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Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa
BACKGROUND: Ethylene is a gaseous plant hormone that acts as a requisite role in many aspects of the plant life cycle, and it is also a regulator of plant responses to abiotic and biotic stresses. In this study, we attempt to provide comprehensive information through analyses of existing data using...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Berlin Heidelberg
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7572930/ https://www.ncbi.nlm.nih.gov/pubmed/33074438 http://dx.doi.org/10.1186/s43141-020-00083-1 |
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author | Ahmadizadeh, Mostafa Chen, Jen-Tsung Hasanzadeh, Soosan Ahmar, Sunny Heidari, Parviz |
author_facet | Ahmadizadeh, Mostafa Chen, Jen-Tsung Hasanzadeh, Soosan Ahmar, Sunny Heidari, Parviz |
author_sort | Ahmadizadeh, Mostafa |
collection | PubMed |
description | BACKGROUND: Ethylene is a gaseous plant hormone that acts as a requisite role in many aspects of the plant life cycle, and it is also a regulator of plant responses to abiotic and biotic stresses. In this study, we attempt to provide comprehensive information through analyses of existing data using bioinformatics tools to compare the identified ethylene biosynthesis genes between Arabidopsis (as dicotyledonous) and rice (as monocotyledonous). RESULTS: The results exposed that the Arabidopsis proteins of the ethylene biosynthesis pathway had more potential glycosylation sites than rice, and 1-aminocyclopropane-1-carboxylate oxidase proteins were less phosphorylated than 1-aminocyclopropane-1-carboxylate synthase and S-adenosylmethionine proteins. According to the gene expression patterns, S-adenosylmethionine genes were more involved in the rice-ripening stage while in Arabidopsis, ACS2, and 1-aminocyclopropane-1-carboxylate oxidase genes were contributed to seed maturity. Furthermore, the result of miRNA targeting the transcript sequences showed that ath-miR843 and osa-miR1858 play a key role to regulate the post-transcription modification of S-adenosylmethionine genes in Arabidopsis and rice, respectively. The discovered cis- motifs in the promoter site of all the ethylene biosynthesis genes of A. thaliana genes were engaged to light-induced response in the cotyledon and root genes, sulfur-responsive element, dehydration, cell cycle phase-independent activation, and salicylic acid. The ACS4 protein prediction demonstrated strong protein-protein interaction in Arabidopsis, as well as, SAM2, Os04T0578000, Os01T0192900, and Os03T0727600 predicted strong protein-protein interactions in rice. CONCLUSION: In the current study, the complex between miRNAs with transcript sequences of ethylene biosynthesis genes in A. thaliana and O. sativa were identified, which could be helpful to understand the gene expression regulation after the transcription process. The binding sites of common transcription factors such as MYB, WRKY, and ABRE that control target genes in abiotic and biotic stresses were generally distributed in promoter sites of ethylene biosynthesis genes of A. thaliana. This was the first time to wide explore the ethylene biosynthesis pathway using bioinformatics tools that markedly showed the capability of the in silico study to integrate existing data and knowledge and furnish novel insights into the understanding of underlying ethylene biosynthesis pathway genes that will be helpful for more dissection. |
format | Online Article Text |
id | pubmed-7572930 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Springer Berlin Heidelberg |
record_format | MEDLINE/PubMed |
spelling | pubmed-75729302020-11-02 Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa Ahmadizadeh, Mostafa Chen, Jen-Tsung Hasanzadeh, Soosan Ahmar, Sunny Heidari, Parviz J Genet Eng Biotechnol Research BACKGROUND: Ethylene is a gaseous plant hormone that acts as a requisite role in many aspects of the plant life cycle, and it is also a regulator of plant responses to abiotic and biotic stresses. In this study, we attempt to provide comprehensive information through analyses of existing data using bioinformatics tools to compare the identified ethylene biosynthesis genes between Arabidopsis (as dicotyledonous) and rice (as monocotyledonous). RESULTS: The results exposed that the Arabidopsis proteins of the ethylene biosynthesis pathway had more potential glycosylation sites than rice, and 1-aminocyclopropane-1-carboxylate oxidase proteins were less phosphorylated than 1-aminocyclopropane-1-carboxylate synthase and S-adenosylmethionine proteins. According to the gene expression patterns, S-adenosylmethionine genes were more involved in the rice-ripening stage while in Arabidopsis, ACS2, and 1-aminocyclopropane-1-carboxylate oxidase genes were contributed to seed maturity. Furthermore, the result of miRNA targeting the transcript sequences showed that ath-miR843 and osa-miR1858 play a key role to regulate the post-transcription modification of S-adenosylmethionine genes in Arabidopsis and rice, respectively. The discovered cis- motifs in the promoter site of all the ethylene biosynthesis genes of A. thaliana genes were engaged to light-induced response in the cotyledon and root genes, sulfur-responsive element, dehydration, cell cycle phase-independent activation, and salicylic acid. The ACS4 protein prediction demonstrated strong protein-protein interaction in Arabidopsis, as well as, SAM2, Os04T0578000, Os01T0192900, and Os03T0727600 predicted strong protein-protein interactions in rice. CONCLUSION: In the current study, the complex between miRNAs with transcript sequences of ethylene biosynthesis genes in A. thaliana and O. sativa were identified, which could be helpful to understand the gene expression regulation after the transcription process. The binding sites of common transcription factors such as MYB, WRKY, and ABRE that control target genes in abiotic and biotic stresses were generally distributed in promoter sites of ethylene biosynthesis genes of A. thaliana. This was the first time to wide explore the ethylene biosynthesis pathway using bioinformatics tools that markedly showed the capability of the in silico study to integrate existing data and knowledge and furnish novel insights into the understanding of underlying ethylene biosynthesis pathway genes that will be helpful for more dissection. Springer Berlin Heidelberg 2020-10-19 /pmc/articles/PMC7572930/ /pubmed/33074438 http://dx.doi.org/10.1186/s43141-020-00083-1 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Research Ahmadizadeh, Mostafa Chen, Jen-Tsung Hasanzadeh, Soosan Ahmar, Sunny Heidari, Parviz Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa |
title | Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa |
title_full | Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa |
title_fullStr | Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa |
title_full_unstemmed | Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa |
title_short | Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa |
title_sort | insights into the genes involved in the ethylene biosynthesis pathway in arabidopsis thaliana and oryza sativa |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7572930/ https://www.ncbi.nlm.nih.gov/pubmed/33074438 http://dx.doi.org/10.1186/s43141-020-00083-1 |
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