/metabolismo , Ácidos Carboxílicos/metabolismo , Carica/metabolismo , Glucosinolatos/metabolismo , Redes e Vias Metabólicas/fisiologia , Polifenóis/metabolismo , Alcaloides/química , Alcaloides/classificação , Alcaloides/isolamento & purificação , Ácidos Carboxílicos/química , Ácidos Carboxílicos/classificação , Ácidos Carboxílicos/isolamento & purificação , Carica/química , Cromatografia Líquida , Culinária/métodos , Frutas/química , Frutas/metabolismo , Alimento Funcional/análise , Glucosinolatos/química , Glucosinolatos/classificação , Glucosinolatos/isolamento & purificação , Humanos , Extratos Vegetais/química , Polifenóis/química , Polifenóis/classificação , Polifenóis/isolamento & purificação , Análise de Componente Principal , Espectrometria de Massas em Tandem
5.
Plant Cell Physiol ; 61(2): 276-282, 2020 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-31593237

RESUMO

For carotenogenesis, two biosynthetic pathways from phytoene to lycopene are known. Most bacteria and fungi require only phytoene desaturase (PDS, CrtI), whereas land plants require four enzymes: PDS (CrtP), ζ-carotene desaturase (ZDS, CrtQ), ζ-carotene isomerase (Z-ISO) and cis-carotene isomerase (CrtISO, CrtH). The gene encoding Z-ISO has been functionally identified in only two species, Arabidopsis thaliana and Zea mays, and has been little studied in other organisms. In this study, we found that the deduced amino acid sequences of Arthrospira Z-ISO and Euglena Z-ISO have 58% and 62% identity, respectively, with functional Z-ISO from Arabidopsis. We studied the function of Z-ISO genes from the cyanobacterium Arthrospira platensis and eukaryotic microalga Euglena gracilis. The Z-ISO genes of Arthrospira and Euglena were transformed into Escherichia coli strains that produced mainly 9,15,9'-tri-cis-ζ-carotene in darkness. In the resulting E. coli transformants cultured under darkness, 9,9'-di-cis-ζ-carotene was accumulated predominantly as Z-ISO in Arabidopsis. This indicates that the Z-ISO genes were involved in the isomerization of 9,15,9'-tri-cis-ζ-carotene to 9,9'-di-cis-ζ-carotene in darkness. This is the first functional analysis of Z-ISO as a ζ-carotene isomerase in cyanobacteria and eukaryotic microalgae. Green sulfur bacteria and Chloracidobacterium also use CrtP, CrtQ and CrtH for lycopene synthesis as cyanobacteria, but their genomes did not comprise Z-ISO genes. Consequently, Z-ISO is needed in oxygenic phototrophs, whereas it is not found in anoxygenic species.


Assuntos
Carotenoides/metabolismo , Euglena/metabolismo , Oxigênio/metabolismo , Spirulina/metabolismo , cis-trans-Isomerases/metabolismo , Acidobacteria/enzimologia , Acidobacteria/genética , Arabidopsis/enzimologia , Arabidopsis/genética , Proteínas de Arabidopsis , Bactérias/enzimologia , Bactérias/genética , Vias Biossintéticas/genética , Clonagem Molecular , Escherichia coli/genética , Euglena/enzimologia , Euglena/genética , Filogenia , Análise de Sequência de Proteína , Spirulina/enzimologia , Spirulina/genética , Zea mays/embriologia , Zea mays/genética , cis-trans-Isomerases/classificação , cis-trans-Isomerases/genética , zeta Caroteno/metabolismo
6.
Biosci Biotechnol Biochem ; 83(9): 1782-1789, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31045477

RESUMO

Activation of the adipose lipolytic pathway during lipid metabolism is mediated by protein kinase A (PKA), which responds to ß-adrenergic stimulation, leading to increased lipolysis. Soy is well known as a functional food and it is able to affect lipolysis in adipocytes. However, the mechanism by which soy components contribute to the lipolytic pathway remains to be fully elucidated. Here, we show that hydrolyzed soy enhances isoproterenol-stimulated lipolysis and activation of PKA in 3T3-L1 adipocytes. We also found that the expression of ß-adrenergic receptors, which coordinate the activation of PKA, is elevated in adipocytes differentiated in the presence of soy hydrolysate. The activity of the soy hydrolysate towards ß-adrenergic receptor expression was detected in its hydrophilic fraction. Our results suggest that the soy hydrolysate enhances the PKA pathway through the upregulation of ß-adrenergic receptor expression and thereby, increase lipolysis in adipocytes.


Assuntos
Adipócitos/metabolismo , Agonistas Adrenérgicos beta/farmacologia , Glycine max/metabolismo , Isoproterenol/farmacologia , Lipólise/efeitos dos fármacos , Receptores Adrenérgicos beta/metabolismo , Células 3T3-L1 , Animais , Cromatografia Líquida de Alta Pressão/métodos , Proteínas Quinases Dependentes de AMP Cíclico/metabolismo , Hidrólise , Camundongos
7.
Int J Mol Sci ; 20(2)2019 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-30641938

RESUMO

Endoplasmic reticulum (ER) homeostasis is critical in maintaining metabolic regulation. Once it is disrupted due to accumulated unfolded proteins, ER homeostasis is restored via activation of the unfolded protein response (UPR); hence, the UPR affects diverse physiological processes. However, how ER stress influences adipocyte functions is not well known. In this study, we investigated the effect of ER stress in thermogenic capacity of mice beige adipocytes. Here, we show that the expression of uncoupling protein 1 (Ucp1) involved in thermoregulation is severely suppressed under ER stress conditions (afflicted by tunicamycin) in inguinal white adipose tissue (IWAT) both in vitro and in vivo. Further investigation showed that extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK) were both activated after ER stress stimulation and regulated the mRNA levels of Ucp1 and peroxisome proliferator-activated receptor γ (Pparγ), which is known as a Ucp1 transcriptional activator, in vitro and ex vivo. We also found that Pparγ protein was significantly degraded, reducing its recruitment to the Ucp1 enhancer, thereby downregulating Ucp1 expression. Additionally, only JNK inhibition, but not ERK, rescued the Pparγ protein. These findings provide novel insights into the regulatory effect of ER stress on Ucp1 expression via Pparγ suppression in beige adipocytes.


Assuntos
Adipócitos Bege/metabolismo , Estresse do Retículo Endoplasmático , PPAR gama/genética , PPAR gama/metabolismo , Proteína Desacopladora 1/genética , Adipócitos Bege/citologia , Animais , Células Cultivadas , MAP Quinases Reguladas por Sinal Extracelular/metabolismo , Proteínas Quinases JNK Ativadas por Mitógeno/metabolismo , Masculino , Camundongos , Ligação Proteica , Proteólise , Tunicamicina/farmacologia , Proteína Desacopladora 1/metabolismo , Resposta a Proteínas não Dobradas
8.
Int J Mol Sci ; 19(8)2018 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-30126161

RESUMO

Browning of adipose tissue has been prescribed as a potential way to treat obesity, marked by the upregulation of uncoupling protein 1 (Ucp1). Several reports have suggested that histone deacetylase (HDAC) might regulate Ucp1 by remodelling chromatin structure, although the mechanism remains unclear. Herein, we investigate the effect of ß-adrenergic receptor (ß-AR) activation on the chromatin state of beige adipocyte. ß-AR-stimulated Ucp1 expression via cold (in vivo) and isoproterenol (in vitro) resulted in acetylation of histone activation mark H3K27. H3K27 acetylation was also seen within Ucp1 promoter upon isoproterenol addition, favouring open chromatin for Ucp1 transcriptional activation. This result was found to be associated with the downregulation of class I HDAC mRNA, particularly Hdac3 and Hdac8. Further investigation showed that although HDAC8 activity decreased, Ucp1 expression was not altered when HDAC8 was activated or inhibited. In contrast, HDAC3 mRNA and protein levels were simultaneously downregulated upon isoproterenol addition, resulting in reduced recruitment of HDAC3 to the Ucp1 enhancer region, causing an increased H3K27 acetylation for Ucp1 upregulation. The importance of HDAC3 inhibition was confirmed through the enhanced Ucp1 expression when the cells were treated with HDAC3 inhibitor. This study highlights the novel mechanism of HDAC3-regulated Ucp1 expression during ß-AR stimulation.


Assuntos
Adipócitos Bege/metabolismo , Histona Desacetilases/metabolismo , Receptores Adrenérgicos beta/metabolismo , Transdução de Sinais , Proteína Desacopladora 1/genética , Regulação para Cima , Acetilação , Adipócitos Bege/citologia , Animais , Regulação para Baixo , Histona Desacetilases/genética , Histonas/metabolismo , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Regiões Promotoras Genéticas , Ativação Transcricional
9.
Biochem Biophys Res Commun ; 493(1): 108-114, 2017 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-28919422

RESUMO

Peroxisome proliferator-activated receptor α (PPARα) is important in the regulation of lipid metabolism and expressed at high levels in the liver. Although PPARα is also expressed in adipose tissue, little is known about the relationship between its activation and the regulation of glucose metabolism. In this study, we developed adipose tissue specific PPARα over-expression (OE) mice. Metabolomics and insulin tolerance tests showed that OE induces branched-chain amino acid (BCAA) profile and improvement of insulin sensitivity. Furthermore, LC-MS and PCR analyses revealed that OE changes free fatty acid (FFA) profile and reduces obesity-induced inflammation. These findings suggested that PPARα activation in adipose tissue contributes to the improvement of glucose metabolism disorders via the enhancement of BCAA and FFA metabolism.


Assuntos
Tecido Adiposo/metabolismo , Glicemia/metabolismo , Ácidos Graxos não Esterificados/metabolismo , Resistência à Insulina , Insulina/metabolismo , Obesidade/metabolismo , PPAR alfa/metabolismo , Animais , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Regulação para Cima
10.
Bioinformatics ; 29(2): 290-1, 2013 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-23162084

RESUMO

SUMMARY: High-accuracy mass values detected by high-resolution mass spectrometry analysis enable prediction of elemental compositions, and thus are used for metabolite annotations in metabolomic studies. Here, we report an application of a relational database to significantly improve the rate of elemental composition predictions. By searching a database of pre-calculated elemental compositions with fixed kinds and numbers of atoms, the approach eliminates redundant evaluations of the same formula that occur in repeated calculations with other tools. When our approach is compared with HR2, which is one of the fastest tools available, our database search times were at least 109 times shorter than those of HR2. When a solid-state drive (SSD) was applied, the search time was 488 times shorter at 5 ppm mass tolerance and 1833 times at 0.1 ppm. Even if the search by HR2 was performed with 8 threads in a high-spec Windows 7 PC, the database search times were at least 26 and 115 times shorter without and with the SSD. These improvements were enhanced in a low spec Windows XP PC. We constructed a web service 'MFSearcher' to query the database in a RESTful manner. AVAILABILITY AND IMPLEMENTATION: Available for free at http://webs2.kazusa.or.jp/mfsearcher. The web service is implemented in Java, MySQL, Apache and Tomcat, with all major browsers supported. CONTACT: sakurai@kazusa.or.jp SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Bases de Dados de Compostos Químicos , Espectrometria de Massas/métodos , Metabolômica/métodos , Algoritmos
11.
Nucleic Acids Res ; 39(Database issue): D677-84, 2011 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-21097783

RESUMO

Correlations of gene-to-gene co-expression and metabolite-to-metabolite co-accumulation calculated from large amounts of transcriptome and metabolome data are useful for uncovering unknown functions of genes, functional diversities of gene family members and regulatory mechanisms of metabolic pathway flows. Many databases and tools are available to interpret quantitative transcriptome and metabolome data, but there are only limited ones that connect correlation data to biological knowledge and can be utilized to find biological significance of it. We report here a new metabolic pathway database, KaPPA-View4 (http://kpv.kazusa.or.jp/kpv4/), which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. This representation would help to discover, for example, novel functions of a transcription factor that regulates genes on a metabolic pathway. Pathway maps of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and maps generated from their gene classifications are available at KaPPA-View4 KEGG version (http://kpv.kazusa.or.jp/kpv4-kegg/). At present, gene co-expression data from the databases ATTED-II, COXPRESdb, CoP and MiBASE for human, mouse, rat, Arabidopsis, rice, tomato and other plants are available.


Assuntos
Bases de Dados Genéticas , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Redes e Vias Metabólicas/genética , Metaboloma/genética , Animais , Humanos , Internet , Camundongos , Ratos
12.
PLoS One ; 17(7): e0267248, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35776737

RESUMO

Adiponectin, an adipokine, regulates glucose metabolism and insulin sensitivity through the adiponectin receptor (AdipoR). In this study, we searched for metabolites that activate the adiponectin signaling pathway from tomato (Solanum lycopersicu). Metabolites of mature tomato were separated into 55 fractions by liquid chromatography, and then each fraction was examined using the phosphorylation assay of AMP-protein kinase (AMPK) in C2C12 myotubes and in AdipoR-knockdown cells by small interfering RNA (siRNA). Several fractions showed AMPK phosphorylation in C2C12 myotubes and siRNA-mediated abrogation of the effect. Non-targeted metabolite analysis revealed the presence of 721 diverse metabolites in tomato. By integrating the activity of fractions on AMPK phosphorylation and the 721 metabolites based on their retention times of liquid chromatography, we performed a comprehensive screen for metabolites that possess adiponectin-like activity. As the screening suggested that the active fractions contained four carotenoids, we further analyzed ß-carotene and lycopene, the major carotenoids of food. They induced AMPK phosphorylation via the AdipoR, Ca2+/calmodulin-dependent protein kinase kinase and Ca2+ influx, in addition to activating glucose uptake via AdipoR in C2C12 myotubes. All these events were characteristic adiponectin actions. These results indicated that the food-derived carotenoids, ß-carotene and lycopene, activate the adiponectin signaling pathway, including AMPK phosphorylation.


Assuntos
Adiponectina , Solanum lycopersicum , Proteínas Quinases Ativadas por AMP/metabolismo , Adenilato Quinase/metabolismo , Adiponectina/metabolismo , Bioensaio , Cálcio/metabolismo , Licopeno/metabolismo , Solanum lycopersicum/genética , Fosforilação , RNA Interferente Pequeno/metabolismo , Receptores de Adiponectina/metabolismo , Transdução de Sinais , beta Caroteno/metabolismo
13.
Plant Biotechnol (Tokyo) ; 38(1): 167-171, 2021 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-34177338

RESUMO

Depository of low-molecular-weight compounds or metabolites detected in various organisms in a non-targeted manner is indispensable for metabolomics research. Due to the diverse chemical compounds, various mass spectrometry (MS) setups with state-of-the-art technologies have been used. Over the past two decades, we have analyzed various biological samples by using gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, or capillary electrophoresis-mass spectrometry, and archived the datasets in the depository MassBase (http://webs2.kazusa.or.jp/massbase/). As the format of MS datasets depends on the MS setup used, we converted each raw binary dataset of the mass chromatogram to text file format, and thereafter, information of the chromatograph peak was extracted in the text file from the converted file. In total, the depository comprises 46,493 datasets, of which 38,750 belong to the plant species and 7,743 are authentic or mixed chemicals as well as other sources (microorganisms, animals, and foods), as on August 1, 2020. All files in the depository can be downloaded in bulk from the website. Mass chromatograms of 90 plant species obtained by LC-Fourier transform ion cyclotron resonance MS or Orbitrap MS, which detect the ionized molecules with high accuracy allowing speculation of chemical compositions, were converted to text files by the software PowerGet, and the chemical annotation of each peak was added. The processed datasets were deposited in the annotation database KomicMarket2 (http://webs2.kazusa.or.jp/km2/). The archives provide fundamental resources for comparative metabolomics and functional genomics, which may result in deeper understanding of living organisms.

14.
Plant Direct ; 5(4): e00318, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33969254

RESUMO

The total number of low-molecular-weight compounds in the plant kingdom, most of which are secondary metabolites, is hypothesized to be over one million, although only a limited number of plant compounds have been characterized. Untargeted analysis, especially using mass spectrometry (MS), has been useful for understanding the plant metabolome; however, due to the limited availability of authentic compounds for MS-based identification, the identities of most of the ion peaks detected by MS remain unknown. Accurate mass values of peaks obtained by high accuracy mass measurement and, if available, MS/MS fragmentation patterns provide abundant annotation for each peak. Here, we carried out an untargeted analysis of compounds in the mature fruit of 25 tomato cultivars using liquid chromatography-Orbitrap MS for accurate mass measurement, followed by manual curation to construct the metabolome database TOMATOMET (http://metabolites.in/tomato-fruits/). The database contains 7,118 peaks with accurate mass values, in which 1,577 ion peaks are annotated as members of a chemical group. Remarkably, 71% of the mass values are not found in the accurate masses detected previously in Arabidopsis thaliana, Medicago truncatula or Jatropha curcas, indicating significant chemical diversity among plant species that remains to be solved. Interestingly, substantial chemical diversity exists also among tomato cultivars, indicating that chemical profiling from distinct cultivars contributes towards understanding the metabolome, even in a single organ of a species, and can prioritize some desirable metabolic targets for further applications such as breeding.

15.
Mol Biol Evol ; 26(2): 327-34, 2009 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-18984903

RESUMO

Of the 1.1 million Alu retroposons in the human genome, about 10,000 are inserted in the 3' untranslated regions (UTR) of protein-coding genes and 1% of these (107 events) are active as polyadenylation sites (PASs). Strikingly, although Alu's in 3' UTR are indifferently inserted in the forward or reverse direction, 99% of polyadenylation-active Alu sequences are forward oriented. Consensus Alu+ sequences contain sites that can give rise to polyadenylation signals and enhancers through a few point mutations. We found that the strand bias of polyadenylation-active Alu's reflects a radical difference in the fitness of sense and antisense Alu's toward cleavage/polyadenylation activity. In contrast to previous beliefs, Alu inserts do not necessarily represent weak or cryptic PASs; instead, they often constitute the major or the unique PAS in a gene, adding to the growing list of Alu exaptations. Finally, some Alu-borne PASs are intronic and produce truncated transcripts that may impact gene function and/or contribute to gene remodeling.


Assuntos
Elementos Alu , Poliadenilação , Animais , Sequência de Bases , Elementos Facilitadores Genéticos , Humanos , Camundongos , Dados de Sequência Molecular , Sítios de Splice de RNA
16.
Genomics ; 93(3): 213-20, 2009 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-19059335

RESUMO

The Alternative Splicing and Transcript Diversity database (ASTD) gives access to a vast collection of alternative transcripts that integrate transcription initiation, polyadenylation and splicing variant data. Alternative transcripts are derived from the mapping of transcribed sequences to the complete human, mouse and rat genomes using an extension of the computational pipeline developed for the ASD (Alternative Splicing Database) and ATD (Alternative Transcript Diversity) databases, which are now superseded by ASTD. For the human genome, ASTD identifies splicing variants, transcription initiation variants and polyadenylation variants in 68%, 68% and 62% of the gene set, respectively, consistent with current estimates for transcription variation. Users can access ASTD through a variety of browsing and query tools, including expression state-based queries for the identification of tissue-specific isoforms. Participating laboratories have experimentally validated a subset of ASTD-predicted alternative splice forms and alternative polyadenylation forms that were not previously reported. The ASTD database can be accessed at http://www.ebi.ac.uk/astd.


Assuntos
Processamento Alternativo/genética , Bases de Dados Genéticas , Animais , Sistemas de Gerenciamento de Base de Dados , Humanos , Armazenamento e Recuperação da Informação/métodos , Camundongos , Ratos , Reprodutibilidade dos Testes , Software , Interface Usuário-Computador
17.
Plant Biotechnol (Tokyo) ; 37(3): 377-381, 2020 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-33088205

RESUMO

The model land plant Physcomitrella patens synthesizes flavonoids which may act as protectant of ultraviolet-B radiation. We aimed to uncover its flavonoid profile, for which metabolome analysis using liquid chromatography coupled with Ion trap/Orbitrap mass spectrometry was performed. From the 80% methanol extracts, 661 valid peaks were detected. Prediction of the elemental compositions within a mass accuracy of 2 ppm indicated that 217 peaks had single elemental composition. A compound database search revealed 47 peaks to be annotated as secondary metabolites based on the compound database search. Comprehensive substituent search by ShiftedIonsFinder showed there were 13 peaks of potential flavonoid derivatives. Interestingly, a peak having m/z 287.0551, corresponding to that of luteolin, was detected, even though flavone synthase has never been identified in P. patens. Using P. patens labeled with stable isotopes (13C-, 15N-, 18O-, and 34S), we confirmed the elemental composition of the peak as C15H10O6. By a comparison of MS/MS spectra with that of authentic standard, the peak was identified as luteolin or related flavone isomers. This is the first report of luteolin or related flavones synthesis and the possibility of the existence of an unknown enzyme with flavone synthase activity in P. patens.

18.
Plant Biotechnol (Tokyo) ; 37(3): 383-387, 2020 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-33088206

RESUMO

Metabolome analysis of flavored vegetables, green spring onion (Allium fistulosum), Chinese chive (A. tuberosum), and their interspecies hybrid Negi-Nira chive, was conducted using liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry, with ca. 2 ppm mass accuracy. Ion peaks in the chromatograms of four biological replicates of the vegetable leaves were processed using the alignment software PowerGet for metabolite comparison, from which we obtained the potential chemical formulae. In total, 860 ion peaks were reproducibly detected; of these, 506, 525, and 336 peaks were found in the hybrid, A. tuberosum, and A. fistulosum, respectively. There were 130 peaks specific to the hybrid; from these, 31 metabolites were annotated by searching compound databases. The sulfur-containing compounds and flavonoids were further analyzed using bioinformatics, to examine the sulfur metabolism of Allium volatiles and the flavonoid pathways in these species. In conclusion, our metabolome analysis of this interspecies hybrid and its parents provides a unique opportunity to elucidate their metabolic background.

19.
Nucleic Acids Res ; 35(6): 1947-57, 2007.
Artigo em Inglês | MEDLINE | ID: mdl-17339231

RESUMO

High throughput EST and full-length cDNA sequencing have revealed extensive variations at the 3' ends of mammalian transcripts. Whether all of these changes are biologically meaningful has been the subject of controversy, as such, results may reflect in part transcription or polyadenylation leakage. We selected here a set of tandem poly(A) sites predicted from EST/cDNA sequence analysis that (i) are conserved between human and mouse, (ii) produce alternative 3' isoforms with unusual size features and (iii) are not documented in current genome databases, and we submitted these sites to experimental validation in mouse tissues. Out of 86 tested poly(A) sites from 44 genes, 84 were individually confirmed using a specially devised RT-PCR strategy. We then focused on validating the exon structure between distant tandem poly(A) sites separated by over 3 kb, and between stop codons and alternative poly(A) sites located at 4.5 kb or more, using a long-distance RT-PCR strategy. In most cases, long transcripts spanning the whole poly(A)-poly(A) or stop-poly(A) distance were detected, confirming that tandem sites were part of the same transcription unit. Given the apparent conservation of these long alternative 3' ends, different regulatory functions can be foreseen, depending on the location where transcription starts.


Assuntos
Regiões 3' não Traduzidas/química , Poli A/análise , Animais , Sequência de Bases , Células Cultivadas , Sequência Conservada , DNA Complementar/química , Bases de Dados de Ácidos Nucleicos , Etiquetas de Sequências Expressas/química , Humanos , Camundongos , Camundongos Endogâmicos BALB C , Poliadenilação , Isoformas de Proteínas/biossíntese , Isoformas de Proteínas/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa
20.
FEBS Lett ; 593(11): 1201-1212, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31074834

RESUMO

Mitochondrial uncoupling protein 1 (UCP1) is well known for its thermogenic function in brown adipose tissue (BAT). Since UCP1 expends energy on thermogenesis, UCP1 activation has been considered an approach to ameliorate obesity. As a tool for uncovering yet unknown mechanisms of UCP1 activation, we generated a transgenic mouse model in which UCP1 expression levels are reflected in fluorescence derived from monomeric red fluorescent protein 1 (mRFP1). In these UCP1-mRFP1 BAC transgenic mice, fluorescence intensity mimics the change in UCP1 expression levels evoked through physiological or pharmacological stimulation. This transgenic mouse model will be useful in the search for bioactive compounds with the ability to induce UCP1 and for revealing undiscovered mechanisms of BAT activation.


Assuntos
Proteínas Luminescentes/metabolismo , Mitocôndrias/metabolismo , Imagem Óptica/métodos , Proteína Desacopladora 1/metabolismo , Tecido Adiposo Marrom/metabolismo , Animais , Cromossomos Artificiais Bacterianos/genética , Fluorescência , Genes Reporter , Proteínas Luminescentes/genética , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteína Desacopladora 1/genética , Proteína Vermelha Fluorescente
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