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Registro Completo |
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Biblioteca(s): |
Embrapa Recursos Genéticos e Biotecnologia; Embrapa Semiárido. |
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Data corrente: |
19/02/2021 |
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Data da última atualização: |
07/02/2022 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
ARRAES, F. B. M.; MARTINS-DE-SA, D; VASQUEZ, D. D. N.; MELO, B. P.; FAHEEM, M.; MACEDO, L. L. P. de; MORGANTE, C. V.; BARBOSA, J. A. R. G.; TOGAWA, R. C.; MOREIRA, V. J. V.; DANCHIN, E. G. J.; SA, M. F. G. de. |
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Afiliação: |
FABRICIO BARBOSA MONTEIRO ARRAES; DIOGO MARTINS-DE-SA; DANIEL D. NORIEGA VASQUEZ; BRUNO PAES MELO; MUHAMMAD FAHEEM; LEONARDO LIMA PEPINO DE MACEDO; CAROLINA VIANNA MORGANTE, CPATSA; JOÃO ALEXANDRE R. G. BARBOSA; ROBERTO COITI TOGAWA; VALDEIR JUNIO VAZ MOREIRA; ETIENNE G. J. DANCHIN; MARIA FATIMA GROSSI DE SA. |
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Título: |
Dissecting protein domain variability in the core rna interference machinery of five insect orders. |
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Ano de publicação: |
2021 |
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Fonte/Imprenta: |
RNA Biology, v. 18, n. 11, p. 1653-1681, 2021. |
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DOI: |
https://doi.org/10.1080/15476286.2020.1861816 |
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Idioma: |
Inglês |
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Conteúdo: |
RNA interference (RNAi)-mediated gene silencing can be used to control specific insect pest populations. Unfortunately, the variable efficiency in the knockdown levels of target genes has narrowed the applicability of this technology to a few species. Here, we examine the current state of knowledge regarding the miRNA (micro RNA) and siRNA (small interfering RNA) pathways in insects and investigate the structural variability at key protein domains of the RNAi machinery. Our goal was to correlate domain variability with mechanisms affecting the gene silencing efficiency. To this end, the protein domains of 168 insect species, encompassing the orders Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera, were analysed using our pipeline, which takes advantage of meticulous structure-based sequence alignments. We used phylogenetic inference and the evolutionary rate coefficient (K) to outline the variability across domain regions and surfaces. Our results show that four domains, namely dsrm, Helicase, PAZ and Ribonuclease III, are the main contributors of protein variability in the RNAi machinery across different insect orders. We discuss the potential roles of these domains in regulating RNAi-mediated gene silencing and the role of loop regions in fine-tuning RNAi efficiency. Additionally, we identified several order-specific singularities which indicate that lepidopterans have evolved differently from other insect orders, possibly due to constant coevolution with plants and viruses. In conclusion, our results highlight several variability hotspots that deserve further investigation in order to improve the application of RNAi technology in the control of insect pests. MenosRNA interference (RNAi)-mediated gene silencing can be used to control specific insect pest populations. Unfortunately, the variable efficiency in the knockdown levels of target genes has narrowed the applicability of this technology to a few species. Here, we examine the current state of knowledge regarding the miRNA (micro RNA) and siRNA (small interfering RNA) pathways in insects and investigate the structural variability at key protein domains of the RNAi machinery. Our goal was to correlate domain variability with mechanisms affecting the gene silencing efficiency. To this end, the protein domains of 168 insect species, encompassing the orders Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera, were analysed using our pipeline, which takes advantage of meticulous structure-based sequence alignments. We used phylogenetic inference and the evolutionary rate coefficient (K) to outline the variability across domain regions and surfaces. Our results show that four domains, namely dsrm, Helicase, PAZ and Ribonuclease III, are the main contributors of protein variability in the RNAi machinery across different insect orders. We discuss the potential roles of these domains in regulating RNAi-mediated gene silencing and the role of loop regions in fine-tuning RNAi efficiency. Additionally, we identified several order-specific singularities which indicate that lepidopterans have evolved differently from other insect orders, possibly due to constant coevolution with plant... Mostrar Tudo |
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Palavras-Chave: |
Argonaute; DCR1; Dicer; Drosha; DsRBDs; Evolução da proteína; In silico analysis; Loquacious; Pasha; Protein evolution; R2D2; RIIID II; Sequência de proteínas inteira; Structure-function relationship. |
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Thesagro: |
Controle Genético; Genoma; Inseto; Praga; Proteína. |
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Thesaurus Nal: |
Insect control; Pest control; Protein structure; Proteins. |
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Categoria do assunto: |
--
G Melhoramento Genético |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/230917/1/Dissecting-protein-domain-variability-2021.pdf
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Marc: |
LEADER 03184naa a2200541 a 4500
001 2130159
005 2022-02-07
008 2021 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1080/15476286.2020.1861816$2DOI
100 1 $aARRAES, F. B. M.
245 $aDissecting protein domain variability in the core rna interference machinery of five insect orders.$h[electronic resource]
260 $c2021
520 $aRNA interference (RNAi)-mediated gene silencing can be used to control specific insect pest populations. Unfortunately, the variable efficiency in the knockdown levels of target genes has narrowed the applicability of this technology to a few species. Here, we examine the current state of knowledge regarding the miRNA (micro RNA) and siRNA (small interfering RNA) pathways in insects and investigate the structural variability at key protein domains of the RNAi machinery. Our goal was to correlate domain variability with mechanisms affecting the gene silencing efficiency. To this end, the protein domains of 168 insect species, encompassing the orders Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera, were analysed using our pipeline, which takes advantage of meticulous structure-based sequence alignments. We used phylogenetic inference and the evolutionary rate coefficient (K) to outline the variability across domain regions and surfaces. Our results show that four domains, namely dsrm, Helicase, PAZ and Ribonuclease III, are the main contributors of protein variability in the RNAi machinery across different insect orders. We discuss the potential roles of these domains in regulating RNAi-mediated gene silencing and the role of loop regions in fine-tuning RNAi efficiency. Additionally, we identified several order-specific singularities which indicate that lepidopterans have evolved differently from other insect orders, possibly due to constant coevolution with plants and viruses. In conclusion, our results highlight several variability hotspots that deserve further investigation in order to improve the application of RNAi technology in the control of insect pests.
650 $aInsect control
650 $aPest control
650 $aProtein structure
650 $aProteins
650 $aControle Genético
650 $aGenoma
650 $aInseto
650 $aPraga
650 $aProteína
653 $aArgonaute
653 $aDCR1
653 $aDicer
653 $aDrosha
653 $aDsRBDs
653 $aEvolução da proteína
653 $aIn silico analysis
653 $aLoquacious
653 $aPasha
653 $aProtein evolution
653 $aR2D2
653 $aRIIID II
653 $aSequência de proteínas inteira
653 $aStructure-function relationship
700 1 $aMARTINS-DE-SA, D
700 1 $aVASQUEZ, D. D. N.
700 1 $aMELO, B. P.
700 1 $aFAHEEM, M.
700 1 $aMACEDO, L. L. P. de
700 1 $aMORGANTE, C. V.
700 1 $aBARBOSA, J. A. R. G.
700 1 $aTOGAWA, R. C.
700 1 $aMOREIRA, V. J. V.
700 1 $aDANCHIN, E. G. J.
700 1 $aSA, M. F. G. de
773 $tRNA Biology$gv. 18, n. 11, p. 1653-1681, 2021.
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Esconder MarcMostrar Marc Completo |
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Registro original: |
Embrapa Semiárido (CPATSA) |
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 | Acesso ao texto completo restrito à biblioteca da Embrapa Florestas. Para informações adicionais entre em contato com cnpf.biblioteca@embrapa.br. |
Registro Completo
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Biblioteca(s): |
Embrapa Florestas. |
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Data corrente: |
19/03/2024 |
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Data da última atualização: |
19/03/2024 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 1 |
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Autoria: |
BARTZ, M. L. C.; DUDAS, R. T.; DEMETRIO, W. C.; BROWN, G. G. |
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Afiliação: |
MARIE LUISE CAROLINA BARTZ, CENTRO MUNICIPAL DE CULTURA DE DESENVOLVIMENTO - ORGANIC FARMING, UNIVERSITY OF COIMBRA; RAFAELA TAVARES DUDAS, UNIVERSIDADE FEDERAL DO PARANÁ; WILIAN CARLO DEMETRIO, UNIVERSIDADE DE SÃO PAULO; GEORGE GARDNER BROWN, CNPF. |
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Título: |
Earthworms as soil health indicators in no-tillage agroecosystems. |
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Ano de publicação: |
2024 |
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Fonte/Imprenta: |
European Journal of Soil Biology, v. 121, 103605, 2024. |
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DOI: |
https://doi.org/10.1016/j.ejsobi.2024.103605 |
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Idioma: |
Português |
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Conteúdo: |
No-tillage (NT) and no-tillage systems (NTS) are widely used conservation agriculture practices in Brazil, and in the state of Paran´a, nearly 80% of annual crops are cultivated using these methods. Compared with NT, NTS sites permanently include: minimum soil disturbance, soil cover (straw and living vegetation) and crop rotation and diversification with cover crops. These practices often increase earthworm populations, that can be used to indicate soil health. Herein, we review soil health classification of NT sites, and the species found in Paran´a state. We compiled information from 130 sites with NT or NTS, located in 29 counties, of which 93 had biomass and 91 had species richness data, aiming to compare NT with NTS sites, and the effect of the age of these practices on earthworm populations. Overall, 29 earthworm species were recorded, of which 17 were native, including many new to science. Mean abundance and biomass in NT + NTS were 104 ind m 2 and 2.5 g m 2, respectively, and richness 2.5 species per site. Abundance was significantly higher in NT than NTS in the initial phase of adoption, and both abundance and biomass decreased with increasing age of NT. Earthworm abundance and species richness were positively correlated with clayey soils and phosphorus content, while higher biomass was asso- ciated with soil carbon content and pH. A new classification system was proposed, with the categories poor (<50 ind. m 2, 1 species), moderate (≥50 to <100 ind m 2, 2 species), good (≥100 to <150 ind m 2, 3 species), very good (≥150 to 200 ind m 2, 4 species) and excellent (≥200 ind m 2, ≥5 species) soil health, using earthworm abundance and species richness, respectively. Most of the sites sampled showed poor or moderate soil health, with few displaying very good or excellent health, indicating the need for improved management practices, in order to promote earthworm populations and their potential benefits to soil fertility and plant production. MenosNo-tillage (NT) and no-tillage systems (NTS) are widely used conservation agriculture practices in Brazil, and in the state of Paran´a, nearly 80% of annual crops are cultivated using these methods. Compared with NT, NTS sites permanently include: minimum soil disturbance, soil cover (straw and living vegetation) and crop rotation and diversification with cover crops. These practices often increase earthworm populations, that can be used to indicate soil health. Herein, we review soil health classification of NT sites, and the species found in Paran´a state. We compiled information from 130 sites with NT or NTS, located in 29 counties, of which 93 had biomass and 91 had species richness data, aiming to compare NT with NTS sites, and the effect of the age of these practices on earthworm populations. Overall, 29 earthworm species were recorded, of which 17 were native, including many new to science. Mean abundance and biomass in NT + NTS were 104 ind m 2 and 2.5 g m 2, respectively, and richness 2.5 species per site. Abundance was significantly higher in NT than NTS in the initial phase of adoption, and both abundance and biomass decreased with increasing age of NT. Earthworm abundance and species richness were positively correlated with clayey soils and phosphorus content, while higher biomass was asso- ciated with soil carbon content and pH. A new classification system was proposed, with the categories poor (<50 ind. m 2, 1 species), moderate (≥50 to <100 ind m 2, 2 species)... Mostrar Tudo |
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Palavras-Chave: |
Agroecossistemas; Bioindicator; Conservation agriculture; Crassiclitellata; Soil health. |
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Thesagro: |
Minhoca; Plantio Direto. |
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Categoria do assunto: |
K Ciência Florestal e Produtos de Origem Vegetal |
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Marc: |
LEADER 02742naa a2200253 a 4500
001 2162984
005 2024-03-19
008 2024 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1016/j.ejsobi.2024.103605$2DOI
100 1 $aBARTZ, M. L. C.
245 $aEarthworms as soil health indicators in no-tillage agroecosystems.$h[electronic resource]
260 $c2024
520 $aNo-tillage (NT) and no-tillage systems (NTS) are widely used conservation agriculture practices in Brazil, and in the state of Paran´a, nearly 80% of annual crops are cultivated using these methods. Compared with NT, NTS sites permanently include: minimum soil disturbance, soil cover (straw and living vegetation) and crop rotation and diversification with cover crops. These practices often increase earthworm populations, that can be used to indicate soil health. Herein, we review soil health classification of NT sites, and the species found in Paran´a state. We compiled information from 130 sites with NT or NTS, located in 29 counties, of which 93 had biomass and 91 had species richness data, aiming to compare NT with NTS sites, and the effect of the age of these practices on earthworm populations. Overall, 29 earthworm species were recorded, of which 17 were native, including many new to science. Mean abundance and biomass in NT + NTS were 104 ind m 2 and 2.5 g m 2, respectively, and richness 2.5 species per site. Abundance was significantly higher in NT than NTS in the initial phase of adoption, and both abundance and biomass decreased with increasing age of NT. Earthworm abundance and species richness were positively correlated with clayey soils and phosphorus content, while higher biomass was asso- ciated with soil carbon content and pH. A new classification system was proposed, with the categories poor (<50 ind. m 2, 1 species), moderate (≥50 to <100 ind m 2, 2 species), good (≥100 to <150 ind m 2, 3 species), very good (≥150 to 200 ind m 2, 4 species) and excellent (≥200 ind m 2, ≥5 species) soil health, using earthworm abundance and species richness, respectively. Most of the sites sampled showed poor or moderate soil health, with few displaying very good or excellent health, indicating the need for improved management practices, in order to promote earthworm populations and their potential benefits to soil fertility and plant production.
650 $aMinhoca
650 $aPlantio Direto
653 $aAgroecossistemas
653 $aBioindicator
653 $aConservation agriculture
653 $aCrassiclitellata
653 $aSoil health
700 1 $aDUDAS, R. T.
700 1 $aDEMETRIO, W. C.
700 1 $aBROWN, G. G.
773 $tEuropean Journal of Soil Biology$gv. 121, 103605, 2024.
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