Edição de RNA plastidial em Glycine max: caracterização de sítios de edição, componentes do editossomo e efeitos de estresse abiótico

Soja, uma cultura conhecida por sua importância econômica e nutricional, tem sido objeto de vários estudos que avaliam o impacto e as respostas efetivas das plantas aos estresses abióticos. O estresse salino é um dos principais estresses ambientais e afeta negativamente o crescimento e o rendimento das culturas, incluindo a soja. A edição de RNA é um processo pelo qual as sequências de nucleotídeos podem ser alteradas, revertendo mutações que podem mudar as sequências de proteínas para manter suas funções conservadas. As proteínas pentatricopeptide repeat (PPRs) são trans-elementos de edição caracterizados por reconhecer cis-elementos específicos de RNA e realizar a reação de edição. Vários estudos descreveram estes trans-elementos e seus sítios de edição cognatos, mas nem todas as proteínas que compõem o complexo de edição foram identificadas. A perda de eventos de edição de plastídios, resultante de mutações em fatores de edição de RNA ou através de interferência por estresse, leva a alterações de desenvolvimento, de fisiologia e da fotossíntese. O objetivo do presente trabalho é caracterizar os sítios de edição e os fatores associados à edição de RNA em Glycine max e a influência de estresses abióticos no processo de edição de RNA em cloroplastos. No capítulo 1, um método é apresentado para triar a edição de RNA de cloroplasto usando bibliotecas públicas de sRNAs de Arabidopsis, soja e arroz. Entre os sítios de edição previstos, 40,57, 34,78 e 25,31% foram confirmados utilizando sRNAs de Arabidopsis, soja e arroz, respectivamente. A análise de SNPs revelou alterações de C-to-U de 58,2, 43,9 e 37,5% nas respectivas espécies e identificou conhecidas e possíveis novas edições de RNA de adenosina para inosina (A-to-I) em tRNAs. O método e os dados revelam o potencial do uso de sRNA como uma fonte confiável para identificar novos e confirmar sítios de edição conhecidos. No capítulo 2, o processo de edição de RNA foi avaliado em cloroplastos de plantas de soja sob estresse salino. A abordagem de bioinformática utilizando bibliotecas de sRNAs e mRNAs foi empregada para detectar sítios específicos que mostram diferenças na taxa de edição. RT-qPCR foi usado para medir a taxa de edição nos sítios selecionados. Observamos diferenças nas taxas de edição nos transcritos dos genes ndhA, ndhB, rps14 e rps16 ao comparar os dados das bibliotecas controle e das tratadas com NaCl. Os ensaios de RT-qPCR 9 demonstraram um aumento na edição dos genes selecionados. Esses aumentos podem ser uma resposta para manter a homeostase das funções das proteínas do cloroplasto em resposta ao estresse salino. No capítulo 3, para identificar os fatores relacionados aos sítios de edição analisados, sondas biotiniladas de RNA foram projetadas com base nos sítios de edição de RNA de plastídio de soja para realizar um isolamento proteico específico do fator de edição. Proteínas que interagiram com as sondas foram isoladas através da ligação das sondas à biotina e foram identificadas utilizando espectrometria de massa. Entre os peptídeos detectados, cinco corresponderam a proteínas PPR. A comparação dos genes de Arabidopsis com as proteínas PPR da soja permitiu a identificação dos homólogos mais próximos. O presente estudo representa a primeira identificação do conjunto de sítios de edição de RNA, de fatores associados aos sítios de edição de RNA e a caracterização dos efeitos do estresse abiótico na edição de RNA em Glycine max.Soybean, a crop known by its economic and nutritional importance, has been the subject of several studies that assess the impact and the effective plant responses to abiotic stresses. Salt stress is one of the main environmental stresses and negatively impacts crop growth and yield. RNA editing is a process whereby nucleotide sequences can be altered, reverting mutations that could change protein sequences to maintain their conserved functions. Pentatricopeptide repeat proteins are editing trans-elements characterized by recognize specific RNA cis-elements and perform the editing reaction. Several studies have described these trans-elements and their cognate editing sites, but not all proteins that compose the editing complex were identified. The loss of plastid editing events, resulting from mutations in RNA editing factors or through stress interference, leads to developmental, physiological and photosynthetic alterations. The aim of the present work is to characterize the editing sites and factors associated with RNA editing in Glycine max and the influence of abiotic stresses on the process of RNA editing in chloroplasts. In chapter 1, a method is presented to screen chloroplast RNA editing using public sRNA libraries from Arabidopsis, soybean and rice. Among the predicted editing sites, 40.57, 34.78, and 25.31% were confirmed using sRNAs from Arabidopsis, soybean and rice, respectively. SNP analysis revealed 58.2, 43.9, and 37.5% new C-to-U changes in the respective species and identified known and new putative adenosine to inosine (A-to-I) RNA editing in tRNAs. The method and data reveal the potential of sRNA as a reliable source to identify new and confirm known editing sites. In chapter 2, RNA editing process was evaluated in the chloroplast of soybean plants under salt stress. Bioinformatics approach using sRNA and mRNA libraries was employed to detect specific sites showing differences in editing efficiency. RT-qPCR was used to measure editing efficiency at selected sites. We observed differences in ndhA, ndhB, rps14 and rps16 editing rates between control and salt-treated libraries. RT-qPCR assays demonstrated an increase in editing efficiency of selected genes. These increases can be a response to keep the homeostasis of chloroplast protein functions in response to NaCl stress. In chapter 3, to identify the trans-acting factors of editing sites analyzed, we have designed RNA biotinylated probes based in soybean plastid RNA editing sites to perform 11 specific isolation of proteins associated to editosomes. Proteins that interacted with the probes were isolated by binding the probes to biotin and were identified using mass spectrometry. Among the detected peptides, five corresponded to PPR proteins. Comparison of Arabidopsis genes to the soybean PPR proteins allow identification of the closest related homologs. The present study represents the first identification of RNA editing sites set, associated factors to RNA editing sites and characterization of effects from abiotic stress in RNA editing in Glycine max

Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies

Myrtaceae is a large and species-rich family of woody eudicots, with prevalent distribution in the Southern Hemisphere. Classification and taxonomy of species belonging to this family is quite challenging, sometimes with difficulty in species identification and producing phylogenies with low support for species relationships. Most of the current knowledge comes from few molecular markers, such as plastid genes and intergenic regions, which can be difficult to handle and produce conflicting results. Based on plastid protein-coding sequences and nuclear markers, we present a topology for the phylogenetic relationships among Myrtaceae tribes. Our phylogenetic estimate offers a contrasting topology over previous analysis with fewer markers. Plastome phylogeny groups the tribes Syzygieae and Eucalypteae and individual chloroplast genes produce divergent topologies, especially among species within Myrteae tribe, but also in regard to the grouping of Syzygieae and Eucalypteae. Results are consistent and reproducible with both nuclear and organellar datasets. It confronts previous data about the deep nodes of Myrtaceae phylogeny

Análise metagenômica de comunidades microbianas do aparelho genital de bovinos sadios e acometidos por distúrbios reprodutivos

Reproductive disorders in bovines can be caused by various pathogens, which might already be present in the reproductive tract. The microbial community of the reproductive apparatus, when known, can provide information about the health of the host. The metagenomics has been used to characterize and obtain genetics information about microbial communities in various environments and can relate certain diseases with changes in community composition. In this study, samples were collected from the secretion of mucosa of vaginal surface of 05 healthy cows and 05 cows that showed symptoms of reproductive disorders. Metagenomics DNA samples were extracted of secretion samples and amplified with primers for the V5-V6 regions of the 16S rRNA and sequenced on the platform "Ion Torrent Personal Genome Machine - PGM". The data were processed to remove low quality sequences and chimeras, with the Mothur program, then the data were released in the Ribosomal Database Project for classification of OTU's. Local blastn was performed and this results was loaded in MEGAN program, for viewing profiles and taxonomic microbial attributes. The control profile showed a total of 15 taxa, being the taxa Bacteroides, Enterobacteriaceae and Victivallis, with the highest representation of OTU's; the positive profile showed 68 taxa, and Bacteroides, Enterobacteriaceae, Histophilus, Victivallis, Alistipes and Coriobacteriaceae, the taxa with more OTU's representation. The genus Histophilus have pathogenics species in reproductive tract of cattle. There was a change in the community composition, well as in microbial attributes of profiles there may be a relationship between the pathogen and of other representatives taxa, in production of metabolites to disease progression.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPESDistúrbios reprodutivos em bovinos podem ser causados por diversos patógenos, que poderiam já estar presentes no trato reprodutivos. A comunidade microbiana dos aparelhos reprodutivos, quando conhecida, pode fornecer informações a respeito da saúde do hospedeiro. A metagenômica tem sido utilizada para caracterizar e obter informações genéticas a respeito de comunidades microbianas de diversos ambientes, podendo relacionar determinadas doenças com alterações na composição das comunidades. Nesse trabalho, foram coletadas amostras de secreção de mucosa da superfície vaginal de 05 vacas sadias e 05 vacas que apresentaram sintomas de distúrbios reprodutivos. Amostras de DNA metagenômico foram extraídas das amostras de secreção e amplificadas com primers para as regiões V5-V6 do gene 16S rRNA e sequenciadas na plataforma Ion Torrent Personal Genome Machine PGM . Os dados foram tratados para retirada de sequencias de baixa qualidade e quimeras, com o programa Mothur; em seguida, os dados foram lançados no Ribosomal Database Project para classificação das OTU´s. Blastn local foi efetuado e seus resultados foram carregados no programa MEGAN, para visualização de perfis taxonômicos e atributos microbianos. O perfil controle apresentou um total de 15 taxa, sendo os taxa Bacteroides, Enterobacteriaceae e Victivallis, os de maior representação de OTU´s; o perfil com distúrbios apresentou 68 taxa, sendo Bacteroides, Enterobacteriaceae, Histophilus, Victivallis, Alistipes, e Coriobacteriaceae, os taxa com maior representação de OTU´s. O gênero Histophilus possui espécies patogênicas em trato reprodutivo de bovinos. Observou-se uma alteração na composição das comunidades estudadas, bem como nos atributos microbianos dos perfis podendo haver uma relação entre patógenos e representantes de outros taxa, na produção de metabólitos para progressão da doença

Edição de RNA plastidial em Glycine max: caracterização de sítios de edição, componentes do editossomo e efeitos de estresse abiótico

Soja, uma cultura conhecida por sua importância econômica e nutricional, tem sido objeto de vários estudos que avaliam o impacto e as respostas efetivas das plantas aos estresses abióticos. O estresse salino é um dos principais estresses ambientais e afeta negativamente o crescimento e o rendimento das culturas, incluindo a soja. A edição de RNA é um processo pelo qual as sequências de nucleotídeos podem ser alteradas, revertendo mutações que podem mudar as sequências de proteínas para manter suas funções conservadas. As proteínas pentatricopeptide repeat (PPRs) são trans-elementos de edição caracterizados por reconhecer cis-elementos específicos de RNA e realizar a reação de edição. Vários estudos descreveram estes trans-elementos e seus sítios de edição cognatos, mas nem todas as proteínas que compõem o complexo de edição foram identificadas. A perda de eventos de edição de plastídios, resultante de mutações em fatores de edição de RNA ou através de interferência por estresse, leva a alterações de desenvolvimento, de fisiologia e da fotossíntese. O objetivo do presente trabalho é caracterizar os sítios de edição e os fatores associados à edição de RNA em Glycine max e a influência de estresses abióticos no processo de edição de RNA em cloroplastos. No capítulo 1, um método é apresentado para triar a edição de RNA de cloroplasto usando bibliotecas públicas de sRNAs de Arabidopsis, soja e arroz. Entre os sítios de edição previstos, 40,57, 34,78 e 25,31% foram confirmados utilizando sRNAs de Arabidopsis, soja e arroz, respectivamente. A análise de SNPs revelou alterações de C-to-U de 58,2, 43,9 e 37,5% nas respectivas espécies e identificou conhecidas e possíveis novas edições de RNA de adenosina para inosina (A-to-I) em tRNAs. O método e os dados revelam o potencial do uso de sRNA como uma fonte confiável para identificar novos e confirmar sítios de edição conhecidos. No capítulo 2, o processo de edição de RNA foi avaliado em cloroplastos de plantas de soja sob estresse salino. A abordagem de bioinformática utilizando bibliotecas de sRNAs e mRNAs foi empregada para detectar sítios específicos que mostram diferenças na taxa de edição. RT-qPCR foi usado para medir a taxa de edição nos sítios selecionados. Observamos diferenças nas taxas de edição nos transcritos dos genes ndhA, ndhB, rps14 e rps16 ao comparar os dados das bibliotecas controle e das tratadas com NaCl. Os ensaios de RT-qPCR 9 demonstraram um aumento na edição dos genes selecionados. Esses aumentos podem ser uma resposta para manter a homeostase das funções das proteínas do cloroplasto em resposta ao estresse salino. No capítulo 3, para identificar os fatores relacionados aos sítios de edição analisados, sondas biotiniladas de RNA foram projetadas com base nos sítios de edição de RNA de plastídio de soja para realizar um isolamento proteico específico do fator de edição. Proteínas que interagiram com as sondas foram isoladas através da ligação das sondas à biotina e foram identificadas utilizando espectrometria de massa. Entre os peptídeos detectados, cinco corresponderam a proteínas PPR. A comparação dos genes de Arabidopsis com as proteínas PPR da soja permitiu a identificação dos homólogos mais próximos. O presente estudo representa a primeira identificação do conjunto de sítios de edição de RNA, de fatores associados aos sítios de edição de RNA e a caracterização dos efeitos do estresse abiótico na edição de RNA em Glycine max.Soybean, a crop known by its economic and nutritional importance, has been the subject of several studies that assess the impact and the effective plant responses to abiotic stresses. Salt stress is one of the main environmental stresses and negatively impacts crop growth and yield. RNA editing is a process whereby nucleotide sequences can be altered, reverting mutations that could change protein sequences to maintain their conserved functions. Pentatricopeptide repeat proteins are editing trans-elements characterized by recognize specific RNA cis-elements and perform the editing reaction. Several studies have described these trans-elements and their cognate editing sites, but not all proteins that compose the editing complex were identified. The loss of plastid editing events, resulting from mutations in RNA editing factors or through stress interference, leads to developmental, physiological and photosynthetic alterations. The aim of the present work is to characterize the editing sites and factors associated with RNA editing in Glycine max and the influence of abiotic stresses on the process of RNA editing in chloroplasts. In chapter 1, a method is presented to screen chloroplast RNA editing using public sRNA libraries from Arabidopsis, soybean and rice. Among the predicted editing sites, 40.57, 34.78, and 25.31% were confirmed using sRNAs from Arabidopsis, soybean and rice, respectively. SNP analysis revealed 58.2, 43.9, and 37.5% new C-to-U changes in the respective species and identified known and new putative adenosine to inosine (A-to-I) RNA editing in tRNAs. The method and data reveal the potential of sRNA as a reliable source to identify new and confirm known editing sites. In chapter 2, RNA editing process was evaluated in the chloroplast of soybean plants under salt stress. Bioinformatics approach using sRNA and mRNA libraries was employed to detect specific sites showing differences in editing efficiency. RT-qPCR was used to measure editing efficiency at selected sites. We observed differences in ndhA, ndhB, rps14 and rps16 editing rates between control and salt-treated libraries. RT-qPCR assays demonstrated an increase in editing efficiency of selected genes. These increases can be a response to keep the homeostasis of chloroplast protein functions in response to NaCl stress. In chapter 3, to identify the trans-acting factors of editing sites analyzed, we have designed RNA biotinylated probes based in soybean plastid RNA editing sites to perform 11 specific isolation of proteins associated to editosomes. Proteins that interacted with the probes were isolated by binding the probes to biotin and were identified using mass spectrometry. Among the detected peptides, five corresponded to PPR proteins. Comparison of Arabidopsis genes to the soybean PPR proteins allow identification of the closest related homologs. The present study represents the first identification of RNA editing sites set, associated factors to RNA editing sites and characterization of effects from abiotic stress in RNA editing in Glycine max

Salt stress affects mRNA editing in soybean chloroplasts

Soybean, a crop known by its economic and nutritional importance, has been the subject of several studies that assess the impact and the effective plant responses to abiotic stresses. Salt stress is one of the main environmental stresses and negatively impacts crop growth and yield. In this work, the RNA editing process in the chloroplast of soybean plants was evaluated in response to a salt stress. Bioinformatics approach using sRNA and mRNA libraries were employed to detect specific sites showing differences in editing efficiency. RT-qPCR was used to measure editing efficiency at selected sites. We observed that transcripts of NDHA, NDHB, RPS14 and RPS16 genes presented differences in coverage and editing rates between control and salt-treated libraries. RT-qPCR assays demonstrated an increase in editing efficiency of selected genes. The salt stress enhanced the RNA editing process in transcripts, indicating responses to components of the electron transfer chain, photosystem and translation complexes. These increases can be a response to keep the homeostasis of chloroplast protein functions in response to salt stress

Salt stress affects mRNA editing in soybean chloroplasts

Soybean, a crop known by its economic and nutritional importance, has been the subject of several studies that assess the impact and the effective plant responses to abiotic stresses. Salt stress is one of the main environmental stresses and negatively impacts crop growth and yield. In this work, the RNA editing process in the chloroplast of soybean plants was evaluated in response to a salt stress. Bioinformatics approach using sRNA and mRNA libraries were employed to detect specific sites showing differences in editing efficiency. RT-qPCR was used to measure editing efficiency at selected sites. We observed that transcripts of NDHA, NDHB, RPS14 and RPS16 genes presented differences in coverage and editing rates between control and salt-treated libraries. RT-qPCR assays demonstrated an increase in editing efficiency of selected genes. The salt stress enhanced the RNA editing process in transcripts, indicating responses to components of the electron transfer chain, photosystem and translation complexes. These increases can be a response to keep the homeostasis of chloroplast protein functions in response to salt stress

Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora

Plinia trunciflora is a Brazilian native fruit tree from the Myrtaceae family, also known as jaboticaba. This species has great potential by its fruit production. Due to the high content of essential oils in their leaves and of anthocyanins in the fruits, there is also an increasing interest by the pharmaceutical industry. Nevertheless, there are few studies focusing on its molecular biology and genetic characterization. We herein report the complete chloroplast (cp) genome of P. trunciflora using high-throughput sequencing and compare it to other previously sequenced Myrtaceae genomes. The cp genome of P. trunciflora is 159,512 bp in size, comprising inverted repeats of 26,414 bp and single-copy regions of 88,097 bp (LSC) and 18,587 bp (SSC). The genome contains 111 single-copy genes (77 protein-coding, 30 tRNA and four rRNA genes). Phylogenetic analysis using 57 cp protein-coding genes demonstrated that P. trunciflora, Eugenia uniflora and Acca sellowiana form a cluster with closer relationship to Syzygium cumini than with Eucalyptus. The complete cp sequence reported here can be used in evolutionary and population genetics studies, contributing to resolve the complex taxonomy of this species and fill the gap in genetic characterization

Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora

<div><p>Abstract Plinia trunciflora is a Brazilian native fruit tree from the Myrtaceae family, also known as jaboticaba. This species has great potential by its fruit production. Due to the high content of essential oils in their leaves and of anthocyanins in the fruits, there is also an increasing interest by the pharmaceutical industry. Nevertheless, there are few studies focusing on its molecular biology and genetic characterization. We herein report the complete chloroplast (cp) genome of P. trunciflora using high-throughput sequencing and compare it to other previously sequenced Myrtaceae genomes. The cp genome of P. trunciflora is 159,512 bp in size, comprising inverted repeats of 26,414 bp and single-copy regions of 88,097 bp (LSC) and 18,587 bp (SSC). The genome contains 111 single-copy genes (77 protein-coding, 30 tRNA and four rRNA genes). Phylogenetic analysis using 57 cp protein-coding genes demonstrated that P. trunciflora, Eugenia uniflora and Acca sellowiana form a cluster with closer relationship to Syzygium cumini than with Eucalyptus. The complete cp sequence reported here can be used in evolutionary and population genetics studies, contributing to resolve the complex taxonomy of this species and fill the gap in genetic characterization.</p></div