“…7a, and b ). In a recent study, we have shown that abscisic acid (ABA) treatment also induced a significant increase of Am nucleosides in rice seedlings [ 28 ]. Fig.…”
Section: Resultsmentioning
confidence: 99%
“…Small RNAs (< 200 bp) were extracted using microRNA Extraction Kit (Omega Bio-tek Inc.), digested into nucleosides and analyzed by LC-MS/MS with an LC-20A HPLC system and a diode array UV detector (190-400 nm). Details for LC-MS/MS analysis was described previously [ 28 ]. The abundance of each nucleoside under stress conditions was normalized to that in control set, the ratio (fold of change) of each nucleoside was calculated and used for heatmap generation.…”
Section: Methodsmentioning
confidence: 99%
“…The mutants of AtTRM4B , m 5 C (5-methylcytidine) methylation modification gene, had shorter primary roots and increased sensitivity to oxidative stress [ 27 ]. Our recent study showed that Am nucleoside (2’-O-methyladenosine) was induced by salt stress in a variety of plants including Rice, Poplar, Arabidopsis and Brachypodium [ 28 ]. Overexpression of OsTRM13 , the corresponding gene for Am and Cm modification at position 4, improved salt stress tolerance in rice [ 28 ].…”
Section: Introductionmentioning
confidence: 99%
“…Our recent study showed that Am nucleoside (2’-O-methyladenosine) was induced by salt stress in a variety of plants including Rice, Poplar, Arabidopsis and Brachypodium [ 28 ]. Overexpression of OsTRM13 , the corresponding gene for Am and Cm modification at position 4, improved salt stress tolerance in rice [ 28 ].…”
BackgroundModification of nucleosides on transfer RNA (tRNA) is important either for correct mRNA decoding process or for tRNA structural stabilization. Nucleoside methylations catalyzed by MTase (methyltransferase) are the most common type among all tRNA nucleoside modifications. Although tRNA modified nucleosides and modification enzymes have been extensively studied in prokaryotic systems, similar research remains preliminary in higher plants, especially in crop species, such as rice (Oryza sativa). Rice is a monocot model plant as well as an important cereal crop, and stress tolerance and yield are of great importance for rice breeding.ResultsIn this study, we investigated how the composition and abundance of tRNA modified nucleosides could change in response to drought, salt and cold stress, as well as in different tissues during the whole growth season in two model plants–O. sativa and Arabidopsis thaliana. Twenty two and 20 MTase candidate genes were identified in rice and Arabidopsis, respectively, by protein sequence homology and conserved domain analysis. Four methylated nucleosides, Am, Cm, m1A and m7G, were found to be very important in stress response both in rice and Arabidopsis. Additionally, three nucleosides,Gm, m5U and m5C, were involved in plant development. Hierarchical clustering analysis revealed consistency on Am, Cm, m1A and m7G MTase candidate genes, and the abundance of the corresponding nucleoside under stress conditions. The same is true for Gm, m5U and m5C modifications and corresponding methylation genes in different tissues during different developmental stages.ConclusionsWe identified candidate genes for various tRNA modified nucleosides in rice and Arabidopsis, especially on MTases for methylated nucleosides. Based on bioinformatics analysis, nucleoside abundance assessments and gene expression profiling, we propose four methylated nucleosides (Am, Cm, m1A and m7G) that are critical for stress response in rice and Arabidopsis, and three methylated nucleosides (Gm, m5U and m5C) that might be important during development.Electronic supplementary materialThe online version of this article (10.1186/s12870-017-1206-0) contains supplementary material, which is available to authorized users.
“…7a, and b ). In a recent study, we have shown that abscisic acid (ABA) treatment also induced a significant increase of Am nucleosides in rice seedlings [ 28 ]. Fig.…”
Section: Resultsmentioning
confidence: 99%
“…Small RNAs (< 200 bp) were extracted using microRNA Extraction Kit (Omega Bio-tek Inc.), digested into nucleosides and analyzed by LC-MS/MS with an LC-20A HPLC system and a diode array UV detector (190-400 nm). Details for LC-MS/MS analysis was described previously [ 28 ]. The abundance of each nucleoside under stress conditions was normalized to that in control set, the ratio (fold of change) of each nucleoside was calculated and used for heatmap generation.…”
Section: Methodsmentioning
confidence: 99%
“…The mutants of AtTRM4B , m 5 C (5-methylcytidine) methylation modification gene, had shorter primary roots and increased sensitivity to oxidative stress [ 27 ]. Our recent study showed that Am nucleoside (2’-O-methyladenosine) was induced by salt stress in a variety of plants including Rice, Poplar, Arabidopsis and Brachypodium [ 28 ]. Overexpression of OsTRM13 , the corresponding gene for Am and Cm modification at position 4, improved salt stress tolerance in rice [ 28 ].…”
Section: Introductionmentioning
confidence: 99%
“…Our recent study showed that Am nucleoside (2’-O-methyladenosine) was induced by salt stress in a variety of plants including Rice, Poplar, Arabidopsis and Brachypodium [ 28 ]. Overexpression of OsTRM13 , the corresponding gene for Am and Cm modification at position 4, improved salt stress tolerance in rice [ 28 ].…”
BackgroundModification of nucleosides on transfer RNA (tRNA) is important either for correct mRNA decoding process or for tRNA structural stabilization. Nucleoside methylations catalyzed by MTase (methyltransferase) are the most common type among all tRNA nucleoside modifications. Although tRNA modified nucleosides and modification enzymes have been extensively studied in prokaryotic systems, similar research remains preliminary in higher plants, especially in crop species, such as rice (Oryza sativa). Rice is a monocot model plant as well as an important cereal crop, and stress tolerance and yield are of great importance for rice breeding.ResultsIn this study, we investigated how the composition and abundance of tRNA modified nucleosides could change in response to drought, salt and cold stress, as well as in different tissues during the whole growth season in two model plants–O. sativa and Arabidopsis thaliana. Twenty two and 20 MTase candidate genes were identified in rice and Arabidopsis, respectively, by protein sequence homology and conserved domain analysis. Four methylated nucleosides, Am, Cm, m1A and m7G, were found to be very important in stress response both in rice and Arabidopsis. Additionally, three nucleosides,Gm, m5U and m5C, were involved in plant development. Hierarchical clustering analysis revealed consistency on Am, Cm, m1A and m7G MTase candidate genes, and the abundance of the corresponding nucleoside under stress conditions. The same is true for Gm, m5U and m5C modifications and corresponding methylation genes in different tissues during different developmental stages.ConclusionsWe identified candidate genes for various tRNA modified nucleosides in rice and Arabidopsis, especially on MTases for methylated nucleosides. Based on bioinformatics analysis, nucleoside abundance assessments and gene expression profiling, we propose four methylated nucleosides (Am, Cm, m1A and m7G) that are critical for stress response in rice and Arabidopsis, and three methylated nucleosides (Gm, m5U and m5C) that might be important during development.Electronic supplementary materialThe online version of this article (10.1186/s12870-017-1206-0) contains supplementary material, which is available to authorized users.
“…Over the past few decades, with the continuous development of biological technologies and high-throughput sequencing technologies (Goff et al 2002;Yu et al 2002;International Barley Genome Sequencing Consortium et al 2012;International Wheat Genome Sequencing Consortium et al 2014;Schnable et al 2009), more and more researchers have been able to identify and clone genes or transcription factors related to stress resistance in these crops (Mickelbart et al 2015;. As a large number of genes and transcription factors were found to be related to the stress resistance of crops (Güre et al 2016;Barnawal et al 2017;Wang et al 2017;Gao et al 2018),researchers published the research results through the display of articles in major academic journals for reference by other researchers. Mass research were scattered across different journals' websites or public document data websites.…”
Numerous studies have shown that many genes and proteins in plants are involved in the regulation of plant resistance to abiotic and biotic stresses. The researches on the stress tolerance of crops are also the focus of many researchers. To provides a reliable platform for collecting and retrieving genetic and protein information related to stress tolerance found in crops, we constructed CSTDB(Crops Stress-tolerance Database), an integrated database that includes stress-tolerance genes and proteins for many crop species. The database was developed based on convolutional neural network technology. It is a web-accessible database that contains detailed information on the stress-tolerance genes and proteins of major crop species. Currently, the database records four major crops containing 1,371 abiotic stress-tolerance genes or proteins, and 207 genes or proteins associated with biotic stress. Each gene and protein has detailed functional information and sequence information, such as stress types, Genbank ID, Pubmed ID，Protein ID，3D model picture and FASTA files. As a user-friendly browsing tool, this database provides search functions, BALST functions and file download functions. CSTDB can be a valuable resource，which is designed to meet the broad needs of researchers working on crops stress-tolerance experiments. Database URL: http://pcsb.ahau.edu.cn:8080/CSTDB
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