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1.
J Forensic Sci ; 65(1): 259-265, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31411746

RESUMO

DNA is one of the fastest growing tools in forensic sciences, increasing reliability in forensic reports and judgments. The use of DNA has increased in different areas of the forensic sciences, such as investigation of plant species, where plastid DNA has been used to elucidate and generate evidence in cases of traceability of genetically modified and controlled plants. Even with several advances and the practice of using DNA in forensic investigations, there are just few studies related to the identification of genetic tools for the characterization of drug and nondrug-types of Cannabis. Herein, the whole plastomes of two drug-type Cannabis are presented and have their structures compared with other Cannabis plastomes deposited in the GenBank, focusing in the forensic use of plastome sequences. The plastomes of Cannabis sativa "Brazuka" and of the hybrid Cannabis AK Royal Automatic presented general structure that does not differs from the reported for other C. sativa cultivars. A phylogenomic analyses grouped C. sativa "Brazuka" with the nondrug C. sativa cultivars, while the hybrid Cannabis AK Royal Automatic placed isolated, basal to this group. This suggests that the analysis of plastomes is useful toward genetic identification of hybrids in relation to C. sativa.


Assuntos
Cannabis/genética , Genomas de Plastídeos , Plastídeos/genética , DNA de Plantas , Bases de Dados de Ácidos Nucleicos , Ciências Forenses , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Análise de Sequência de DNA
2.
BMC Evol Biol ; 19(1): 224, 2019 12 09.
Artigo em Inglês | MEDLINE | ID: mdl-31818253

RESUMO

BACKGROUND: Eukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data. RESULTS: Using Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies ("phyloclassifies") cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data. CONCLUSIONS: Phylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies.


Assuntos
Cianobactérias/genética , Eucariotos/citologia , Eucariotos/genética , Plastídeos/genética , Evolução Biológica , Modelos Biológicos , Fotossíntese , Filogenia , RNA de Transferência , Simbiose
3.
Nat Commun ; 10(1): 4823, 2019 10 23.
Artigo em Inglês | MEDLINE | ID: mdl-31645564

RESUMO

The common ancestor of red algae (Rhodophyta) has undergone massive genome reduction, whereby 25% of the gene inventory has been lost, followed by its split into the species-poor extremophilic Cyanidiophytina and the broadly distributed mesophilic red algae. Success of the mesophile radiation is surprising given their highly reduced gene inventory. To address this latter issue, we combine an improved genome assembly from the unicellular red alga Porphyridium purpureum with a diverse collection of other algal genomes to reconstruct ancient endosymbiotic gene transfers (EGTs) and gene duplications. We find EGTs associated with the core photosynthetic machinery that may have played important roles in plastid establishment. More significant are the extensive duplications and diversification of nuclear gene families encoding phycobilisome linker proteins that stabilize light-harvesting functions. We speculate that the origin of these complex families in mesophilic red algae may have contributed to their adaptation to a diversity of light environments.


Assuntos
Fotossíntese/genética , Ficobilissomas/genética , Porphyridium/genética , Evolução Molecular , Duplicação Gênica , Transferência Genética Horizontal , Genomas de Plastídeos , Genômica , Filogenia , Plastídeos/genética , Rodófitas/genética , Simbiose
4.
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
5.
Protist ; 170(4): 358-373, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31415953

RESUMO

The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed "minicircles". These minicircles may contain genes, or no recognisable coding information. Transcripts produced from minicircles may undergo unusual processing events, such as the addition of a 3' poly(U) tail. To date, little is known about the genetic or transcriptional diversity of non-coding sequences in peridinin dinoflagellate plastids. These sequences include empty minicircles, and regions of non-coding DNA in coding minicircles. Here, we present an integrated plastid genome and transcriptome for the model peridinin dinoflagellate Amphidinium carterae, identifying a previously undescribed minicircle. We also profile transcripts covering non-coding regions of the psbA and petB/atpA minicircles. We present evidence that antisense transcripts are produced within the A. carterae plastid, but show that these transcripts undergo different end cleavage events from sense transcripts, and do not receive 3' poly(U) tails. The difference in processing events between sense and antisense transcripts may enable the removal of non-coding transcripts from peridinin dinoflagellate plastid transcript pools.


Assuntos
Dinoflagelados/classificação , Dinoflagelados/genética , Genoma de Protozoário/genética , Plastídeos/genética , Transcriptoma/genética , Perfilação da Expressão Gênica , Genômica
6.
Dokl Biochem Biophys ; 486(1): 163-167, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31367812

RESUMO

The treatment of Arabidopsis thaliana plants with exogenous cytokinin (CK) followed by heat shock (HS) activated the expression of the genes for the plastid transcription machinery but adversely affected the plant viability. Abscisic acid (ABA), conversely, promoted maintaining the resistance to HS and had differentially affected different components of the plastid transcriptional complex. This hormone suppressed the accumulation of transcripts of PEP genes and the genes encoding PAP proteins, which are involved in DNA-RNA metabolism. However, it had no effect or activated the expression of NEP genes and PAP genes, which are involved in the redox regulation, as well as the genes encoding the stress-inducible trans-factor (SIG5) and the plastid transcription Ser/Thr protein kinase (cpCK2). Thus, for the adaptation of plants to elevated temperatures, both increase and decrease in the expression of the genes for the plastid transcriptional machinery with the involvement of various regulatory systems, including phytohormones, are equally significant.


Assuntos
Ácido Abscísico/farmacologia , Arabidopsis/efeitos dos fármacos , Citocininas/farmacologia , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Resposta ao Choque Térmico/genética , Plastídeos/genética , Transcrição Genética/efeitos dos fármacos , Arabidopsis/citologia , Arabidopsis/genética , Arabidopsis/fisiologia , Resposta ao Choque Térmico/efeitos dos fármacos , Plastídeos/efeitos dos fármacos
7.
Int J Mol Sci ; 20(16)2019 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-31426439

RESUMO

Epimedium wushanense (Berberidaceae) is recorded as the source plant of Epimedii Wushanensis Folium in the Chinese Pharmacopoeia. However, controversies exist on the classification of E. wushanense and its closely related species, namely, E. pseudowushanense, E. chlorandrum, E. mikinorii, E. ilicifolium, and E. borealiguizhouense. These species are often confused with one another because of their highly similar morphological characteristics. This confusion leads to misuse in the medicinal market threatening efficiency and safety. Here, we studied the plastid genomes of these Epimedium species. Results show that the plastid genomes of E. wushanense and its relative species are typical circular tetramerous structure, with lengths of 156,855-158,251 bp. A total of 112 genes were identified from the Epimedium plastid genomes, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. A loss of rpl32 gene in E. chlorandrum was found for the first time in this study. The phylogenetic trees constructed indicated that E. wushanense can be distinguished from its closely related species. E. wushanense shows a closer relationship to species in ser. Dolichocerae. In conclusion, the use of plastid genomes contributes useful genetic information for identifying medicinally important species E. wushanense and provides new evidence for understanding phylogenetic relationships within the Epimedium genus.


Assuntos
Epimedium/genética , Genomas de Plastídeos , DNA de Plantas/genética , Epimedium/classificação , Genômica , Filogenia , Plastídeos/classificação , Plastídeos/genética
8.
Int J Mol Sci ; 20(15)2019 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-31382526

RESUMO

Many Salicaceae s.l. plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family Salicaceae s.l. remain poorly understood. In this study, we compare 24 species representing 18 genera of the family. Simple sequence repeats (SSRs) are considered effective molecular markers for plant species identification and population genetics. Among them, a total of 1798 SSRs were identified, among which mononucleotide repeat was the most common with 1455 accounts representing 80.92% of the total. Most of the SSRs are located in the non-coding region. We also identified five other types of repeats, including 1750 tandems, 434 forward, 407 palindromic, 86 reverse, and 30 complementary repeats. The species in Salicaceae s.l. have a conserved plastid genome. Each plastome presented a typical quadripartite structure and varied in size due to the expansion and contraction of the inverted repeat (IR) boundary, lacking major structural variations, but we identified six divergence hotspot regions. We obtained phylogenetic relationships of 18 genera in Salicaceae s.l. and the 24 species formed a highly supported lineage. Casearia was identified as the basal clade. The divergence time between Salicaceae s.l. and the outgroup was estimated as ~93 Mya; Salix, and Populus diverged around 34 Mya, consistent with the previously reported time. Our research will contribute to a better understanding of the phylogenetic relationships among the members of the Salicaceae s.l.


Assuntos
Genomas de Plastídeos , Filogenia , Plastídeos/genética , Salicaceae/genética , Evolução Molecular , Sequências Repetidas Invertidas , Repetições de Microssatélites
9.
Nat Commun ; 10(1): 2904, 2019 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-31266952

RESUMO

Plant survival necessitates constant monitoring of fluctuating light and balancing growth demands with adaptive responses, tasks mediated via interconnected sensing and signaling networks. Photoreceptor phytochrome B (phyB) and plastidial retrograde signaling metabolite methylerythritol cyclodiphosphate (MEcPP) are evolutionarily conserved sensing and signaling components eliciting responses through unknown connection(s). Here, via a suppressor screen, we identify two phyB mutant alleles that revert the dwarf and high salicylic acid phenotypes of the high MEcPP containing mutant ceh1. Biochemical analyses show high phyB protein levels in MEcPP-accumulating plants resulting from reduced expression of phyB antagonists and decreased auxin levels. We show that auxin treatment negatively regulates phyB abundance. Additional studies identify CAMTA3, a MEcPP-activated calcium-dependent transcriptional regulator, as critical for maintaining phyB abundance. These studies provide insights into biological organization fundamentals whereby a signal from a single plastidial metabolite is transduced into an ensemble of regulatory networks controlling the abundance of phyB, positioning plastids at the information apex directing adaptive responses.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Fitocromo B/metabolismo , Plastídeos/metabolismo , Arabidopsis/genética , Arabidopsis/efeitos da radiação , Proteínas de Arabidopsis/genética , Eritritol/análogos & derivados , Eritritol/metabolismo , Regulação da Expressão Gênica de Plantas/efeitos da radiação , Ácidos Indolacéticos/metabolismo , Luz , Fitocromo B/genética , Plastídeos/genética , Transdução de Sinais/efeitos da radiação , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
10.
BMC Evol Biol ; 19(1): 152, 2019 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-31340752

RESUMO

BACKGROUND: With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus. RESULTS: We generated 1856 sequence tags in putative single-copy orthologous nuclear loci. Associated in silico primer pairs can potentially amplify fragments able to resolve a wide range of speciation events within the genus Rosa. Analysis of parsimony-informative site content showed the value of non-coding genomic regions to obtain variable sequences despite the fact that they may be more difficult to target in less related species. Dozens of nuclear loci outperform the conventional plastid phylogenetic markers in terms of phylogenetic informativeness, for both recent and ancient evolutionary divergences. However, conflicting phylogenetic signals were found between nuclear gene tree topologies and the species-tree topology, shedding light on the many patterns of hybridization and/or incomplete lineage sorting that occur in the genus Rosa. CONCLUSIONS: With recently published genome sequence data, we developed a set of single-copy orthologous nuclear loci to resolve species-level phylogenomics in the genus Rosa. This genome-wide scale dataset contains hundreds of highly variable loci which phylogenetic interest was assessed in terms of phylogenetic informativeness and topological conflict. Our target identification procedure can easily be reproduced to identify new highly informative loci for other taxonomic groups and ranks.


Assuntos
Núcleo Celular/genética , Dosagem de Genes , Loci Gênicos , Genômica , Filogenia , Rosa/genética , Primers do DNA/metabolismo , Genoma de Planta , Funções Verossimilhança , Plastídeos/genética
11.
Int J Mol Sci ; 20(14)2019 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-31337110

RESUMO

Buckwheat is an important functional food material with high nutritional value. However, it is still a difficult task for the taxonomy studies of wild buckwheat that are only based on morphology. In order to demonstrate the most efficient DNA barcode in the phylogenetic research of buckwheat, promote the investigation of wild buckwheat, and also reveal the phylogenetic relationship between Fagopyrum species, psbE-psbL and ndhA intron were validated here, which previously have been proved to be promising DNA barcode candidates for phylogenetic studies in genera Fagopyrum. Meanwhile, ndhA intron + psbE-psbL and matK + psbE-psbL could distinguish the relationship between species clearly. Combining the results of morphology and molecular markers, we suggested the buckwheat species should be divided into two subgroups, one subgroup consisted of F. tataricum, F. esculentum, F. cymosum and its related wild species, and the other subgroup included other wild buckwheat species. Our results could fulfill molecular markers of taxonomy research in genera Fagopyrum, promote wild buckwheat species identification, and assist in the use of wild buckwheat resources in the future. Additionally, the phylogenetic relationship revealed here could provide valuable information for molecular breeding of buckwheat and provide reference for inter-species hybridization.


Assuntos
Código de Barras de DNA Taxonômico , DNA de Plantas , Fagopyrum/classificação , Fagopyrum/genética , Genes de Plantas , Íntrons , Plastídeos/genética , Marcadores Genéticos , Fenótipo , Filogenia
12.
Plant Biol (Stuttg) ; 21(6): 1072-1082, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31349366

RESUMO

Introgression is a poorly understood evolutionary outcome of hybridisation because it may remain largely undetected whenever it involves the transfer of small parts of the genome from one species to another. Aiming to understand the early stages of this process, a putative case from the southernmost border of the Armeria pungens range from its congener A. macrophylla is revisited following the discovery of a subpopulation that does not show phenotypic signs of introgression and resembles typical A. pungens. We analysed morphometrics, nuclear ribosomal DNA ITS and plastid DNA (trnL-trnF) sequences, genome size, 45S and 5S rDNA loci-FISH data and nrDNA IGS sequences. Within the study site, most individuals match morphologies of either of the two hybridising species, particularly the new subpopulation, with intermediate phenotypes being scarce. This pattern does not fully fit molecular evidence revealing two ITS ribotypes co-occurring intragenomically in most plants from the study site and one single plastid haplotype. Genome size and structural features of the IGS sequences both indicate that A. pungens from the study site is genetically more similar to its sympatric congener than to the remainder of its conspecifics. Introgression of A. macrophylla into A. pungens and plastid capture explain all the evidence analysed. However, important features to understand the origin and fate of the introgressed population, such as the degree and direction of introgression, which are important for understanding early stages of hybridisation in plants with low reproductive barriers, should be addressed with new data.


Assuntos
DNA Ribossômico/metabolismo , Plumbaginaceae/metabolismo , DNA Ribossômico/genética , Evolução Molecular , Genoma de Planta/genética , Hibridização Genética , Plastídeos/genética , Plastídeos/metabolismo , Plumbaginaceae/genética , Análise de Sequência de DNA
13.
Plant Cell Physiol ; 60(11): 2436-2448, 2019 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-31350548

RESUMO

Protoporphyrinogen IX oxidase1 (PPO1) catalyzes the oxidation of protoporphyrinogen IX to form protoporphyrin IX in the plastid tetrapyrrole biosynthesis pathway and is also essential for plastid RNA editing in Arabidopsis thaliana. The Arabidopsis ppo1-1 mutation was previously shown to be seedling lethal; however, in this study, we showed that the heterozygous ppo1-1/+ mutant exhibited reproductive growth defects characterized by reduced silique length and seed set, as well as aborted pollen development. In this mutant, the second mitotic division was blocked during male gametogenesis, whereas female gametogenesis was impaired at the one-nucleate stage. Before perishing at the seedling stage, the homozygous ppo1-1 mutant displayed reduced hypocotyl and root length, increased levels of reactive oxygen species accumulation and elevated cell death, especially under light conditions. Wild-type seedlings treated with acifluorfen, a PPO1 inhibitor, showed similar phenotypes to the ppo1-1 mutants, and both plants possessed a high proportion of 2C nuclei and a low proportion of 8C nuclei compared with the untreated wild type. Genome-wide RNA-seq analysis showed that a number of genes, including cell cycle-related genes, were differentially regulated by PPO1. Consistently, PPO1 was highly expressed in the pollen, anther, pistil and root apical meristem cells actively undergoing cell division. Our study reveals a role for PPO1 involved in the mitotic cell cycle during gametogenesis and seedling development.


Assuntos
Arabidopsis/metabolismo , Ciclo Celular/fisiologia , Cloroplastos/metabolismo , Arabidopsis/genética , Ciclo Celular/genética , Gametogênese/genética , Gametogênese/fisiologia , Regulação da Expressão Gênica de Plantas/genética , Regulação da Expressão Gênica de Plantas/fisiologia , Plastídeos/genética , Plastídeos/metabolismo
14.
Mol Ecol Resour ; 19(5): 1333-1345, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31237984

RESUMO

Complete plastid genome (plastome) sequences and nuclear ribosomal DNA (nrDNA) regions have been proposed as candidates for the next generation of DNA barcodes for plant species discrimination. However, the efficacy of this approach still lacks comprehensive evaluation. We carried out a case study in the economically important but phylogenetically and taxonomically difficult genus Panax (Araliaceae). We generated a large data set of plastomes and nrDNA sequences from multiple accessions per species. Our data improved the phylogenetic resolution and levels of species discrimination in Panax, compared to any previous studies using standard DNA barcodes. This provides new insights into the speciation, lineage diversification and biogeography of the genus. However, both plastome and nrDNA failed to completely resolve the phylogenetic relationships in the Panax bipinnatifidus species complex, and only half of the species within it were recovered as monophyletic units. The results suggest that complete plastome and ribosomal DNA sequences can substantially increase species discriminatory power in plants, but they are not powerful enough to fully resolve phylogenetic relationships and discriminate all species, particularly in evolutionarily young and complex plant groups. To gain further resolving power for closely related species, the addition of substantial numbers of nuclear markers is likely to be required.


Assuntos
Código de Barras de DNA Taxonômico/métodos , DNA de Plantas/genética , DNA Ribossômico/genética , Panax/classificação , Panax/genética , Plastídeos/genética , Análise de Sequência de DNA/métodos
15.
Food Chem ; 297: 124964, 2019 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-31253313

RESUMO

Broccoli undergoes yellowing in unfavorable conditions, thereby diminishing the sensory quality and commodity value. This study aimed to investigate systematically cellular and/or biomolecular changes involved in broccoli yellowing by analyzing changes in microstructural integrity, pigment content, and gene expression. On day-5 of storage at 20 °C, the buds turned yellow without blooming and showed structural damage; ultrastructural analysis revealed plastid transformation and abnormal chloroplast development. Genes regulating pigment content and chloroplast structure directly were identified. More specifically, BoCAO and BoNYC1 regulated chlorophyll turnover, affecting chlorophyll a and b contents. Changes in the ß-cryptoxanthin content were influenced by the combined action of up- (BoHYD) and downstream (BoZEP) genes. BoZEP and BoVDE were activated after cold-temperature induction. High BoHO1 expression delayed yellowing at low temperature, inducing BoZEP expression. Color intensity correlated significantly with the chlorophyll b, ß-cryptoxanthin, and ß-carotene contents, which were associated with increased yellowing of plant tissues.


Assuntos
Brassica/fisiologia , Carotenoides/metabolismo , Clorofila/metabolismo , Armazenamento de Alimentos , beta-Criptoxantina/genética , beta-Criptoxantina/metabolismo , Vias Biossintéticas , Brassica/ultraestrutura , Cloroplastos/metabolismo , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plastídeos/genética , Plastídeos/metabolismo , Temperatura Ambiente
16.
Nat Commun ; 10(1): 2834, 2019 06 27.
Artigo em Inglês | MEDLINE | ID: mdl-31249292

RESUMO

Environmental information perceived by chloroplasts can be translated into retrograde signals that alter the expression of nuclear genes. Singlet oxygen (1O2) generated by photosystem II (PSII) can cause photo-oxidative damage of PSII but has also been implicated in retrograde signaling. We previously reported that a nuclear-encoded chloroplast FtsH2 metalloprotease coordinates 1O2-triggered retrograde signaling by promoting the degradation of the EXECUTER1 (EX1) protein, a putative 1O2 sensor. Here, we show that a 1O2-mediated oxidative post-translational modification of EX1 is essential for initiating 1O2-derived signaling. Specifically, the Trp643 residue in DUF3506 domain of EX1 is prone to oxidation by 1O2. Both the substitution of Trp643 with 1O2-insensitive amino acids and the deletion of the DUF3506 domain abolish the EX1-mediated 1O2 signaling. We thus provide mechanistic insight into how EX1 senses 1O2 via Trp643 located in the DUF3506 domain.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Plastídeos/metabolismo , Oxigênio Singlete/metabolismo , Motivos de Aminoácidos , Substituição de Aminoácidos , Arabidopsis/química , Arabidopsis/genética , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , Oxirredução , Plastídeos/química , Plastídeos/genética , Domínios Proteicos , Processamento de Proteína Pós-Traducional , Transdução de Sinais
17.
Nat Commun ; 10(1): 2630, 2019 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-31201314

RESUMO

Phytochromes initiate chloroplast biogenesis by activating genes encoding the photosynthetic apparatus, including photosynthesis-associated plastid-encoded genes (PhAPGs). PhAPGs are transcribed by a bacterial-type RNA polymerase (PEP), but how phytochromes in the nucleus activate chloroplast gene expression remains enigmatic. We report here a forward genetic screen in Arabidopsis that identified NUCLEAR CONTROL OF PEP ACTIVITY (NCP) as a necessary component of phytochrome signaling for PhAPG activation. NCP is dual-targeted to plastids and the nucleus. While nuclear NCP mediates the degradation of two repressors of chloroplast biogenesis, PIF1 and PIF3, NCP in plastids promotes the assembly of the PEP complex for PhAPG transcription. NCP and its paralog RCB are non-catalytic thioredoxin-like proteins that diverged in seed plants to adopt nonredundant functions in phytochrome signaling. These results support a model in which phytochromes control PhAPG expression through light-dependent double nuclear and plastidial switches that are linked by evolutionarily conserved and dual-localized regulatory proteins.


Assuntos
Proteínas de Arabidopsis/metabolismo , Cloroplastos/metabolismo , Chaperonas Moleculares/metabolismo , Fitocromo/metabolismo , Transcrição Genética/fisiologia , Arabidopsis/fisiologia , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Núcleo Celular/genética , Núcleo Celular/metabolismo , Cloroplastos/genética , RNA Polimerases Dirigidas por DNA/metabolismo , Regulação da Expressão Gênica de Plantas/efeitos da radiação , Luz , Fotossíntese/fisiologia , Plantas Geneticamente Modificadas , Plastídeos/genética , Plastídeos/metabolismo , Transdução de Sinais/fisiologia , Transcrição Genética/efeitos da radiação
18.
Nat Commun ; 10(1): 2629, 2019 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-31201355

RESUMO

Light initiates chloroplast biogenesis by activating photosynthesis-associated genes encoded by not only the nuclear but also the plastidial genome, but how photoreceptors control plastidial gene expression remains enigmatic. Here we show that the photoactivation of phytochromes triggers the expression of photosynthesis-associated plastid-encoded genes (PhAPGs) by stimulating the assembly of the bacterial-type plastidial RNA polymerase (PEP) into a 1000-kDa complex. Using forward genetic approaches, we identified REGULATOR OF CHLOROPLAST BIOGENESIS (RCB) as a dual-targeted nuclear/plastidial phytochrome signaling component required for PEP assembly. Surprisingly, RCB controls PhAPG expression primarily from the nucleus by interacting with phytochromes and promoting their localization to photobodies for the degradation of the transcriptional regulators PIF1 and PIF3. RCB-dependent PIF degradation in the nucleus signals the plastids for PEP assembly and PhAPG expression. Thus, our findings reveal the framework of a nucleus-to-plastid anterograde signaling pathway by which phytochrome signaling in the nucleus controls plastidial transcription.


Assuntos
Proteínas de Arabidopsis/metabolismo , Cloroplastos/metabolismo , RNA Polimerases Dirigidas por DNA/metabolismo , Fitocromo/metabolismo , Tiorredoxinas/metabolismo , Transcrição Genética/fisiologia , Arabidopsis/fisiologia , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Núcleo Celular/metabolismo , Cloroplastos/genética , Regulação da Expressão Gênica de Plantas/efeitos da radiação , Luz , Fotossíntese/fisiologia , Plantas Geneticamente Modificadas , Plastídeos/genética , Plastídeos/metabolismo , Proteólise , Transdução de Sinais/fisiologia , Transcrição Genética/efeitos da radiação
19.
Plant Cell Physiol ; 60(10): 2141-2151, 2019 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-31150097

RESUMO

Amborella trichopoda is placed close to the base of the angiosperm lineage (basal angiosperm). By genome-wide RNA sequencing, we identified 184C-to-U RNA editing sites in the plastid genome of Amborella. This number is much higher than that observed in other angiosperms including maize (44 sites), rice (39 sites) and grape (115 sites). Despite the high frequency of RNA editing, the biased distribution of RNA editing sites in the genome, target codon preference and nucleotide preference adjacent to the edited cytidine are similar to that in other angiosperms, suggesting a common editing machinery. Consistent with this idea, the Amborella nuclear genome encodes 2-3 times more of the E- and DYW-subclass members of pentatricopeptide repeat proteins responsible for RNA editing site recognition in plant organelles. Among 165 editing sites in plastid protein coding sequences in Amborella, 100 sites were conserved at least in one out of 38 species selected to represent key branching points of the angiosperm phylogenetic tree. We assume these 100 sites represent at least a subset of the sites in the plastid editotype of ancestral angiosperms. We then mapped the loss and gain of editing sites on the phylogenetic tree of angiosperms. Our results support the idea that the evolution of angiosperms has led to the loss of RNA editing sites in plastids.


Assuntos
Evolução Molecular , Genoma de Planta/genética , Magnoliopsida/genética , Edição de RNA , Transcriptoma , Plastídeos/genética , RNA de Plantas/genética , Análise de Sequência de RNA , Sequenciamento Completo do Genoma
20.
Planta ; 250(4): 1229-1246, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31222493

RESUMO

MAIN CONCLUSION: The plastomes of Astrocaryum murumuru and A. aculeatum revealed a lineage-specific structural feature originated by flip-flop recombination, non-synonymous substitutions in conserved genes and several molecular markers. Astrocaryum murumuru Mart. and A. aculeatum G.Mey. are two palm species of Amazon forest that are economically important as source of food, oil and raw material for several applications. Genetic studies aiming to establish strategies for conservation and domestication of both species are still in the beginning given that the exploitation is mostly by extractive activity. The identification and characterization of molecular markers are essential to assess the genetic diversity of natural populations of both species. Therefore, we sequenced and characterized in detail the plastome of both species. We compared both species and identified 32 polymorphic SSR loci, 150 SNPs, 46 indels and eight hotspots of nucleotide diversity. Additionally, we reported a specific RNA editing site found in the ccsA gene, which is exclusive to A. murumuru. Moreover, the structural analysis in the plastomes of both species revealed a 4.6-kb inversion encompassing a set of genes involved in chlororespiration and plastid translation. This 4.6-kb inversion is a lineage-specific structural feature of the genus Astrocaryum originated by flip-flop recombination between two short inverted repeats. Furthermore, our phylogenetic analysis using whole plastomes of 39 Arecaceae species placed the Astrocaryum species sister to Acrocomia within the tribe Cocoseae. Finally, our data indicated substantial changes in the plastome structure and sequence of both species of the genus Astrocaryum, bringing new molecular markers, several structural and evolving features, which can be applied in several areas such as genetic, evolution, breeding, phylogeny and conservation strategies for both species.


Assuntos
Arecaceae/genética , Sequências Repetidas Invertidas/genética , Plastídeos/genética , Evolução Molecular , Filogenia , Edição de RNA , Recombinação Genética
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