Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 28
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
Front Immunol ; 12: 709986, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34512630

RESUMO

Background: Nowadays, researchers are leveraging the mRNA-based vaccine technology used to develop personalized immunotherapy for cancer. However, its application against glioma is still in its infancy. In this study, the applicable candidates were excavated for mRNA vaccine treatment in the perspective of immune regulation, and suitable glioma recipients with corresponding immune subtypes were further investigated. Methods: The RNA-seq data and clinical information of 702 and 325 patients were recruited from TCGA and CGGA, separately. The genetic alteration profile was visualized and compared by cBioPortal. Then, we explored prognostic outcomes and immune correlations of the selected antigens to validate their clinical relevance. The prognostic index was measured via GEPIA2, and infiltration of antigen-presenting cells (APCs) was calculated and visualized by TIMER. Based on immune-related gene expression, immune subtypes of glioma were identified using consensus clustering analysis. Moreover, the immune landscape was visualized by graph learning-based dimensionality reduction analysis. Results: Four glioma antigens, namely ANXA5, FKBP10, MSN, and PYGL, associated with superior prognoses and infiltration of APCs were selected. Three immune subtypes IS1-IS3 were identified, which fundamentally differed in molecular, cellular, and clinical signatures. Patients in subtypes IS2 and IS3 carried immunologically cold phenotypes, whereas those in IS1 carried immunologically hot phenotype. Particularly, patients in subtypes IS3 and IS2 demonstrated better outcomes than that in IS1. Expression profiles of immune checkpoints and immunogenic cell death (ICD) modulators showed a difference among IS1-IS3 tumors. Ultimately, the immune landscape of glioma elucidated considerable heterogeneity not only between individual patients but also within the same immune subtype. Conclusions: ANXA5, FKBP10, MSN, and PYGL are identified as potential antigens for anti-glioma mRNA vaccine production, specifically for patients in immune subtypes 2 and 3. In summary, this study may shed new light on the promising approaches of immunotherapy, such as devising mRNA vaccination tailored to applicable glioma recipients.

2.
BMC Plant Biol ; 21(1): 364, 2021 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-34376143

RESUMO

BACKGROUND: Improving the overall production of rice with high quality is a major target of breeders. Mining potential yield-related loci have been geared towards developing efficient rice breeding strategies. In this study, one single-locus genome-wide association studies (SL-GWAS) method (MLM) in conjunction with five multi-locus genome-wide association studies (ML-GWAS) approaches (mrMLM, FASTmrMLM, pLARmEB, pKWmEB, and ISIS EM-BLASSO) were conducted in a panel consisting of 529 rice core varieties with 607,201 SNPs. RESULTS: A total of 152, 106, 12, 111, and 64 SNPs were detected by the MLM model associated with the five yield-related traits, namely grain length (GL), grain width (GW), grain thickness (GT), thousand-grain weight (TGW), and yield per plant (YPP), respectively. Furthermore, 74 significant quantitative trait nucleotides (QTNs) were presented across at least two ML-GWAS methods to be associated with the above five traits successively. Finally, 20 common QTNs were simultaneously discovered by both SL-GWAS and ML-GWAS methods. Based on genome annotation, gene expression analysis, and previous studies, two candidate key genes (LOC_Os09g02830 and LOC_Os07g31450) were characterized to affect GW and TGW, separately. CONCLUSIONS: These outcomes will provide an indication for breeding high-yielding rice varieties in the immediate future.


Assuntos
Estudo de Associação Genômica Ampla , Oryza/crescimento & desenvolvimento , Oryza/genética , Desequilíbrio de Ligação , Fenótipo , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas
3.
BMC Genomics ; 22(1): 86, 2021 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-33509071

RESUMO

BACKGROUND: The number of panicles per plant, number of grains per panicle, and 1000-grain weight are important factors contributing to the grain yield per plant in rice. The Rice Diversity Panel 1 (RDP1) contains a total of 421 purified, homozygous rice accessions representing diverse genetic variations within O. sativa. The release of High-Density Rice Array (HDRA, 700 k SNPs) dataset provides a new opportunity to discover the genetic variants of panicle architectures in rice. RESULTS: In this report, a new method genome-phenome wide association study (GPWAS) was performed with 391 individuals and 27 traits derived from RDP1 to scan the relationship between the genes and multi-traits. A total of 1985 gene models were linked to phenomic variation with a p-value cutoff of 4.49E-18. Besides, 406 accessions derived from RDP1 with 411,066 SNPs were used to identify QTLs associated with the total spikelets number per panicle (TSNP), grain number per panicle (GNP), empty grain number per panicle (EGNP), primary branch number (PBN), panicle length (PL), and panicle number per plant (PN) by GLM, MLM, FarmCPU, and BLINK models for genome-wide association study (GWAS) analyses. A total of 18, 21, 18, 17, 15, and 17 QTLs were identified tightly linked with TSNP, GNP, EGNP, PBN, PL, and PN, respectively. Then, a total of 23 candidate genes were mapped simultaneously using both GWAS and GPWAS methods, composed of 6, 4, 5, 4, and 4 for TSNP, GNP, EGNP, PBN, and PL. Notably, one overlapped gene (Os01g0140100) were further investigated based on the haplotype and gene expression profile, indicating this gene might regulate the TSNP or panicle architecture in rice. CONCLUSIONS: Nearly 30 % (30/106) QTLs co-located with the previous published genes or QTLs, indicating the power of GWAS. Besides, GPWAS is a new method to discover the relationship between genes and traits, especially the pleiotropy genes. Through comparing the results from GWAS and GPWAS, we identified 23 candidate genes related to panicle architectures in rice. This comprehensive study provides new insights into the genetic basis controlling panicle architectures in rice, which lays a foundation in rice improvement.


Assuntos
Estudo de Associação Genômica Ampla , Oryza , Grão Comestível/genética , Humanos , Oryza/genética , Fenômica , Locos de Características Quantitativas
4.
Artigo em Inglês | MEDLINE | ID: mdl-33213038

RESUMO

This research was conducted to study the growth performance, arsenic (As) tissue distribution, and As excretion of pigs fed As-containing rice bran. Twenty gilts (26.3 kg) were randomly assigned to 3 dietary treatments (n = 6 or 7) with Diets I, II, and III containing 0, 36.7, and 73.5% rice bran and 0, 306, and 612 ppb As, respectively. Pigs were fed for 6 weeks, and their growth performance and daily activities were examined. Fecal, blood, and hair samples were collected immediately before and after the 6-weeks. At the end of the 6-weeks, pigs were slaughtered; the liver, kidney, muscle, and urine samples were collected. No pig showed any unhealthy signs throughout the trial. The average daily feed intake, average daily gain, and final body weight of Diet III pigs were lower (p ≤ 0.001) than Diet I pigs. The gain to feed ratios were not different among the treatments. The fecal, hair, kidney, and urinary As concentrations of both Diets II and III pigs were higher than Diet I pigs. The hair As concentration of Diet III pigs was higher than Diet II pigs, but no difference was found in the fecal, urinary, kidney, or muscle As concentrations between Diets II and III pigs. The blood and muscle As concentrations were below 10 ppb. These results suggest that 73.5% dietary rice bran inclusion compromised growth performance, whereas the 36.7% inclusion did not. The fecal As data imply that dietary As was poorly absorbed by the gastrointestinal tract. The tissue As data indicate that the absorbed As was rapidly cleared from the blood with some retained in various organs and others eliminated via urine. The hair As concentration was much higher than that of liver and kidney. The muscle As data suggest that the pork produced from the pigs fed a typical As-containing rice bran as used in this study is safe for human consumption.


Assuntos
Ração Animal/análise , Arsênio/efeitos adversos , Dieta/efeitos adversos , Exposição Ambiental/análise , Contaminação de Alimentos/análise , Oryza/química , Suínos/crescimento & desenvolvimento , Fenômenos Fisiológicos da Nutrição Animal , Animais , Arsênio/administração & dosagem , Dieta/veterinária , Feminino , Masculino , Suínos/metabolismo , Distribuição Tecidual
5.
BMC Plant Biol ; 20(1): 441, 2020 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-32972357

RESUMO

BACKGROUND: Rice is an important human staple food vulnerable to heavy metal contamination leading to serious concerns. High yield with low heavy metal contamination is a common but highly challenging goal for rice breeders worldwide due to lack of genetic knowledge and markers. RESULTS: To identify candidate QTLs and develop molecular markers for rice yield and heavy metal content, a total of 191 accessions from the USDA Rice mini-core collection with over 3.2 million SNPs were employed to investigate the QTLs. Sixteen ionomic and thirteen agronomic traits were analyzed utilizing two univariate (GLM and MLM) and two multivariate (MLMM and FarmCPU) GWAS methods. 106, 47, and 97 QTLs were identified for ionomics flooded, ionomics unflooded, and agronomic traits, respectively, with the criterium of p-value < 1.53 × 10- 8, which was determined by the Bonferroni correction for p-value of 0.05. While 49 (~ 20%) of the 250 QTLs were coinciding with previously reported QTLs/genes, about 201 (~ 80%) were new. In addition, several new candidate genes involved in ionomic and agronomic traits control were identified by analyzing the DNA sequence, gene expression, and the homologs of the QTL regions. Our results further showed that each of the four GWAS methods can identify unique as well as common QTLs, suggesting that using multiple GWAS methods can complement each other in QTL identification, especially by combining univariate and multivariate methods. CONCLUSIONS: While 49 previously reported QTLs/genes were rediscovered, over 200 new QTLs for ionomic and agronomic traits were found in the rice genome. Moreover, multiple new candidate genes for agronomic and ionomic traits were identified. This research provides novel insights into the genetic basis of both ionomic and agronomic variations in rice, establishing the foundation for marker development in breeding and further investigation on reducing heavy-metal contamination and improving crop yields. Finally, the comparative analysis of the GWAS methods showed that each method has unique features and different methods can complement each other.


Assuntos
Mapeamento Cromossômico/métodos , Cromossomos de Plantas/genética , Produtos Agrícolas/genética , Marcadores Genéticos , Estudo de Associação Genômica Ampla , Oryza/genética , Locos de Características Quantitativas/genética , Fenótipo , Banco de Sementes , Estados Unidos , United States Department of Agriculture
6.
Mol Cell Proteomics ; 18(12): 2359-2372, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31492684

RESUMO

Lysine succinylation has been recognized as a post-translational modification (PTM) in recent years. It is plausible that succinylation may have a vaster functional impact than acetylation because of bulkier structural changes and more significant charge differences on the modified lysine residue. Currently, however, the quantity and identity of succinylated proteins and their corresponding functions in cereal plants remain largely unknown. In this study, we estimated the native succinylation occupancy on lysine was between 2% to 10% in developing rice seeds. Eight hundred fifty-four lysine succinylation sites on 347 proteins have been identified by a thorough investigation in developing rice seeds. Six motifs were revealed as preferred amino acid sequence arrangements for succinylation sites, and a noteworthy motif preference was identified in proteins associated with different biological processes, molecular functions, pathways, and domains. Remarkably, heavy succinylation was detected on major seed storage proteins, in conjunction with critical enzymes involved in central carbon metabolism and starch biosynthetic pathways for rice seed development. Meanwhile, our results showed that the modification pattern of in vitro nonenzymatically succinylated proteins was different from those of the proteins isolated from cells in Western blots, suggesting that succinylation is not generated via nonenzymatic reaction in the cells, at least not completely. Using the acylation data obtained from the same rice tissue, we mapped many sites harboring lysine succinylation, acetylation, malonylation, crotonylation, and 2-hydroxisobutyrylation in rice seed proteins. A striking number of proteins with multiple modifications were shown to be involved in critical metabolic events. Given that these modification moieties are intermediate products of multiple cellular metabolic pathways, these targeted lysine residues may mediate the crosstalk between different metabolic pathways via modifications by different moieties. Our study exhibits a platform for extensive investigation of molecular networks administrating cereal seed development and metabolism via PTMs.


Assuntos
Lisina/metabolismo , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Processamento de Proteína Pós-Traducional , Succinatos/metabolismo , Acetilação , Acil Coenzima A/metabolismo , Western Blotting , Domínio Catalítico , Sementes/metabolismo
7.
Biochim Biophys Acta Proteins Proteom ; 1866(3): 451-463, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29313810

RESUMO

Protein lysine acetylation is a highly conserved post-translational modification with various biological functions. However, only a limited number of acetylation sites have been reported in plants, especially in cereals, and the function of non-histone protein acetylation is still largely unknown. In this report, we identified 1003 lysine acetylation sites in 692 proteins of developing rice seeds, which greatly extended the number of known acetylated sites in plants. Seven distinguished motifs were detected flanking acetylated lysines. Functional annotation analyses indicated diverse biological processes and pathways engaged in lysine acetylation. Remarkably, we found that several key enzymes in storage starch synthesis pathway and the main storage proteins were heavily acetylated. A comprehensive comparison of the rice acetylome, succinylome, ubiquitome and phosphorylome with available published data was conducted. A large number of proteins carrying multiple kinds of modifications were identified and many of these proteins are known to be key enzymes of vital metabolic pathways. Our study provides extending knowledge of protein acetylation. It will have critical reference value for understanding the mechanisms underlying PTM mediated multiple signal integration in the regulation of metabolism and development in plants.


Assuntos
Lisina/metabolismo , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Proteoma/metabolismo , Sementes/metabolismo , Acetilação , Sequência de Aminoácidos , Vias Biossintéticas , Oryza/crescimento & desenvolvimento , Peptídeos/metabolismo , Fosforilação , Processamento de Proteína Pós-Traducional , Proteômica/métodos , Sementes/crescimento & desenvolvimento , Amido/biossíntese , Ácido Succínico/metabolismo , Espectrometria de Massas em Tandem , Ubiquitinação
8.
J Proteomics ; 170: 88-98, 2018 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-28882676

RESUMO

In recent years, lysine malonylation has garnered wide spread interest due to its potential regulatory roles. While studies have been performed in bacteria, mouse, and human, the involvement and the biological function of this modification in plant are still largely unknown. We examined the global proteome profile of lysine malonylation in developing rice seeds using affinity enrichment followed by LC-MS/MS analysis. We identified 421 malonylated lysine sites across 247 proteins. Functional analyses showed predominant presence of malonylated proteins in metabolic processes, including carbon metabolism, glycolysis/gluconeogenesis, TCA cycle, as well as photosynthesis. Malonylation was also detected on enzymes in starch biosynthesis pathway in developing rice seeds. In addition, we found a remarkable overlap among the malonylated, succinylated and acetylated sites identified in rice. Furthermore, malonylation at conserved sites of homologous proteins was observed across organisms of different kingdoms, including mouse, human, and bacteria. Finally, distinct motifs were identified when the rice malonylation sites were analyzed and conserved motifs were observed from bacterium to human and rice. Our results provide an initial understanding of the lysine malonylome in plants. The study has critical reference value for future understanding of the biological function of protein lysine malonylation in plants. BIOLOGICAL SIGNIFICANCE: Lysine malonylation is a newly discovered acylation with functional potential in regulating cellular metabolisms and activities. However, the malonylation status has not been reported in plants. Grain yield and quality, mainly determined during cereal seed development, are closely related to food security, human health and economic value. To evaluate malonylation level in plants and the possible regulatory functions of malonylation in seed development, we conducted comprehensive analyses of malonylome in developing rice seeds. A total of 421 malonylated lysine sites from 247 proteins were identified, which involved in multiple critical metabolic processes, including central carbon metabolism, lipid metabolism, photosynthesis, and starch biosynthesis. We found that charged amino acids, lysine and arginine, were the preferred residues in positions flanking the modified lysines. Highly conserved modification sites on both histone and non-histone proteins were observed among different organisms through sequence alignment analysis. More interestingly, a large number of modification sites shared by malonylation, acetylation and succinylation were identified in rice. The study presents a comprehensive understanding of malonylome in plants, which will serve as an initial platform for further investigation of the functions of lysine malonylation, especially in cereal seeds development.


Assuntos
Oryza/metabolismo , Proteínas de Plantas/metabolismo , Processamento de Proteína Pós-Traducional/fisiologia , Sementes/metabolismo , Acetilação , Lisina/metabolismo
9.
Sci Rep ; 7(1): 17486, 2017 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-29235492

RESUMO

Lysine 2-hydroxyisobutyrylation is a recently identified protein post-translational modification that is known to affect the association between histone and DNA. However, non-histone protein lysine 2-hydroxyisobutyrylation remains largely unexplored. Utilizing antibody-based affinity enrichment and nano-HPLC/MS/MS analyses of 2-hydroxyisobutyrylation peptides, we efficaciously identified 9,916 2-hydroxyisobutyryl lysine sites on 2,512 proteins in developing rice seeds, representing the first lysine 2-hydroxyisobutyrylome dataset in plants. Functional annotation analyses indicated that a wide variety of vital biological processes were preferably targeted by lysine 2-hydroxyisobutyrylation, including glycolysis/gluconeogenesis, TCA cycle, starch biosynthesis, lipid metabolism, protein biosynthesis and processing. Our finding showed that 2-hydroxyisobutyrylated histone sites were conserved across plants, human, and mouse. A number of 2-hydroxyisobutyryl sites were shared with other lysine acylations in both histone and non-histone proteins. Comprehensive analysis of the lysine 2-hydroxyisobutyrylation sites illustrated that the modification sites were highly sequence specific with distinct motifs, and they had less surface accessibility than other lysine residues in the protein. Overall, our study provides the first systematic analysis of lysine 2-hydroxyisobutyrylation proteome in plants, and it serves as an important resource for future investigations of the regulatory mechanisms and functions of lysine 2-hydroxyisobutyrylation.


Assuntos
Oryza/metabolismo , Proteínas de Plantas/metabolismo , Processamento de Proteína Pós-Traducional , Proteoma , Sementes/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Lisina/análogos & derivados , Lisina/metabolismo , Oryza/genética , Oryza/crescimento & desenvolvimento , Proteínas de Plantas/genética , Proteômica , Sementes/genética , Sementes/crescimento & desenvolvimento
10.
PLoS One ; 11(12): e0168467, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27992503

RESUMO

Starch is the most important food energy source in cereals. Many of the known enzymes involved in starch biosynthesis are partially or entirely granule-associated in the endosperm. Studying the proteome of rice starch granules is critical for us to further understand the mechanisms underlying starch biosynthesis and packaging of starch granules in rice amyloplasts, consequently for the improvement of rice grain quality. In this article, we developed a protocol to purify starch granules from mature rice endosperm and verified the quality of purified starch granules by microscopy observations, I2 staining, and Western blot analyses. In addition, we found the phenol extraction method was superior to Tris-HCl buffer extraction method with respect to the efficiency in recovery of starch granule associated proteins. LC-MS/MS analysis showed identification of already known starch granule associated proteins with high confidence. Several proteins reported to be involved in starch synthesis in prior genetic studies in plants were also shown to be enriched with starch granules, either directly or indirectly, in our studies. In addition, our results suggested that a few additional candidate proteins may also be involved in starch synthesis. Furthermore, our results indicated that some starch synthesis pathway proteins are subject to protein acetylation modification. GO analysis and KEGG pathway enrichment analysis showed that the identified proteins were mainly located in plastids and involved in carbohydrate metabolism. This study substantially advances the understanding of the starch granule associated proteome in rice and post translational regulation of some starch granule associated proteins.


Assuntos
Endosperma/metabolismo , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Plastídeos/metabolismo , Proteoma/metabolismo , Amido/metabolismo , Proteômica
11.
BMC Genomics ; 17: 350, 2016 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-27169379

RESUMO

BACKGROUND: Nitrogen (N) is an essential and often limiting nutrient to plant growth and development. Previous studies have shown that the mRNA expressions of numerous genes are regulated by nitrogen supplies; however, little is known about the expressed non-coding elements, for example long non-coding RNAs (lncRNAs) that control the response of maize (Zea mays L.) to nitrogen. LncRNAs are a class of non-coding RNAs larger than 200 bp, which have emerged as key regulators in gene expression. RESULTS: In this study, we surveyed the intergenic/intronic lncRNAs in maize B73 leaves at the V7 stage under conditions of N-deficiency and N-sufficiency using ribosomal RNA depletion and ultra-deep total RNA sequencing approaches. By integration with mRNA expression profiles and physiological evaluations, 7245 lncRNAs and 637 nitrogen-responsive lncRNAs were identified that exhibited unique expression patterns. Co-expression network analysis showed that the nitrogen-responsive lncRNAs were enriched mainly in one of the three co-expressed modules. The genes in the enriched module are mainly involved in NADH dehydrogenase activity, oxidative phosphorylation and the nitrogen compounds metabolic process. CONCLUSIONS: We identified a large number of lncRNAs in maize and illustrated their potential regulatory roles in response to N stress. The results lay the foundation for further in-depth understanding of the molecular mechanisms of lncRNAs' role in response to nitrogen stresses.


Assuntos
Nitrogênio/metabolismo , RNA Longo não Codificante/genética , Análise de Sequência de RNA/métodos , Zea mays/crescimento & desenvolvimento , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Folhas de Planta/genética , Folhas de Planta/crescimento & desenvolvimento , RNA de Plantas/genética , Ribossomos/genética , Zea mays/genética
12.
Proteomes ; 4(1)2016 Feb 03.
Artigo em Inglês | MEDLINE | ID: mdl-28248216

RESUMO

The distinct stages of cotton fiber development and maturation serve as a single-celled model for studying the molecular mechanisms of plant cell elongation, cell wall development and cellulose biosynthesis. However, this model system of plant cell development is compromised for proteomic studies due to a lack of an efficient protein extraction method during the later stages of fiber development, because of a recalcitrant cell wall and the presence of abundant phenolic compounds. Here, we compared the quality and quantities of proteins extracted from 25 dpa (days post anthesis) fiber with multiple protein extraction methods and present a comprehensive quantitative proteomic study of fiber development from 10 dpa to 25 dpa. Comparative analysis using a label-free quantification method revealed 287 differentially-expressed proteins in the 10 dpa to 25 dpa fiber developmental period. Proteins involved in cell wall metabolism and regulation, cytoskeleton development and carbohydrate metabolism among other functional categories in four fiber developmental stages were identified. Our studies provide protocols for protein extraction from maturing fiber tissues for mass spectrometry analysis and expand knowledge of the proteomic profile of cotton fiber development.

13.
PLoS One ; 9(2): e89283, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24586658

RESUMO

Lysine acetylation is a reversible, dynamic protein modification regulated by lysine acetyltransferases and deacetylases. Recent advances in high-throughput proteomics have greatly contributed to the success of global analysis of lysine acetylation. A large number of proteins of diverse biological functions have been shown to be acetylated in several reports in human cells, E.coli, and dicot plants. However, the extent of lysine acetylation in non-histone proteins remains largely unknown in monocots, particularly in the cereal crops. Here we report the mass spectrometric examination of lysine acetylation in rice (Oryza sativa). We identified 60 lysine acetylated sites on 44 proteins of diverse biological functions. Immunoblot studies further validated the presence of a large number of acetylated non-histone proteins. Examination of the amino acid composition revealed substantial amino acid bias around the acetylation sites and the amino acid preference is conserved among different organisms. Gene ontology analysis demonstrates that lysine acetylation occurs in diverse cytoplasmic, chloroplast and mitochondrial proteins in addition to the histone modifications. Our results suggest that lysine acetylation might constitute a regulatory mechanism for many proteins, including both histones and non-histone proteins of diverse biological functions.


Assuntos
Lisina/química , Proteínas de Plantas/metabolismo , Processamento de Proteína Pós-Traducional , Proteoma/análise , Acetilação , Sequência de Aminoácidos , Fenômenos Biológicos , Western Blotting , Cromatografia de Afinidade , Ontologia Genética , Humanos , Lisina/metabolismo , Dados de Sequência Molecular , Oryza , Proteínas de Plantas/genética , Proteômica , Espectrometria de Massas em Tandem
14.
Proteome Sci ; 11(1): 26, 2013 Jun 19.
Artigo em Inglês | MEDLINE | ID: mdl-23777608

RESUMO

Plant cells are routinely exposed to various pathogens and environmental stresses that cause cell wall perturbations. Little is known of the mechanisms that plant cells use to sense these disturbances and transduce corresponding signals to regulate cellular responses to maintain cell wall integrity. Previous studies in rice have shown that removal of the cell wall leads to substantial chromatin reorganization and histone modification changes concomitant with cell wall re-synthesis. But the genes and proteins that regulate these cellular responses are still largely unknown. Here we present an examination of the nuclear proteome differential expression in response to removal of the cell wall in rice suspension cells using multiple nuclear proteome extraction methods. A total of 382 nuclear proteins were identified with two or more peptides, including 26 transcription factors. Upon removal of the cell wall, 142 nuclear proteins were up regulated and 112 were down regulated. The differentially expressed proteins included transcription factors, histones, histone domain containing proteins, and histone modification enzymes. Gene ontology analysis of the differentially expressed proteins indicates that chromatin & nucleosome assembly, protein-DNA complex assembly, and DNA packaging are tightly associated with cell wall removal. Our results indicate that removal of the cell wall imposes a tremendous challenge to the cells. Consequently, plant cells respond to the removal of the cell wall in the nucleus at every level of the regulatory hierarchy.

15.
PLoS Genet ; 9(3): e1003322, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23505380

RESUMO

Cereal endosperm represents 60% of the calories consumed by human beings worldwide. In addition, cereals also serve as the primary feedstock for livestock. However, the regulatory mechanism of cereal endosperm and seed development is largely unknown. Polycomb complex has been shown to play a key role in the regulation of endosperm development in Arabidopsis, but its role in cereal endosperm development remains obscure. Additionally, the enzyme activities of the polycomb complexes have not been demonstrated in plants. Here we purified the rice OsFIE2-polycomb complex using tandem affinity purification and demonstrated its specific H3 methyltransferase activity. We found that the OsFIE2 gene product was responsible for H3K27me3 production specifically in vivo. Genetic studies showed that a reduction of OsFIE2 expression led to smaller seeds, partially filled seeds, and partial loss of seed dormancy. Gene expression and proteomics analyses found that the starch synthesis rate limiting step enzyme and multiple storage proteins are down-regulated in OsFIE2 reduction lines. Genome wide ChIP-Seq data analysis shows that H3K27me3 is associated with many genes in the young seeds. The H3K27me3 modification and gene expression in a key helix-loop-helix transcription factor is shown to be regulated by OsFIE2. Our results suggest that OsFIE2-polycomb complex positively regulates rice endosperm development and grain filling via a mechanism highly different from that in Arabidopsis.


Assuntos
Grão Comestível , Oryza , Proteínas do Grupo Polycomb , Sementes , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Grão Comestível/genética , Grão Comestível/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Histona-Lisina N-Metiltransferase , Complexos Multiproteicos , Oryza/genética , Oryza/crescimento & desenvolvimento , Dormência de Plantas/genética , Proteínas do Grupo Polycomb/genética , Proteínas do Grupo Polycomb/metabolismo , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Sementes/genética , Sementes/crescimento & desenvolvimento
16.
PLoS One ; 6(9): e25260, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21984925

RESUMO

Chromatin immunoprecipitation coupled with high throughput DNA Sequencing (ChIP-Seq) has emerged as a powerful tool for genome wide profiling of the binding sites of proteins associated with DNA such as histones and transcription factors. However, no peak calling program has gained consensus acceptance by the scientific community as the preferred tool for ChIP-Seq data analysis. Analyzing the large data sets generated by ChIP-Seq studies remains highly challenging for most molecular biology laboratories.Here we profile H3K27me3 enrichment sites in rice young endosperm using the ChIP-Seq approach and analyze the data using four peak calling algorithms (FindPeaks, PeakSeq, USeq, and MACS). Comparison of the four algorithms reveals that these programs produce very different peaks in terms of peak size, number, and position relative to genes. We verify the peak predictions using ChIP-PCR to evaluate the accuracy of peak prediction of the four algorithms. We discuss the approach of each algorithm and compare similarities and differences in the results. Despite their differences in the peaks identified, all of the programs reach similar conclusions about the effect of H3K27me3 on gene expression. Its presence either upstream or downstream of a gene is predominately associated with repression of the gene. Additionally, GO analysis finds that a substantially higher ratio of genes associated with H3K27me3 were involved in multicellular organism development, signal transduction, response to external and endogenous stimuli, and secondary metabolic pathways than the rest of the rice genome.


Assuntos
Algoritmos , Metilação de DNA/genética , Endosperma/genética , Histonas/genética , Oryza/genética , Imunoprecipitação da Cromatina , Análise de Sequência de DNA
17.
Plant Mol Biol ; 77(4-5): 391-406, 2011 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21887580

RESUMO

Efficient and cost-effective conversion of plant biomass to usable forms of energy requires a thorough understanding of cell wall biosynthesis, modification and degradation. To elucidate these processes, we assessed the expression dynamics during enzymatic removal and regeneration of rice cell walls in suspension cells over time. In total, 928 genes exhibited significant up-regulation during cell wall removal, whereas, 79 genes were up-regulated during cell wall regeneration. Both gene sets are enriched for kinases, transcription factors and genes predicted to be involved in cell wall-related functions. Integration of the gene expression datasets with a catalog of known and/or predicted biochemical pathways from rice, revealed metabolic and hormonal pathways involved in cell wall degradation and regeneration. Rice lines carrying Tos17 mutations in genes up-regulated during cell wall removal exhibit dwarf phenotypes. Many of the genes up-regulated during cell wall development are also up-regulated in response to infection and environmental perturbations indicating a coordinated response to diverse types of stress.


Assuntos
Parede Celular/genética , Oryza/genética , Proteínas de Plantas/genética , Parede Celular/metabolismo , Parede Celular/ultraestrutura , Células Cultivadas , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Lignina/biossíntese , Mutação , Oryza/metabolismo , Oryza/ultraestrutura , Pectinas/biossíntese , Fenótipo , Proteínas de Plantas/metabolismo , Proteínas de Plantas/fisiologia , Polissacarídeos/biossíntese , Estresse Fisiológico/genética , Transcrição Genética
18.
Proc Natl Acad Sci U S A ; 108(37): 15498-503, 2011 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-21896764

RESUMO

DNA 5-methylcytosine (5-meC) is an important epigenetic mark for transcriptional gene silencing in many eukaryotes. In Arabidopsis, 5-meC DNA glycosylase/lyases actively remove 5-meC to counteract transcriptional gene silencing in a locus-specific manner, and have been suggested to maintain the expression of transposons. However, it is unclear whether plant DNA demethylases can promote the transposition of transposons. Here we report the functional characterization of the DNA glycosylase/lyase DNG701 in rice. DNG701 encodes a large (1,812 amino acid residues) DNA glycosylase domain protein. Recombinant DNG701 protein showed 5-meC DNA glycosylase and lyase activities in vitro. Knockout or knockdown of DNG701 in rice plants led to DNA hypermethylation and reduced expression of the retrotransposon Tos17. Tos17 showed less transposition in calli derived from dng701 knockout mutant seeds compared with that in wild-type calli. Overexpression of DNG701 in both rice calli and transgenic plants substantially reduced DNA methylation levels of Tos17 and enhanced its expression. The overexpression also led to more frequent transposition of Tos17 in calli. Our results demonstrate that rice DNG701 is a 5-meC DNA glycosylase/lyase responsible for the demethylation of Tos17 and this DNA demethylase plays a critical role in promoting Tos17 transposition in rice calli.


Assuntos
DNA Glicosilases/metabolismo , Metilação de DNA , Liases/metabolismo , Oryza/enzimologia , Oryza/genética , Retroelementos/genética , 5-Metilcitosina/metabolismo , DNA de Plantas/metabolismo , Regulação da Expressão Gênica de Plantas , Técnicas de Silenciamento de Genes , Técnicas de Inativação de Genes , Plantas Geneticamente Modificadas
19.
J Proteome Res ; 10(2): 551-63, 2011 Feb 04.
Artigo em Inglês | MEDLINE | ID: mdl-20958091

RESUMO

The cell wall is a critical extracellular structure that provides protection and structural support in plant cells. To study the biological function of the cell wall and the regulation of cell wall resynthesis, we examined cellular responses to enzymatic removal of the cell wall in rice (Oryza sativa) suspension cells using proteomic approaches. We find that removal of cell wall stimulates cell wall synthesis from multiple sites in protoplasts instead of from a single site as in cytokinesis. Nucleus DAPI stain and MNase digestion further show that removal of the cell wall is concomitant with substantial chromatin reorganization. Histone post-translational modification studies using both Western blots and isotope labeling assisted quantitative mass spectrometry analyses reveal that substantial histone modification changes, particularly H3K18(AC) and H3K23(AC), are associated with the removal and regeneration of the cell wall. Label-free quantitative proteome analyses further reveal that chromatin associated proteins undergo dramatic changes upon removal of the cell wall, along with cytoskeleton, cell wall metabolism, and stress-response proteins. This study demonstrates that cell wall removal is associated with substantial chromatin change and may lead to stimulation of cell wall synthesis using a novel mechanism.


Assuntos
Parede Celular/metabolismo , Montagem e Desmontagem da Cromatina/fisiologia , Histonas/metabolismo , Oryza/fisiologia , Proteínas de Plantas/metabolismo , Acetilação , Sequência de Aminoácidos , Western Blotting , Parede Celular/química , Microscopia de Fluorescência , Dados de Sequência Molecular , Oryza/metabolismo , Mapeamento de Peptídeos , Extratos Vegetais/química , Processamento de Proteína Pós-Traducional , Proteômica , Protoplastos/química , Protoplastos/metabolismo
20.
Plant J ; 64(4): 604-17, 2010 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-20822505

RESUMO

MADS-box transcription factors are known for their roles in plant growth and development. The regulatory mechanisms of spatial and temporal specific expression of MADS-box genes and the function of MADS-box genes in other biological processes are still to be explored. Here, we report that OsMADS6 is highly expressed in flower and endosperm in Oryza sativa (rice). In addition to displaying a homeotic organ identity phenotype in all the four whorls of the flowers, the endosperm development is severely affected in its mutant. At least 32% of the seeds lacked starch filling and aborted. For seeds that have starch filling and develop to maturity, the starch content is reduced by at least 13%. In addition, the seed shape changes from elliptical to roundish, and the protein content increases from 12.1 to 15.0% (P < 0.05). Further investigation shows that ADP-glucose pyrophosphorylase genes, encoding the rate-limiting step enzyme in the starch synthesis pathway, are subject to the regulation of OsMADS6. Chromatin immunoprecipitation (ChIP)-PCR analyses on the chromatin of the OsMADS6 gene find that H3K27 is trimethylated in tissues where OsMADS6 is silenced, and that H3K36 is trimethylated in tissues where OsMADS6 is highly activated. Point mutation analysis reveals that leucine at position 83 is critical to OsMADS6 function.


Assuntos
Endosperma/metabolismo , Epigênese Genética , Flores/metabolismo , Proteínas de Domínio MADS/metabolismo , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Substituição de Aminoácidos , Metilação de DNA , Endosperma/crescimento & desenvolvimento , Flores/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Histonas/metabolismo , Proteínas de Domínio MADS/genética , Oryza/genética , Oryza/crescimento & desenvolvimento , Fenótipo , Proteínas de Plantas/genética , Plantas Geneticamente Modificadas/crescimento & desenvolvimento , Interferência de RNA , Amido/biossíntese
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...