Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa

Abstract

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.

Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress

“…Glycosylation modifications may change the stability and molecular weight of the target protein [73,74]. In addition, phosphorylation modifications play critical roles in protein activity, protein-protein interactions, and the regulation of signal transduction [65,75,76]. Previous studies have revealed that posttranslational modifications such as phosphorylation are involved in activating the K+ channel AKT1 [1,21,31].…”

Phosphate transporter genes: genome-wide identification and characterization in Camelina sativa

“…The recognized genes were belonged to ,PHT2,PHT4,PHO1,PHO1 homologs,inorganic PHTs, xylulose 5-PHTs, glucose-6-phosphate translocators, and phosphoenolpyruvate translocators. Regarding the physicochemical properties, the PHT proteins were stated with high diversity in terms of pI, molecular weight, GRAVY value, and exon number, indicating that these transporter genes may be associated with various cellular pathways (Ahmadizadeh et al, 2020a(Ahmadizadeh et al, , 2020b. Interestingly, all PHO1 homolog proteins were showed a negative GRAVY value, revealing that the PHO1 homolog proteins are hydrophilic (Heidari et al, 2019;Rezaee et al, 2020).…”

“…Post-translation modifications such as phosphorylation processes cause significant effects on protein activities and inducing cell signaling (Heidari et al, 2020a;Silva-Sanchez et al, 2015). The high phosphorylation potential of PHO1 proteins may indicate that these proteins are involved in various cellular processes under signal transduction pathways (Ahmadizadeh et al, 2020a). Regarding the promoter region analysis, various cis-acting elements associated with response to stress conditions and phytohormones were found in the upstream region of PHT genes.…”

Magnesium transporter Gene Family: Genome-Wide Identification and Characterization in Theobroma cacao, Corchorus capsularis, and Gossypium hirsutum of Family Malvaceae

“…Magnesium transporters as well as other ion transporters are not only involved in response to Mg concentrations, but also their activity can be affected by changes in environmental conditions [10,12]. Analysis of gene promoter regions is one of the strategies to predict the response of target genes to various environmental factors [77,78]. MGT genes have a high potential to respond to stresses, both biotic and abiotic, as well as ABA based on the distribution of corresponding cis-regulatory elements in the promoter region.…”