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1.
Arch Virol ; 165(5): 1177-1190, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32232674

RESUMO

Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) play vital roles in plant defense responses against viral infections. However, there is no systematic understanding of lncRNAs and circRNAs and their competing endogenous RNA (ceRNA) networks in watermelon under cucumber green mottle mosaic virus (CGMMV) stress. Here, we present the characterization and expression profiles of lncRNAs and circRNAs in watermelon leaves 48-h post-inoculation (48 hpi) with CGMMV, with mock inoculation as a control. Deep sequencing analysis revealed 2373 lncRNAs and 606 circRNAs in the two libraries. Among them, 67 lncRNAs (40 upregulated and 27 downregulated) and 548 circRNAs (277 upregulated and 271 downregulated) were differentially expressed (DE) in the 48 hpi library compared with the control library. Furthermore, 263 cis-acting matched lncRNA-mRNA pairs were detected for 49 of the DE-lncRNAs. KEGG pathway analysis of the cis target genes of the DE-lncRNAs revealed significant associations with phenylalanine metabolism, the citrate cycle (TCA cycle), and endocytosis. Additionally, 30 DE-lncRNAs were identified as putative target mimics of 33 microRNAs (miRNAs), and 153 DE-circRNAs were identified as putative target mimics of 88 miRNAs. Furthermore, ceRNA networks of lncRNA/circRNA-miRNA-mRNA in response to CGMMV infection are described, with 12 DE-lncRNAs and 65 DE-circRNAs combining with 22 miRNAs and competing for the miRNA binding sites on 29 mRNAs. The qRT-PCR validation of selected lncRNAs and circRNAs showed a general correlation with the high-throughput sequencing results. This study provides a valuable resource of lncRNAs and circRNAs involved in the response to CGMMV infection in watermelon.


Assuntos
Citrullus/virologia , Interações Hospedeiro-Patógeno , Doenças das Plantas/virologia , RNA Circular/metabolismo , RNA Longo não Codificante/metabolismo , RNA de Plantas/metabolismo , Tobamovirus/crescimento & desenvolvimento , Citrullus/imunologia , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Sequenciamento de Nucleotídeos em Larga Escala , Doenças das Plantas/imunologia , Reação em Cadeia da Polimerase em Tempo Real
2.
PLoS One ; 15(2): e0228850, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32069300

RESUMO

Environmental stresses influence the growth and development of plants by influencing patterns of gene expression. Different regulators control gene expression, including transcription factors (TFs) and microRNAs. MicroRNAs (miRNAs: ~21 nucleotides long) are encoded by miRNA genes transcribed by RNA polymerase II (RNP-II) and play key roles in plant development and physiology. There is little knowledge currently available on miRNAs and their function in response to environmental stresses in safflower. To obtain more information on safflower miRNAs, we initially used a comparative genomics approach and succeeded in identifying 126 miRNAs belonging to 29 conserved families, along with their target genes. In this study, we investigated the expression profiles of seven conserved miRNAs related to drought, salinity, heat, and Cd stress in the leaf and root organs using qRT-PCR, for the first time. Gene Ontology (GO) analysis found that target genes of miRNAs are often TFs such as AP2/ERF and HD-ZIP as well as NAC domain-containing proteins. Expression analyses confirmed that miRNAs can play a vital role in keeping safflower stress-tolerant. Differential expression of miR156, miR162, miR164, miR166, miR172, miR398, and miR408 regulate the expression of their respective target genes. These genes activate several pathways leading to physiological and biochemical responses to abiotic stresses. Some conserved miRNAs were regulated by abiotic stresses. Our finding provides valuable information to understand miRNAs in relation to different abiotic stresses in safflower.


Assuntos
Carthamus tinctorius/genética , RNA de Plantas/genética , Carthamus tinctorius/crescimento & desenvolvimento , Carthamus tinctorius/metabolismo , Secas , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Temperatura Alta , MicroRNAs/genética , MicroRNAs/metabolismo , Proteínas de Plantas/genética , RNA de Plantas/metabolismo , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Salinidade , Estresse Fisiológico/genética , Fatores de Transcrição/genética
3.
PLoS Biol ; 18(1): e3000582, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31995554

RESUMO

In most plants, centromeric DNA contains highly repetitive sequences, including tandem repeats and retrotransposons; however, the roles of these sequences in the structure and function of the centromere are unclear. Here, we found that multiple RNA sequences from centromeric retrotransposons (CRMs) were enriched in maize (Zea mays) centromeres, and back-spliced RNAs were generated from CRM1. We identified 3 types of CRM1-derived circular RNAs with the same back-splicing site based on the back-spliced sequences. These circular RNAs bound to the centromere through R-loops. Two R-loop sites inside a single circular RNA promoted the formation of chromatin loops in CRM1 regions. When RNA interference (RNAi) was used to target the back-splicing site of the circular CRM1 RNAs, the levels of R-loops and chromatin loops formed by these circular RNAs decreased, while the levels of R-loops produced by linear RNAs with similar binding sites increased. Linear RNAs with only one R-loop site could not promote chromatin loop formation. Higher levels of R-loops and lower levels of chromatin loops in the CRM1 regions of RNAi plants led to a reduced localization of the centromeric H3 variant (CENH3). Our work reveals centromeric chromatin organization by circular CRM1 RNAs via R-loops and chromatin loops, which suggested that CRM1 elements might help build a suitable chromatin environment during centromere evolution. These results highlight that R-loops are integral components of centromeric chromatin and proper centromere structure is essential for CENH3 localization.


Assuntos
Centrômero/metabolismo , Cromatina , Conformação de Ácido Nucleico , RNA de Plantas/metabolismo , Retroelementos/genética , Zea mays/genética , Sítios de Ligação/genética , Proteína Centromérica A/genética , Proteína Centromérica A/metabolismo , Cromatina/química , Cromatina/genética , Cromatina/metabolismo , DNA de Plantas/química , DNA de Plantas/genética , DNA de Plantas/metabolismo , Regulação da Expressão Gênica de Plantas , Plantas Geneticamente Modificadas , Processamento de RNA/fisiologia , RNA Circular/genética , RNA Circular/metabolismo , RNA de Plantas/genética , Zea mays/metabolismo
4.
Nucleic Acids Res ; 48(5): 2258-2270, 2020 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-31943065

RESUMO

MicroRNAs (miRNAs) are short, non-coding RNAs that modulate the translation-rate of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex to sequence-specific targets. In plants, this typically results in cleavage and subsequent degradation of the mRNA. Degradome sequencing is a high-throughput technique developed to capture cleaved mRNA fragments and thus can be used to support miRNA target prediction. The current criteria used for miRNA target prediction were inferred on a limited number of experimentally validated A. thaliana interactions and were adapted to fit these specific interactions; thus, these fixed criteria may not be optimal across all datasets (organisms, tissues or treatments). We present a new tool, PAREameters, for inferring targeting criteria from small RNA and degradome sequencing datasets. We evaluate its performance using a more extensive set of experimentally validated interactions in multiple A. thaliana datasets. We also perform comprehensive analyses to highlight and quantify the differences between subsets of miRNA-mRNA interactions in model and non-model organisms. Our results show increased sensitivity in A. thaliana when using the PAREameters inferred criteria and that using data-driven criteria enables the identification of additional interactions that further our understanding of the RNA silencing pathway in both model and non-model organisms.


Assuntos
Arabidopsis/genética , Biologia Computacional/métodos , Regulação da Expressão Gênica de Plantas , MicroRNAs/genética , RNA Mensageiro/genética , RNA de Plantas/genética , Software , Arabidopsis/metabolismo , Sequência de Bases , Conjuntos de Dados como Assunto , Flores/genética , Flores/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , MicroRNAs/metabolismo , Folhas de Planta/genética , Folhas de Planta/metabolismo , Clivagem do RNA , RNA Mensageiro/metabolismo , RNA de Plantas/metabolismo , Sensibilidade e Especificidade , Análise de Sequência de RNA , Transcriptoma
5.
Plant Mol Biol ; 102(1-2): 55-72, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31748889

RESUMO

KEY MESSAGE: Differential expression of mi-RNAs targeting developmental processes and progressive downregulation of repeat-associated siRNAs following genome merger and genome duplication in the context of allopolyploid speciation in Spartina. The role of small RNAs on gene expression regulation and genome stability is arousing increased interest and is being explored in various plant systems. In spite of prominence of reticulate evolution and polyploidy that affects the evolutionary history of all plant lineages, very few studies analysed RNAi mechanisms with this respect. Here, we explored small RNAs diversity and expression in the context of recent allopolyploid speciation, using the Spartina system, which offers a unique opportunity to explore the immediate changes following hybridization and genome duplication. Small RNA-Seq analyses were conducted on hexaploid parental species (S. alterniflora and S. maritima), their F1 hybrid S. x townsendii, and the neoallododecaploid S. anglica. We identified 594 miRNAs, 2197 miRNA-target genes, and 3730 repeat-associated siRNAs (mostly targeting Class I/Copia-Ivana- Copia-SIRE and LINEs elements). For both mi- and ra-siRNAs, we detected differential expression patterns following genome merger and genome duplication. These misregulations include non-additive expression of miRNAs in the F1 hybrid and additional changes in the allopolyploid targeting developmental processes. Expression of repeat-associated siRNAs indicates a strengthen of transposable element repression during the allopolyploidization process. Altogether, these results confirm the central role small RNAs play in shaping regulatory changes in naturally formed recent allopolyploids.


Assuntos
Regulação da Expressão Gênica de Plantas , Hibridização Genética , MicroRNAs/genética , MicroRNAs/metabolismo , Poaceae/genética , Poaceae/metabolismo , RNA de Plantas/genética , RNA de Plantas/metabolismo , Sequência de Bases , Elementos de DNA Transponíveis , DNA de Plantas , Genes de Plantas/genética , Genoma de Planta , Instabilidade Genômica , Anotação de Sequência Molecular , Poliploidia
6.
Food Chem ; 309: 125779, 2020 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-31704074

RESUMO

Germinated edible seeds and sprouts are becoming increasingly common in the human diet because they are rich in bioactive compounds and antioxidants and are highly nutritious. In this study, the effects of NaCl stress and supplemental CaCl2 on carotenoid accumulation, antioxidant capacity and expression of key enzymes in yellow maize kernels were investigated. The results showed that the lutein and zeaxanthin contents increased with NaCl treatment, and further increased with supplemental CaCl2. Additionally, germinated yellow maize kernels showed increased antioxidant capacity in response to NaCl and CaCl2. The transcript levels of carotenogenic genes ZmPSY and ZmCYP97C were upregulated and the expression levels of ZmLCYB and ZmBCH1 were downregulated under NaCl stress. The expression of all key carotenogenic genes was upregulated by CaCl2 supplementation. These results suggested that NaCl and CaCl2 contribute to carotenoid accumulation via increased expression of related carotenogenic genes and increased antioxidant capacity in germinated yellow maize kernels.


Assuntos
Carotenoides/metabolismo , Cloreto de Sódio/farmacologia , Zea mays/efeitos dos fármacos , Antioxidantes/química , Antioxidantes/metabolismo , Cloreto de Cálcio/farmacologia , Carotenoides/análise , Cromatografia Líquida de Alta Pressão , Germinação , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA de Plantas/genética , RNA de Plantas/metabolismo , Sementes/efeitos dos fármacos , Sementes/crescimento & desenvolvimento , Sementes/metabolismo , Regulação para Cima/efeitos dos fármacos , Zea mays/metabolismo
7.
Int J Mol Sci ; 21(1)2019 Dec 25.
Artigo em Inglês | MEDLINE | ID: mdl-31881689

RESUMO

Potato is an important food crop and its production is susceptible to drought. Drought stress in crop growth is usually multiple- or long-term. In this study, the drought tolerant potato landrace Jancko Sisu Yari was treated with drought stress, rehydration and re-dehydration, and RNA-seq was applied to analyze the characteristics of gene regulation during these treatments. The results showed that drought-responsive genes mainly involved photosynthesis, signal transduction, lipid metabolism, sugar metabolism, wax synthesis, cell wall regulation, osmotic adjustment. Potato also can be recovered well in the re-emergence of water through gene regulation. The recovery of rehydration mainly related to patatin, lipid metabolism, sugar metabolism, flavonoids metabolism and detoxification besides the reverse expression of the most of drought-responsive genes. The previous drought stress can produce a positive responsive ability to the subsequent drought by drought hardening. Drought hardening was not only reflected in the drought-responsive genes related to the modified structure and cell components, but also in the hardening of gene expression or the "memory" of drought-responsive genes. Abundant genes involved photosynthesis, signal transduction, sugar metabolism, protease and protease inhibitors, flavonoids metabolism, transporters and transcription factors were subject to drought hardening or memorized drought in potato.


Assuntos
Secas , Solanum tuberosum/metabolismo , Transcriptoma , Água/metabolismo , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA de Plantas/química , RNA de Plantas/metabolismo , Solanum tuberosum/genética
8.
Int J Mol Sci ; 21(1)2019 Dec 25.
Artigo em Inglês | MEDLINE | ID: mdl-31881735

RESUMO

The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.


Assuntos
Redes Reguladoras de Genes , Plantas/metabolismo , RNA de Plantas/metabolismo , Análise de Sequência de RNA/métodos , Transcriptoma , Imunoprecipitação da Cromatina , Biblioteca Gênica , Plantas/genética , RNA de Plantas/química
9.
Elife ; 82019 12 17.
Artigo em Inglês | MEDLINE | ID: mdl-31845648

RESUMO

Trans-species small regulatory RNAs (sRNAs) are delivered to host plants from diverse pathogens and parasites and can target host mRNAs. How trans-species sRNAs can be effective on diverse hosts has been unclear. Multiple species of the parasitic plant Cuscuta produce trans-species sRNAs that collectively target many host mRNAs. Confirmed target sites are nearly always in highly conserved, protein-coding regions of host mRNAs. Cuscuta trans-species sRNAs can be grouped into superfamilies that have variation in a three-nucleotide period. These variants compensate for synonymous-site variation in host mRNAs. By targeting host mRNAs at highly conserved protein-coding sites, and simultaneously expressing multiple variants to cover synonymous-site variation, Cuscuta trans-species sRNAs may be able to successfully target multiple homologous mRNAs from diverse hosts.


Assuntos
Arabidopsis/parasitologia , Cuscuta/genética , Regulação da Expressão Gênica de Plantas , Genoma de Planta , RNA Mensageiro/genética , Pequeno RNA não Traduzido/genética , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Sequência de Bases , Códon , Biologia Computacional , Sequência Conservada , Cuscuta/crescimento & desenvolvimento , Cuscuta/metabolismo , Variação Genética , Interações Hospedeiro-Parasita , Fases de Leitura Aberta , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA Mensageiro/classificação , RNA Mensageiro/metabolismo , RNA de Plantas/genética , RNA de Plantas/metabolismo , Pequeno RNA não Traduzido/classificação , Pequeno RNA não Traduzido/metabolismo , Alinhamento de Sequência , Tabaco/genética , Tabaco/crescimento & desenvolvimento , Tabaco/parasitologia
10.
BMC Bioinformatics ; 20(Suppl 25): 687, 2019 Dec 24.
Artigo em Inglês | MEDLINE | ID: mdl-31874613

RESUMO

BACKGROUND: Bamboo is a very important forest resource. However, the prolonged vegetative stages and uncertainty of flowering brings difficulties in bamboo flowers sampling. Until now, the flowering mechanism of bamboo is still unclear. RESULTS: In this study, three successive stages of flowering buds and the corresponding vegetative buds (non-flowering stage) from Lei bamboo (Phyllostachys violascens) were collected for transcriptome analysis using Illumina RNA-Seq method. We generated about 442 million clean reads from the above samples, and 132,678 unigenes were acquired with N50 of 1080 bp. A total of 7266 differentially expressed genes (DEGs) were determined. According to expression profile and gene function analysis, some environmental stress responsive and plant hormone-related DEGs were highly expressed in the inflorescence meristem formation stage (TF_1) while some floral organ development related genes were up-regulated significantly in floral organs determination stage (TF_2) and floral organs maturation (TF_3) stage, implying the essential roles of these DEGs in flower induction and maturation of Lei bamboo. Additionally, a total of 25 MADS-box unigenes were identified. Based on the expression profile, B, C/D and E clade genes were more related to floral organs development compared with A clade genes in Lei bamboo. CONCLUSIONS: This transcriptome data presents fundamental information about the genes and pathways involved in flower induction and development of Lei bamboo. Moreover, a critical sampling method is provided which could be benefit for bamboo flowering mechanism study.


Assuntos
Perfilação da Expressão Gênica/métodos , Poaceae/genética , Flores/genética , Flores/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Proteínas de Domínio MADS/classificação , Proteínas de Domínio MADS/genética , Filogenia , Poaceae/crescimento & desenvolvimento , RNA de Plantas/química , RNA de Plantas/genética , RNA de Plantas/metabolismo , RNA-Seq
11.
BMC Plant Biol ; 19(1): 563, 2019 Dec 18.
Artigo em Inglês | MEDLINE | ID: mdl-31852430

RESUMO

BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level in eukaryotes. In rice, MIR7695 expression is regulated by infection with the rice blast fungus Magnaporthe oryzae with subsequent down-regulation of an alternatively spliced transcript of natural resistance-associated macrophage protein 6 (OsNramp6). NRAMP6 functions as an iron transporter in rice. RESULTS: Rice plants grown under high iron supply showed blast resistance, which supports that iron is a factor in controlling blast resistance. During pathogen infection, iron accumulated in the vicinity of M. oryzae appressoria, the sites of pathogen entry, and in cells surrounding infected regions of the rice leaf. Activation-tagged MIR7695 rice plants (MIR7695-Ac) exhibited enhanced iron accumulation and resistance to M. oryzae infection. RNA-seq analysis revealed that blast resistance in MIR7695-Ac plants was associated with strong induction of defense-related genes, including pathogenesis-related and diterpenoid biosynthetic genes. Levels of phytoalexins during pathogen infection were higher in MIR7695-Ac than wild-type plants. Early phytoalexin biosynthetic genes, OsCPS2 and OsCPS4, were also highly upregulated in wild-type rice plants grown under high iron supply. CONCLUSIONS: Our data support a positive role of miR7695 in regulating rice immunity that further underpin links between defense and iron signaling in rice. These findings provides a basis to better understand regulatory mechanisms involved in rice immunity in which miR7695 participates which has a great potential for the development of strategies to improve blast resistance in rice.


Assuntos
Resistência à Doença/genética , Regulação da Expressão Gênica de Plantas , Magnaporthe/fisiologia , Oryza/genética , Oryza/imunologia , Doenças das Plantas/imunologia , RNA de Plantas/genética , MicroRNAs/genética , MicroRNAs/metabolismo , RNA de Plantas/metabolismo
12.
BMC Plant Biol ; 19(1): 570, 2019 Dec 19.
Artigo em Inglês | MEDLINE | ID: mdl-31856702

RESUMO

BACKGROUND: Oilseed rape is an excellent candidate for phytoremediation of cadmium (Cd) contaminated soils given its advantages of high biomass, fast growth, moderate metal accumulation, ease of harvesting, and metal tolerance, but the cadmium response pathways in this species (Brassica napus) have yet to be fully elucidated. A combined analysis of miRNA and mRNA expression to infer Cd-induced regulation has not been reported in B. napus. RESULTS: We characterized concurrent changes in miRNA and mRNA profiles in the roots and shoots of B. napus seedlings after 10 days of 10 mg/L Cd2+ treatment. Cd treatment significantly affected the expression of 22 miRNAs belonging to 11 families in the root and 29 miRNAs belonging to 14 miRNA families in the shoot. Five miRNA families (MIR395, MIR397, MIR398, MIR408 and MIR858) and three novel miRNAs were differentially expressed in both tissues. A total of 399 differentially expressed genes (DEGs) in the root and 389 DEGs in the shoot were identified, with very little overlap between tissue types. Eight anti-regulation miRNA-mRNA interaction pairs in the root and eight in the shoot were identified in response to Cd and were involved in key plant stress response pathways: for example, four genes targeted by miR398 were involved in a pathway for detoxification of superoxide radicals. Cd stress significantly impacted the photosynthetic pathway. Transcription factor activation, antioxidant response pathways and secondary metabolic processes such as glutathione (GSH) and phenylpropanoid metabolism were identified as major components for Cd-induced response in both roots and shoots. CONCLUSIONS: Combined miRNA and mRNA profiling revealed miRNAs, genes and pathways involved in Cd response which are potentially critical for adaptation to Cd stress in B. napus. Close crosstalk between several Cd-induced miRNAs and mRNAs was identified, shedding light on possible mechanisms for response to Cd stress in underground and aboveground tissues in B. napus. The pathways, genes, and miRNAs identified here will be valuable targets for future improvement of cadmium tolerance in B. napus.


Assuntos
Brassica napus/efeitos dos fármacos , Cádmio/efeitos adversos , MicroRNAs/genética , RNA Mensageiro/genética , RNA de Plantas/genética , Poluentes do Solo/efeitos adversos , Brassica napus/genética , MicroRNAs/metabolismo , RNA Mensageiro/metabolismo , RNA de Plantas/metabolismo , Plântula/efeitos dos fármacos , Plântula/genética , Estresse Fisiológico , Transcriptoma
13.
BMC Genomics ; 20(1): 997, 2019 Dec 19.
Artigo em Inglês | MEDLINE | ID: mdl-31856707

RESUMO

BACKGROUND: Small RNAs (sRNAs) are regulatory molecules impacting on gene expression and transposon activity. MicroRNAs (miRNAs) are responsible for tissue-specific and environmentally-induced gene repression. Short interfering RNAs (siRNA) are constitutively involved in transposon silencing across different type of tissues. The male gametophyte in angiosperms has a unique set of sRNAs compared to vegetative tissues, including phased siRNAs from intergenic or genic regions, or epigenetically activated siRNAs. This is contrasted by a lack of knowledge about the sRNA profile of the male gametophyte of gymnosperms. RESULTS: Here, we isolated mature pollen from male cones of Norway spruce and investigated its sRNA profiles. While 21-nt sRNAs is the major size class of sRNAs in needles, in pollen 21-nt and 24-nt sRNAs are the most abundant size classes. Although the 24-nt sRNAs were exclusively derived from TEs in pollen, both 21-nt and 24-nt sRNAs were associated with TEs. We also investigated sRNAs from somatic embryonic callus, which has been reported to contain 24-nt sRNAs. Our data show that the 24-nt sRNA profiles are tissue-specific and differ between pollen and cell culture. CONCLUSION: Our data reveal that gymnosperm pollen, like angiosperm pollen, has a unique sRNA profile, differing from vegetative leaf tissue. Thus, our results reveal that angiosperm and gymnosperm pollen produce new size classes not present in vegetative tissues; while in angiosperm pollen 21-nt sRNAs are generated, in the gymnosperm Norway spruce 24-nt sRNAs are generated. The tissue-specific production of distinct TE-derived sRNAs in angiosperms and gymnosperms provides insights into the diversification process of sRNAs in TE silencing pathways between the two groups of seed plants.


Assuntos
Sequências Repetitivas Dispersas , Picea/genética , RNA de Plantas/metabolismo , Pequeno RNA não Traduzido/metabolismo , Loci Gênicos , Picea/embriologia , Picea/metabolismo , Pólen/genética , Pólen/metabolismo , RNA de Plantas/fisiologia , Pequeno RNA não Traduzido/fisiologia
14.
Nat Commun ; 10(1): 3916, 2019 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-31477705

RESUMO

Transcription by RNA polymerase V (Pol V) in plants is required for RNA-directed DNA methylation, leading to transcriptional gene silencing. Global chromatin association of Pol V requires components of the DDR complex DRD1, DMS3 and RDM1, but the assembly process of this complex and the underlying mechanism for Pol V recruitment remain unknown. Here we show that all DDR complex components co-localize with Pol V, and we report the cryoEM structures of two complexes associated with Pol V recruitment-DR (DMS3-RDM1) and DDR' (DMS3-RDM1-DRD1 peptide), at 3.6 Å and 3.5 Å resolution, respectively. RDM1 dimerization at the center frames the assembly of the entire complex and mediates interactions between DMS3 and DRD1 with a stoichiometry of 1 DRD1:4 DMS3:2 RDM1. DRD1 binding to the DR complex induces a drastic movement of a DMS3 coiled-coil helix bundle. We hypothesize that both complexes are functional intermediates that mediate Pol V recruitment.


Assuntos
Proteínas de Arabidopsis/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Metilação de DNA , Proteínas de Ligação a DNA/metabolismo , RNA Polimerases Dirigidas por DNA/metabolismo , RNA de Plantas/metabolismo , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/ultraestrutura , Proteínas Cromossômicas não Histona/genética , Proteínas Cromossômicas não Histona/ultraestrutura , Microscopia Crioeletrônica , DNA de Plantas/genética , DNA de Plantas/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/ultraestrutura , RNA Polimerases Dirigidas por DNA/genética , RNA Polimerases Dirigidas por DNA/ultraestrutura , Regulação da Expressão Gênica de Plantas , Modelos Moleculares , Complexos Multiproteicos/química , Complexos Multiproteicos/metabolismo , Complexos Multiproteicos/ultraestrutura , Ligação Proteica , Conformação Proteica , RNA de Plantas/química , RNA de Plantas/genética
15.
Int J Mol Sci ; 20(18)2019 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-31546885

RESUMO

RNA editing in plant mitochondria and plastids converts specific nucleotides from cytidine (C) to uridine (U). These editing events differ among plant species and are relevant to developmental stages or are impacted by environmental conditions. Proteins of the MORF family are essential components of plant editosomes. One of the members, MORF9, is considered the core protein of the editing complex and is involved in the editing of most sites in chloroplasts. In this study, the phenotypes of a T-DNA insertion line with loss of MORF9 and of the genetic complementation line of Arabidopsis were analyzed, and the editing efficiencies of plastid RNAs in roots, rosette leaves, and flowers from the morf9 mutant and the wild-type (WT) control were compared by bulk-cDNA sequencing. The results showed that most of the known MORF9-associated plastid RNA editing events in rosette leaves and flowers were similarly reduced by morf9 mutation, with the exception that the editing rate of the sites ndhB-872 and psbF-65 declined in the leaves and that of ndhB-586 decreased only in the flowers. In the roots, however, the loss of MORF9 had a much lower effect on overall plastid RNA editing, with nine sites showing no significant editing efficiency change, including accD-794, ndhD-383, psbZ-50, ndhF-290, ndhD-878, matK-706, clpP1-559, rpoA-200, and ndhD-674, which were reduced in the other tissues. Furthermore, we found that during plant aging, MORF9 mRNA level, but not the protein level, was downregulated in senescent leaves. On the basis of these observations, we suggest that MORF9-mediated RNA editing is tissue-dependent and the resultant organelle proteomes are pertinent to the specific tissue functions.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Regulação da Expressão Gênica de Plantas/fisiologia , Plastídeos/metabolismo , Edição de RNA/fisiologia , RNA de Plantas/metabolismo , Proteínas de Ligação a RNA/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Mutação , Especificidade de Órgãos/fisiologia , Plastídeos/genética , RNA de Plantas/genética , Proteínas de Ligação a RNA/genética
16.
Int J Mol Sci ; 20(18)2019 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-31514282

RESUMO

The development of floral organs plays a vital role in plant reproduction. In our research, the APETALA3 (AP3) promoter-transgenic lines showed abnormal developmental phenotypes in stamens and petals. The aim of this study is to understand the molecular mechanisms of the morphological defects in transgenic plants. By performing transgenic analysis, it was found that the AP3-promoted genes and the vector had no relation to the morphological defects. Then, we performed the expression analysis of the class A, B, and C genes. A dramatic reduction of transcript levels of class B genes (AP3 and PISTILLATA) was observed. Additionally, we also analyzed the methylation of the promoters of class B genes and found that the promoter of AP3 was hypermethylated. Furthermore, combining mutations in rdr2-2, drm1/2, and nrpd1b-11 with the AP3-silencing lines rescued the abnormal development of stamens and petals. The expression of AP3 was reactivated and the methylation level of AP3 promoter was also reduced in RdDM-defective AP3-silencing lines. Our results showed that the RdDM pathway contributed to the transcriptional silencing in the transgenic AP3-silencing lines. Moreover, the results revealed that fact that the exogenous fragment of a promoter could trigger the methylation of homologous endogenous sequences, which may be ubiquitous in transgenic plants.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Metilação de DNA/genética , Inativação Gênica , Proteínas de Domínio MADS/genética , Regiões Promotoras Genéticas , RNA de Plantas/metabolismo , Proteínas de Arabidopsis/metabolismo , Regulação da Expressão Gênica de Plantas , Teste de Complementação Genética , Proteínas de Domínio MADS/metabolismo , Fenótipo , Plantas Geneticamente Modificadas , RNA de Plantas/genética
18.
Plant Sci ; 288: 110241, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31521215

RESUMO

Fungal pathogens are an important threat for plant crops, being responsible for important reductions of production yields and a consequent economic impact. Among the molecular mediators of fungal infections of plant crops, non-coding RNAs (ncRNAs) have been described as relevant players either in the plant immune responses and mechanism of defense or in the colonization of plant tissues by fungi. Acting as a mechanism of defense, some plant small ncRNAs such as miRNAs and tasiRNAs can be secreted by cells and directed to target the transcriptome of pathogenic fungi, triggering an RNAi-like interference mechanism able to silence the expression of specific fungal genes. The detailed knowledge of this mechanism of defense against fungal pathogens could open new possibilities for the protection of human important crops. To infer putative functional relationships mediated by ncRNA communication, we performed a prospective analysis to determine potential plant miRNAs able to target the genome of fungal pathogens, which resulted in the description of enriched specific plant miRNA families and their putative fungal targets that could be further studied in the context of plant-fungi interactions. The expression profile of specific members of the enriched miRNAs families showed an infection-dependent behavior in laboratory models of infection. Plant miRNAs showed sequence complementarity with coding genes of their cognate fungal pathogens. Plant miRNAs could potentially target fungal genes belonging to functional families related to stress response, membrane architecture, vacuolar transport, membrane traffic, and anabolic processes. Families of specific infection-responsive miRNAs are included in the putative plant defense mechanism.


Assuntos
Magnaporthe/fisiologia , MicroRNAs/genética , Oryza/genética , Imunidade Vegetal/genética , RNA de Plantas/genética , Simulação por Computador , MicroRNAs/metabolismo , Oryza/imunologia , Oryza/microbiologia , RNA de Plantas/metabolismo
19.
Nucleic Acids Res ; 47(16): 8649-8661, 2019 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-31392997

RESUMO

Viroids are naked RNAs that do not code for any known protein and yet are able to infect plants causing severe diseases. Because of their RNA nature, many studies have focused on the involvement of viroids in RNA-mediated gene silencing as being their pathogenesis mechanism. Here, the alterations caused by the Citrus exocortis viroid (CEVd) on the tomato translation machinery were studied as a new aspect of viroid pathogenesis. The presence of viroids in the ribosomal fractions of infected tomato plants was detected. More precisely, CEVd and its derived viroid small RNAs were found to co-sediment with tomato ribosomes in vivo, and to provoke changes in the global polysome profiles, particularly in the 40S ribosomal subunit accumulation. Additionally, the viroid caused alterations in ribosome biogenesis in the infected tomato plants, affecting the 18S rRNA maturation process. A higher expression level of the ribosomal stress mediator NAC082 was also detected in the CEVd-infected tomato leaves. Both the alterations in the rRNA processing and the induction of NAC082 correlate with the degree of viroid symptomatology. Taken together, these results suggest that CEVd is responsible for defective ribosome biogenesis in tomato, thereby interfering with the translation machinery and, therefore, causing ribosomal stress.


Assuntos
Lycopersicon esculentum/genética , Doenças das Plantas/genética , Biossíntese de Proteínas , RNA de Plantas/genética , RNA Ribossômico 18S/genética , Ribossomos/metabolismo , Viroides/genética , Citrus/virologia , Interações Hospedeiro-Patógeno/genética , Lycopersicon esculentum/metabolismo , Lycopersicon esculentum/virologia , Biogênese de Organelas , Doenças das Plantas/virologia , Folhas de Planta/genética , Folhas de Planta/metabolismo , Folhas de Planta/virologia , Interferência de RNA , RNA de Plantas/antagonistas & inibidores , RNA de Plantas/metabolismo , RNA Ribossômico 18S/antagonistas & inibidores , RNA Ribossômico 18S/metabolismo , RNA Viral/genética , RNA Viral/metabolismo , Proteínas Ribossômicas/genética , Proteínas Ribossômicas/metabolismo , Ribossomos/genética , Estresse Fisiológico/genética , Viroides/metabolismo , Viroides/patogenicidade
20.
Int J Mol Sci ; 20(15)2019 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-31370193

RESUMO

Prior experiments illustrated reactive oxygen species (ROS) overproduction in maize plants infested with bird-cherry-oat (Rhopalosiphum padi L.) aphids. However, there is no available data unveiling the impact of aphids feeding on oxidative damages of crucial macromolecules in maize tissues. Therefore, the purpose of the current study was to evaluate the scale of oxidative damages of genomic DNA, total RNA and mRNA, proteins, and lipids in seedling leaves of two maize genotypes (Zlota Karlowa and Waza cvs-susceptible and relatively resistant to the aphids, respectively). The content of oxidized guanosine residues (8-hydroxy-2'-deoxyguanosine; 8-OHdG) in genomic DNA, 8-hydroxyguanosine (8-OHG) in RNA molecules, protein carbonyl groups, total thiols (T-SH), protein-bound thiols (PB-SH), non-protein thiols (NP-SH), malondialdehyde (MDA) and electrolyte leakage (EL) levels in maze plants were determined. In addition, the electrical penetration graphs (EPG) technique was used to monitor and the aphid stylet positioning and feeding modes in the hosts. Maize seedlings were infested with 0 (control), 30 or 60 R. padi adult apterae per plant. Substantial increases in the levels of RNA, protein and lipid oxidation markers in response to aphid herbivory, but no significant oxidative damages of genomic DNA, were found. Alterations in the studied parameters were dependent on maize genotype, insect abundance and infestation time.


Assuntos
Afídeos/fisiologia , Regulação da Expressão Gênica de Plantas , Interações Hospedeiro-Parasita/genética , Folhas de Planta/genética , Proteínas de Plantas/genética , Zea mays/genética , /metabolismo , Animais , Afídeos/patogenicidade , DNA de Plantas/genética , DNA de Plantas/metabolismo , Genótipo , Guanosina/análogos & derivados , Guanosina/metabolismo , Lipídeos/química , Malondialdeído/metabolismo , Oxirredução , Estresse Oxidativo , Doenças das Plantas/genética , Doenças das Plantas/parasitologia , Folhas de Planta/parasitologia , Proteínas de Plantas/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA de Plantas/genética , RNA de Plantas/metabolismo , Plântula/genética , Plântula/parasitologia , Compostos de Sulfidrila/metabolismo , Zea mays/parasitologia
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