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1.
Proc Biol Sci ; 287(1935): 20201397, 2020 09 30.
Artigo em Inglês | MEDLINE | ID: mdl-32962543

RESUMO

Post-transcriptional regulation has far-reaching implications on the fate of RNAs. It is gaining increasing momentum as a critical component in adjusting global cellular transcript levels during development and in response to environmental stresses. In this process, RNA-binding proteins (RBPs) are indispensable chaperones that naturally bind RNA via one or multiple globular RNA-binding domains (RBDs) changing the function or fate of the bound RNAs. Despite the technical challenges faced in plants in large-scale studies, several hundreds of these RBPs have been discovered and elucidated globally over the past few years. Recent discoveries have more than doubled the number of proteins implicated in RNA interaction, including identification of RBPs lacking classical RBDs. This review will discuss these new emerging classes of RBPs, focusing on the current state of the RBP repertoire in Arabidopsis thaliana, including the diverse functional roles derived from quantitative studies implicating RBPs in abiotic stress responses. Notably, this review highlights that 836 RBPs are enriched as Arabidopsis RBPs while 1865 can be classified as candidate RBPs. The review will also outline outstanding areas within this field that require addressing to advance our understanding and potential biotechnological applications of RBPs.


Assuntos
Arabidopsis/fisiologia , Plantas/genética , Proteínas de Ligação a RNA/genética , RNA de Plantas/genética , Estresse Fisiológico
2.
PLoS One ; 15(8): e0236980, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32780737

RESUMO

Global warming induces heat stress in eggplant, seriously affecting its quality and yield. The response to heat stress is a complex regulatory process; however, the exact mechanism in eggplant is unknown. We analyzed the transcriptome of eggplant under different high-temperature treatments using RNA-Seq technology. Three libraries treated at high temperatures were generated and sequenced. There were 40,733,667, 40,833,852, and 40,301,285 clean reads with 83.98%, 79.69%, and 84.42% of sequences mapped to the eggplant reference genome in groups exposed to 28°C (CK), 38°C (T38), and 43°C (T43), respectively. There were 3,067 and 1,456 DEGs in T38 vs CK and T43 vs CK groups, respectively. In these two DEG groups, 315 and 342 genes were up- and down-regulated, respectively, in common. Differential expression patterns of DEGs in antioxidant enzyme systems, detoxication, phytohormones, and transcription factors under heat stress were investigated. We screened heat stress-related genes for further validation by qRT-PCR. Regulation mechanisms may differ under different temperature treatments, in which heat shock proteins and heat stress transcription factors play vital roles. These results provide insight into the molecular mechanisms of the heat stress response in eggplant and may be useful in crop breeding.


Assuntos
Regulação da Expressão Gênica de Plantas , Solanum melongena/genética , Antioxidantes/metabolismo , Perfilação da Expressão Gênica , Genes de Plantas , Proteínas de Choque Térmico/genética , Resposta ao Choque Térmico/genética , Reguladores de Crescimento de Planta/genética , Proteínas de Plantas/genética , RNA de Plantas/genética , RNA-Seq , Solanum melongena/fisiologia , Fatores de Transcrição/genética
3.
PLoS One ; 15(7): e0236588, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32706804

RESUMO

Xanthoceras sorbifolia, a medicinal and oil-rich woody plant, has great potential for biodiesel production. However, little study explores the link between gene expression level and metabolite accumulation of X. sorbifolia in response to cold stress. Herein, we performed both transcriptomic and metabolomic analyses of X. sorbifolia seedlings to investigate the regulatory mechanism of resistance to low temperature (4 °C) based on physiological profile analyses. Cold stress resulted in a significant increase in the malondialdehyde content, electrolyte leakage and activity of antioxidant enzymes. A total of 1,527 common differentially expressed genes (DEGs) were identified, of which 895 were upregulated and 632 were downregulated. Annotation of DEGs revealed that amino acid metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, galactose metabolism, fructose and mannose metabolism, and the citrate cycle (TCA) were strongly affected by cold stress. In addition, DEGs within the plant mitogen-activated protein kinase (MAPK) signaling pathway and TF families of ERF, WRKY, NAC, MYB, and bHLH were transcriptionally activated. Through metabolomic analysis, we found 51 significantly changed metabolites, particularly with the analysis of primary metabolites, such as sugars, amino acids, and organic acids. Moreover, there is an overlap between transcript and metabolite profiles. Association analysis between key genes and altered metabolites indicated that amino acid metabolism and sugar metabolism were enhanced. A large number of specific cold-responsive genes and metabolites highlight a comprehensive regulatory mechanism, which will contribute to a deeper understanding of the highly complex regulatory program under cold stress in X. sorbifolia.


Assuntos
Resposta ao Choque Frio/genética , Metaboloma , Metabolômica/métodos , Sapindaceae/metabolismo , Transcriptoma , Aminoácidos/metabolismo , Catalase/metabolismo , Temperatura Baixa , Regulação da Expressão Gênica de Plantas , Malondialdeído/metabolismo , Folhas de Planta/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/metabolismo , Análise de Componente Principal , RNA de Plantas/genética , RNA de Plantas/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Sapindaceae/genética , Transdução de Sinais/genética , Superóxido Dismutase/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
4.
PLoS One ; 15(7): e0236530, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32706831

RESUMO

Apple trees grafted on different rootstock types, including vigorous rootstock (VR), dwarfing interstock (DIR), and dwarfing self-rootstock (DSR), are widely planted in production, but the molecular determinants of tree branch architecture growth regulation induced by rootstocks are still not well known. In this study, the branch growth phenotypes of three combinations of 'Fuji' apple trees grafted on different rootstocks (VR: Malus baccata; DIR: Malus baccata/T337; DSR: T337) were investigated. The VR trees presented the biggest branch architecture. The results showed that the sugar content, sugar metabolism-related enzyme activities, and hormone content all presented obvious differences in the tender leaves and buds of apple trees grafted on these rootstocks. Transcriptomic profiles of the tender leaves adjacent to the top buds allowed us to identify genes that were potentially involved in signaling pathways that mediate the regulatory mechanisms underlying growth differences. In total, 3610 differentially expressed genes (DEGs) were identified through pairwise comparisons. The screened data suggested that sugar metabolism-related genes and complex hormone regulatory networks involved the auxin (IAA), cytokinin (CK), abscisic acid (ABA) and gibberellic acid (GA) pathways, as well as several transcription factors, participated in the complicated growth induction process. Overall, this study provides a framework for analysis of the molecular mechanisms underlying differential tree branch growth of apple trees grafted on different rootstocks.


Assuntos
Regulação da Expressão Gênica de Plantas , Malus/genética , Transdução de Sinais/genética , Açúcares/metabolismo , Ácido Abscísico/análise , Ácido Abscísico/metabolismo , Cromatografia Líquida de Alta Pressão , Citocininas/análise , Citocininas/metabolismo , Flores/genética , Flores/metabolismo , Giberelinas/análise , Giberelinas/metabolismo , Ácidos Indolacéticos/análise , Ácidos Indolacéticos/metabolismo , Malus/crescimento & desenvolvimento , Fenótipo , Folhas de Planta/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raízes de Plantas/metabolismo , Caules de Planta/genética , Caules de Planta/fisiologia , RNA de Plantas/genética , RNA de Plantas/metabolismo , Açúcares/análise , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , alfa-Glucosidases/genética , alfa-Glucosidases/metabolismo
5.
Gene ; 759: 145002, 2020 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-32726608

RESUMO

Recent evidence has shown that microRNAs are transferred from one species to another through cross-species transmission and exhibit biological activities in the receptor. However, the cross-kingdom regulation of pathogen virulence by plant-derived miRNAs is rarely reported. This study investigated the regulatory role of novel tomato miRNA miR1001 in the growth and development of Botrytis cinerea. Results showed that miR1001 inhibited the virulence of B. cinerea-infected plants, and the inhibitory effect of miR1001/miR1001* was stronger than that of miR1001. Moreover, miR1001 exerted a significant inhibitory effect on the conidiospore germination of B. cinerea. Degradome-seq experiment showed that miR1001 can directly target the Bcin03g02170.1 and Bcin10g01400.1 genes, which respectively encode the ATP-dependent metallopeptidase and cysteine-type endopeptidase, in B. cinerea. The interactions of both targets with miR1001 were further confirmed by using transient co-expression in tobacco. Real-time RT-PCR analysis showed that the expression levels of the two target genes were significantly downregulated in B. cinerea with miR1001 treatment. Our findings provide new evidence into the coevolution of pathogens and host plants, as well as new directions for the use of plant-derived miRNAs to control pathogens.


Assuntos
Botrytis/patogenicidade , Proteínas Fúngicas/genética , Interações Hospedeiro-Patógeno , Lycopersicon esculentum/genética , MicroRNAs/metabolismo , RNA de Plantas/metabolismo , Botrytis/fisiologia , Proteínas Fúngicas/metabolismo , Lycopersicon esculentum/microbiologia , MicroRNAs/genética , RNA de Plantas/genética , Esporos Fúngicos/fisiologia
6.
J Vis Exp ; (159)2020 05 14.
Artigo em Inglês | MEDLINE | ID: mdl-32478728

RESUMO

Secondary base modifications on RNA, such as m5C, affect the structure and function of the modified RNA molecules. Methylated RNA Immunoprecipitation and sequencing (MeRIP-seq) is a method that aims to enrich for methylated RNA and ultimately identify modified transcripts. Briefly, sonicated RNA is incubated with an antibody for 5-methylated cytosines and precipitated with the assistance of protein G beads. The enriched fragments are then sequenced and the potential methylation sites are mapped based on the distribution of the reads and peak detection. MeRIP can be applied to any organism, as it does not require any prior sequence or modifying enzyme knowledge. In addition, besides fragmentation, RNA is not subjected to any other chemical or temperature treatment. However, MeRIP-seq does not provide single-nucleotide prediction of the methylation site as other methods do, although the methylated area can be narrowed down to a few nucleotides. The use of different modification-specific antibodies allows MeRIP to be adjusted for the different base modifications present on RNA, expanding the possible applications of this method.


Assuntos
5-Metilcitosina/metabolismo , Arabidopsis/metabolismo , Imunoprecipitação/métodos , RNA de Plantas/metabolismo , Arabidopsis/genética , Sequência de Bases , Metilação , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA de Plantas/genética , Análise de Sequência de RNA/métodos , Transcrição Genética
7.
Proc Natl Acad Sci U S A ; 117(26): 15316-15321, 2020 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-32541063

RESUMO

Noncoding RNA plays essential roles in transcriptional control and chromatin silencing. At Arabidopsis thaliana FLC, antisense transcription quantitatively influences transcriptional output, but the mechanism by which this occurs is still unclear. Proximal polyadenylation of the antisense transcripts by FCA, an RNA-binding protein that physically interacts with RNA 3' processing factors, reduces FLC transcription. This process genetically requires FLD, a homolog of the H3K4 demethylase LSD1. However, the mechanism linking RNA processing to FLD function had not been established. Here, we show that FLD tightly associates with LUMINIDEPENDENS (LD) and SET DOMAIN GROUP 26 (SDG26) in vivo, and, together, they prevent accumulation of monomethylated H3K4 (H3K4me1) over the FLC gene body. SDG26 interacts with the RNA 3' processing factor FY (WDR33), thus linking activities for proximal polyadenylation of the antisense transcripts to FLD/LD/SDG26-associated H3K4 demethylation. We propose this demethylation antagonizes an active transcription module, thus reducing H3K36me3 accumulation and increasing H3K27me3. Consistent with this view, we show that Polycomb Repressive Complex 2 (PRC2) silencing is genetically required by FCA to repress FLC Overall, our work provides insights into RNA-mediated chromatin silencing.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Regulação da Expressão Gênica de Plantas/fisiologia , RNA Antissenso , RNA de Plantas/metabolismo , Transcrição Genética/fisiologia , Proteínas de Arabidopsis/genética , Cromatina , RNA de Plantas/genética
8.
Nucleic Acids Res ; 48(14): e80, 2020 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-32496547

RESUMO

Small RNAs are important regulators of gene expression and are involved in human development and disease. Next generation sequencing (NGS) allows for scalable, genome-wide studies of small RNA; however, current methods are challenged by low sensitivity and high bias, limiting their ability to capture an accurate representation of the cellular small RNA population. Several studies have shown that this bias primarily arises during the ligation of single-strand adapters during library preparation, and that this ligation bias is magnified by 2'-O-methyl modifications (2'OMe) on the 3' terminal nucleotide. In this study, we developed a novel library preparation process using randomized splint ligation with a cleavable adapter, a design which resolves previous challenges associated with this ligation strategy. We show that a randomized splint ligation based workflow can reduce bias and increase the sensitivity of small RNA sequencing for a wide variety of small RNAs, including microRNA (miRNA) and tRNA fragments as well as 2'OMe modified RNA, including Piwi-interacting RNA and plant miRNA. Finally, we demonstrate that this workflow detects more differentially expressed miRNA between tumorous and matched normal tissues. Overall, this library preparation process allows for highly accurate small RNA sequencing and will enable studies of 2'OMe modified RNA with new levels of detail.


Assuntos
Biblioteca Gênica , Pequeno RNA não Traduzido/isolamento & purificação , Análise de Sequência de RNA/métodos , Eletroforese Capilar , Feminino , Humanos , Masculino , Metilação , MicroRNAs/química , MicroRNAs/genética , MicroRNAs/isolamento & purificação , Hibridização de Ácido Nucleico , Oligorribonucleotídeos/química , RNA Neoplásico/química , RNA Neoplásico/genética , RNA Neoplásico/isolamento & purificação , RNA de Plantas/química , RNA de Plantas/genética , RNA de Plantas/isolamento & purificação , Pequeno RNA não Traduzido/química , Pequeno RNA não Traduzido/genética , RNA de Transferência/química , RNA de Transferência/isolamento & purificação , Distribuição Aleatória , Sensibilidade e Especificidade , Alinhamento de Sequência
9.
Nat Commun ; 11(1): 2912, 2020 06 09.
Artigo em Inglês | MEDLINE | ID: mdl-32518237

RESUMO

Small RNAs play important roles during plant development by regulating transcript levels of target mRNAs, maintaining genome integrity, and reinforcing DNA methylation. Dicer-like 5 (Dcl5) is proposed to be responsible for precise slicing in many monocots to generate diverse 24-nt phased, secondary small interfering RNAs (phasiRNAs), which are exceptionally abundant in meiotic anthers of diverse flowering plants. The importance and functions of these phasiRNAs remain unclear. Here, we characterized several mutants of dcl5, including alleles generated by the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system and a transposon-disrupted allele. We report that dcl5 mutants have few or no 24-nt phasiRNAs, develop short anthers with defective tapetal cells, and exhibit temperature-sensitive male fertility. We propose that DCL5 and 24-nt phasiRNAs are critical for fertility under growth regimes for optimal yield.


Assuntos
Metilação de DNA , Regulação da Expressão Gênica de Plantas , Infertilidade das Plantas/genética , Proteínas de Plantas/fisiologia , Zea mays/genética , Alelos , Sistemas CRISPR-Cas , Edição de Genes , Mutagênese , Mutação , Proteínas de Plantas/genética , RNA de Plantas/genética , RNA Interferente Pequeno/metabolismo , Temperatura
10.
Plant Mol Biol ; 104(1-2): 39-53, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32564178

RESUMO

Plants are exposed to various environmental cues that lead to reactive oxygen species (ROS) accumulation. ROS production and detoxification are tightly regulated to maintain balance. Although studies of glucose (Glc) are always accompanied by ROS in animals, the role of Glc in respect of ROS in plants is unclear. We isolated gsm2 (Glc-hypersensitive mutant 2), a mutant with a notably chlorotic-cotyledon phenotype. The chloroplast-localized GSM2 was characterized as a transaldolase in the pentose phosphate pathway. With 3% Glc treatment, fewer or no thylakoids were observed in gsm2 cotyledon chloroplasts than in wild-type cotyledon chloroplasts, suggesting that GSM2 is required for chloroplast protection under stress. gsm2 also showed evaluated accumulation of ROS with 3% Glc treatment and was more sensitive to exogenous H2O2 than the wild type. Gene expression analysis of the antioxidant enzymes in gsm2 revealed that chloroplast damage to gsm2 cotyledons results from the accumulation of excessive ROS in response to Glc. Moreover, the addition of diphenyleneiodonium chloride or phenylalanine can rescue Glc-induced chlorosis in gsm2 cotyledons. This work suggests that GSM2 functions to maintain ROS balance in response to Glc during early seedling growth and sheds light on the relationship between Glc, the pentose phosphate pathway and ROS.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Homeostase , RNA Helicases/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Transaldolase/metabolismo , Ácido Abscísico/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Clorofila/metabolismo , Cloroplastos/genética , Cloroplastos/metabolismo , Cotilédone/metabolismo , Regulação da Expressão Gênica de Plantas , Germinação , Glucuronidase/metabolismo , Peróxido de Hidrogênio/metabolismo , Via de Pentose Fosfato/genética , Via de Pentose Fosfato/fisiologia , Fenótipo , RNA Helicases/genética , RNA de Plantas/genética , RNA de Plantas/isolamento & purificação , Plântula/genética , Plântula/metabolismo , Transaldolase/genética
11.
Plant Mol Biol ; 104(1-2): 55-65, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32572798

RESUMO

Increase in atmospheric carbon dioxide (CO2) has a significant effect on plant growth and development. To explore the elevated-CO2 response, we generated transcriptional profiles over a time course (2 h-14 days) of exposure to elevated CO2 in Arabidopsis thaliana. Genes related to photosynthesis were down-regulated and circadian rhythm-related genes were abnormally regulated in the early to middle phase of elevated CO2 exposure. To understand the novel mechanism of elevated CO2 signaling, we focused on 42 unknown small coding genes that showed differential expression patterns under elevated CO2 conditions. Four transgenic plants overexpressing the small coding gene exhibited a growth-defective phenotype under elevated CO2 but not under current CO2. Transcriptome analysis showed that circadian rhythm-related genes were commonly regulated in four transgenic plants. These circadian rhythm-related genes were transcribed in the dark when CO2 concentrations in the leaf was high. Taken together, our identified four small coding genes are likely to participate in elevated CO2 signaling to the circadian rhythm.


Assuntos
Arabidopsis/genética , Arabidopsis/metabolismo , Dióxido de Carbono/metabolismo , Ritmo Circadiano/genética , Ritmo Circadiano/fisiologia , Arabidopsis/crescimento & desenvolvimento , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Regulação para Baixo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Fenótipo , Fotossíntese/genética , Desenvolvimento Vegetal , Folhas de Planta/genética , Folhas de Planta/metabolismo , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/metabolismo , RNA de Plantas/genética , RNA de Plantas/isolamento & purificação , Transcriptoma
12.
J Plant Physiol ; 250: 153188, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32450394

RESUMO

Circular RNAs (circRNAs) are a newly characterized type of noncoding RNA and play important roles in microRNA (miRNA) function and transcriptional control. To unravel the mechanism of soybean circRNAs in low-temperature (LT) stress response, genome-wide identification of soybean circRNAs was conducted under LT (4 °C) treatment via deep sequencing. In this study, the existence of backsplicing sites was validated and circRNAs exhibited specific expression patterns in response to LT. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that circRNAs could participate in LT-responsive processes. Our study revealed a new circRNA-miRNA-mRNA network, which is involved in LT responses. Furthermore, soybean circRNAs were predicted to have potential to encode polypeptides or protein. Taken together, our results indicate that soybean circRNAs might encode proteins and be involved in the regulation of LT responses, providing clues regarding the molecular LT-responsive mechanisms in soybean.


Assuntos
Temperatura Baixa , RNA Circular/genética , RNA de Plantas/genética , Soja/fisiologia , Estresse Fisiológico/genética , Biologia Computacional , Sequenciamento de Nucleotídeos em Larga Escala , Folhas de Planta/genética , Folhas de Planta/fisiologia , RNA Circular/metabolismo , RNA de Plantas/metabolismo , Análise de Sequência de RNA , Soja/genética
13.
Nucleic Acids Res ; 48(12): 6481-6490, 2020 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-32463462

RESUMO

Natural antisense transcript-derived small interfering RNAs (nat-siRNAs) are a class of functional small RNA (sRNA) that have been found in both plant and animals kingdoms. In plants, these sRNAs have been shown to suppress the translation of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex (RISC) to their sequence-specific mRNA target(s). Current computational tools for classification of nat-siRNAs are limited in number and can be computationally infeasible to use. In addition, current methods do not provide any indication of the function of the predicted nat-siRNAs. Here, we present a new software pipeline, called NATpare, for prediction and functional analysis of nat-siRNAs using sRNA and degradome sequencing data. Based on our benchmarking in multiple plant species, NATpare substantially reduces the time required to perform prediction with minimal resource requirements allowing for comprehensive analysis of nat-siRNAs in larger and more complex organisms for the first time. We then exemplify the use of NATpare by identifying tissue and stress specific nat-siRNAs in multiple Arabidopsis thaliana datasets.


Assuntos
RNA de Plantas/genética , RNA Interferente Pequeno/química , Análise de Sequência de RNA/métodos , Software , Arabidopsis , Interferência de RNA , RNA de Plantas/metabolismo , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo
14.
Nature ; 581(7806): 89-93, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32376953

RESUMO

Small interfering RNAs (siRNAs) are essential for proper development and immunity in eukaryotes1. Plants produce siRNAs with lengths of 21, 22 or 24 nucleotides. The 21- and 24-nucleotide species mediate cleavage of messenger RNAs and DNA methylation2,3, respectively, but the biological functions of the 22-nucleotide siRNAs remain unknown. Here we report the identification and characterization of a group of endogenous 22-nucleotide siRNAs that are generated by the DICER-LIKE 2 (DCL2) protein in plants. When cytoplasmic RNA decay and DCL4 are deficient, the resulting massive accumulation of 22-nucleotide siRNAs causes pleiotropic growth disorders, including severe dwarfism, meristem defects and pigmentation. Notably, two genes that encode nitrate reductases-NIA1 and NIA2-produce nearly half of the 22-nucleotide siRNAs. Production of 22-nucleotide siRNAs triggers the amplification of gene silencing and induces translational repression both gene specifically and globally. Moreover, these 22-nucleotide siRNAs preferentially accumulate upon environmental stress, especially those siRNAs derived from NIA1/2, which act to restrain translation, inhibit plant growth and enhance stress responses. Thus, our research uncovers the unique properties of 22-nucleotide siRNAs, and reveals their importance in plant adaptation to environmental stresses.


Assuntos
Aclimatação/genética , Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , Biossíntese de Proteínas/genética , RNA de Plantas/genética , RNA Interferente Pequeno/genética , Arabidopsis/crescimento & desenvolvimento , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Proteínas Argonauta/metabolismo , Proteínas de Ciclo Celular , Inativação Gênica , Mutação , Nitrato Redutase/genética , Doenças das Plantas/genética , Estabilidade de RNA , RNA Mensageiro/genética , RNA Interferente Pequeno/biossíntese , Ribonuclease III/metabolismo
15.
PLoS One ; 15(5): e0225564, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32380515

RESUMO

Senna tora is an annual herb with rich source of anthraquinones that have tremendous pharmacological properties. However, there is little mention of genetic information for this species, especially regarding the biosynthetic pathways of anthraquinones. To understand the key genes and regulatory mechanism of anthraquinone biosynthesis pathways, we performed spatial and temporal transcriptome sequencing of S. tora using short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) technologies, and generated two unigene sets composed of 118,635 and 39,364, respectively. A comprehensive functional annotation and classification with multiple public databases identified array of genes involved in major secondary metabolite biosynthesis pathways and important transcription factor (TF) families (MYB, MYB-related, AP2/ERF, C2C2-YABBY, and bHLH). Differential expression analysis indicated that the expression level of genes involved in anthraquinone biosynthetic pathway regulates differently depending on the degree of tissues and seeds development. Furthermore, we identified that the amount of anthraquinone compounds were greater in late seeds than early ones. In conclusion, these results provide a rich resource for understanding the anthraquinone metabolism in S. tora.


Assuntos
Antraquinonas/metabolismo , Sementes/genética , Extrato de Senna/metabolismo , Senna (Planta)/genética , Senna (Planta)/metabolismo , Transcriptoma , Regulação da Expressão Gênica de Plantas , Folhas de Planta/genética , Folhas de Planta/crescimento & desenvolvimento , Proteínas de Plantas/genética , Raízes de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , RNA de Plantas/genética , RNA-Seq , Reação em Cadeia da Polimerase em Tempo Real , Sementes/crescimento & desenvolvimento , Fatores de Transcrição/genética
16.
PLoS One ; 15(5): e0233076, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32428011

RESUMO

Nitrogen is an important nutrient for plant growth and tuber quality of potato. Since potato crop requires high dose of N, improving nitrogen use efficiency (NUE) of plant is an inevitable approach to minimize N fertilization. The aim of this study was to identify and characterize microRNAs (miRNAs) by small RNA sequencing in potato plants grown in aeroponic under two contrasting N (high and low) regimes. A total of 119 conserved miRNAs belonging to 41 miRNAs families, and 1002 putative novel miRNAs were identified. From total, 52 and 54 conserved miRNAs, and 404 and 628 putative novel miRNAs were differentially expressed in roots and shoots, respectively under low N stress. Of total 34,135 predicted targets, the gene ontology (GO) analysis indicated that maximum targets belong to biological process followed by molecular function and cellular component. Eexpression levels of the selected miRNAs and targets were validated by real time-quantitative polymerase chain reaction (RT-qPCR) analysis. Two predicted targets of potential miRNAs (miR397 and miR398) were validated by 5' RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). In general, predicted targets are associated with stress-related, kinase, transporters and transcription factors such as universal stress protein, heat shock protein, salt-tolerance protein, calmodulin binding protein, serine-threonine protein kinsae, Cdk10/11- cyclin dependent kinase, amino acid transporter, nitrate transporter, sugar transporter, transcription factor, F-box family protein, and zinc finger protein etc. Our study highlights that miR397 and miR398 play crucial role in potato during low N stress management. Moreover, study provides insights to modulate miRNAs and their predicted targets to develop N-use efficient potato using transgenic/genome-editing tools in future.


Assuntos
Perfilação da Expressão Gênica/métodos , MicroRNAs/genética , Solanum tuberosum/crescimento & desenvolvimento , Sequenciamento Completo do Genoma/métodos , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Nitrogênio/metabolismo , Proteínas de Plantas/genética , Raízes de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , Raízes de Plantas/metabolismo , Brotos de Planta/genética , Brotos de Planta/crescimento & desenvolvimento , Brotos de Planta/metabolismo , RNA de Plantas/genética , Análise de Sequência de RNA , Solanum tuberosum/genética , Solanum tuberosum/metabolismo , Estresse Fisiológico
17.
Int J Mol Sci ; 21(8)2020 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-32290539

RESUMO

Target of rapamycin (TOR) acts as a master regulator in coordination of cell growth with energy and nutrient availability. Despite the increased appreciation of the essential role of the TOR complex in interaction with phytohormone signaling, little is known about its function on ethylene signaling. Here, through expression analysis, genetic and biochemical approaches, we reveal that TOR functions in the regulation of ethylene signals. Transcriptional analysis indicates that TOR inhibition by AZD8055 upregulated senescence- and ethylene-related genes expression. Furthermore, ethylene insensitive mutants like etr1-1, ein2-5 and ein3 eil1, showed more hyposensitivity to AZD8055 than that of WT in hypocotyl growth inhibition. Similarly, blocking ethylene signals by ethylene action inhibitor Ag+ or biosynthesis inhibitor aminoethoxyvinylglycine (AVG) largely rescued hypocotyl growth even in presence of AZD8055. In addition, we also demonstrated that Type 2A phosphatase-associated protein of 46 kDa (TAP46), a downstream component of TOR signaling, physically interacts with 1-aminocy-clopropane-1-carboxylate (ACC) synthase ACS2 and ACS6. Arabidopsis overexpressing ACS2 or ACS6 showed more hypersensitivity to AZD8055 than WT in hypocotyl growth inhibition. Moreover, ACS2/ACS6 protein was accumulated under TOR suppression, implying TOR modulates ACC synthase protein levels. Taken together, our results indicate that TOR participates in negatively modulating ethylene signals and the molecular mechanism is likely involved in the regulation of ethylene biosynthesis by affecting ACSs in transcription and protein levels.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Etilenos/metabolismo , Fosfatidilinositol 3-Quinases/metabolismo , Regulação da Expressão Gênica de Plantas/fisiologia , Reguladores de Crescimento de Planta/metabolismo , RNA de Plantas/genética , Transdução de Sinais/fisiologia
18.
Plant Mol Biol ; 103(3): 341-354, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32227258

RESUMO

KEY MESSAGE: We employed both metabolomic and transcriptomic approaches to explore the accumulation patterns of physalins, flavonoids and chlorogenic acid in Physalis angulata and revealed the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment. Physalis angulata L. is an annual Solanaceae plant with a number of medicinally active compounds. Despite the potential pharmacological benefits of P. angulata, the scarce genomic information regarding this plant has limited the studies on the mechanisms of bioactive compound biosynthesis. To facilitate the basic understanding of the main chemical constituent biosynthesis pathways, we performed both metabolomic and transcriptomic approaches to reveal the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment. Untargeted metabolome analysis showed that most physalins, flavonoids and chlorogenic acid were significantly upregulated. Targeted HPLC-MS/MS analysis confirmed variations in the contents of two important representative steroid derivatives (physalins B and G), total flavonoids, neochlorogenic acid, and chlorogenic acid between MeJA-treated plants and controls. Transcript levels of a few steroid biosynthesis-, flavonoid biosynthesis-, and chlorogenic acid biosynthesis-related genes were upregulated, providing a potential explanation for MeJA-induced active ingredient synthesis in P. angulata. Systematic correlation analysis identified a number of novel candidate genes associated with bioactive compound biosynthesis. These results may help to elucidate the regulatory mechanism underlying MeJA-induced active compound accumulation and provide several valuable candidate genes for further functional study.


Assuntos
Acetatos/farmacologia , Ciclopentanos/farmacologia , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Oxilipinas/farmacologia , Physalis/efeitos dos fármacos , Physalis/metabolismo , Proteínas de Plantas/metabolismo , Flavonoides/biossíntese , Flavonoides/química , Metaboloma , Estrutura Molecular , Reguladores de Crescimento de Planta/farmacologia , Proteínas de Plantas/genética , Raízes de Plantas/genética , Raízes de Plantas/metabolismo , RNA de Plantas/genética , Transcriptoma
19.
Gene ; 746: 144652, 2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32259631

RESUMO

Circular RNAs (circRNAs), a novel branch of noncoding RNAs, are widespread in eukaryotic cells. Particularly, due to their abilities to bind microRNA (miRNA) and serve as "sponges", circRNAs can regulate gene expression and participate in multiple biological processes. To detect the function of the circRNAs in tomato resistance, in our study, high-throughput sequencing were used to detect the circRNAs in tomatoes before and after Phytophthora infestans (P. infestans) infection. A total of 68 circRNAs were identified, of them, 18 (26%) were termed as exonic circRNAs, 33 (49%) were termed as intergenic circRNAs, 17 (25%) were termed as intronic circRNAs. Thirty-six out of 68 circRNAs differentially expressed in tomatoes after infection, including 9 up- and 27 down-regulated. Among the up-regulated circRNAs, two exoinc circRNAs, circRNA45 and circRNA47 were annotated as whitefly-induced gp91-phox and ethylene-forming enzyme, respectively. Both of them could act as miR477-3p sponge. Transgenic plants transiently overexpressed circRNA45 and circRNA47 both displayed smaller lesion area than the control plants upon infection, accompanied by lower expression levels of miR477-3p. Furthermore, transiently overexpression of miR477-3p in tomatoes leading to a decline in their targeted disease related genes expression. Our results firstly identified circRNAs in tomato upon P. infestans infection and demonstrated that circRNA45 and circRNA47 may act as positive regulators in tomato resistance by regulating miRNA-mRNAs expression levels.


Assuntos
Resistência à Doença/genética , Regulação da Expressão Gênica de Plantas , Lycopersicon esculentum , Phytophthora infestans , Doenças das Plantas , RNA Circular , RNA de Plantas , Lycopersicon esculentum/genética , Lycopersicon esculentum/metabolismo , Lycopersicon esculentum/microbiologia , MicroRNAs/biossíntese , MicroRNAs/genética , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , RNA Circular/biossíntese , RNA Circular/genética , RNA de Plantas/biossíntese , RNA de Plantas/genética
20.
RNA ; 26(7): 784-793, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32241834

RESUMO

Long noncoding RNAs (lncRNAs) have recently emerged as prominent regulators of gene expression in eukaryotes. LncRNAs often drive the modification and maintenance of gene activation or gene silencing states via chromatin conformation rearrangements. In plants, lncRNAs have been shown to participate in gene regulation, and are essential to processes such as vernalization and photomorphogenesis. Despite their prominent functions, only over a dozen lncRNAs have been experimentally and functionally characterized. Similar to its animal counterparts, the rates of sequence divergence are much higher in plant lncRNAs than in protein coding mRNAs, making it difficult to identify lncRNA conservation using traditional sequence comparison methods. Beyond this, little is known about the evolutionary patterns of lncRNAs in plants. Here, we characterized the splicing conservation of lncRNAs in Brassicaceae. We generated a whole-genome alignment of 16 Brassica species and used it to identify synthenic lncRNA orthologs. Using a scoring system trained on transcriptomes from A. thaliana and B. oleracea, we identified splice sites across the whole alignment and measured their conservation. Our analysis revealed that 17.9% (112/627) of all intergenic lncRNAs display splicing conservation in at least one exon, an estimate that is substantially higher than previous estimates of lncRNA conservation in this group. Our findings agree with similar studies in vertebrates, demonstrating that splicing conservation can be evidence of stabilizing selection. We provide conclusive evidence for the existence of evolutionary deeply conserved lncRNAs in plants and describe a generally applicable computational workflow to identify functional lncRNAs in plants.


Assuntos
Sequência Conservada/genética , Processamento de RNA/genética , RNA Longo não Codificante/genética , RNA de Plantas/genética , Arabidopsis/genética , Brassica/genética , Evolução Molecular , Genoma de Planta/genética , RNA Mensageiro/genética
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