N 6 -methyl-adenosine level in Nicotiana tabacum is associated with tobacco mosaic virus

Abstract Background N 6 -methyl-adenosine (m6A) is a prevalent RNA modification in many species. Abnormal m6A methylation levels can lead to RNA dysfunction and can cause diseases. Tobacco mosaic virus (TMV) is one of the most devastating viruses for agricultural plants. It has many hosts, particularly including tobacco and other members the family Solanaceae. However, it remains unclear whether the abnormal growth induced by TMV is associated with the m6A level. Methods A rapid and accurate analytical method using ultra-high-performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC−HR − MS/MS) was developed to analyse the adenosine (A), cytidine (C), guanosine (G), uridine (U), and m6A contents in the tobacco leaf, and the m6A/G ratio was used to evaluate the m6A level. Subsequent protein sequence alignments were used to find the potential methylases and demethylases in Nicotiana tabacum (N. tabacum). Finally, reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) was used to analyse the gene expression levels of the potential methylases and demethylases in the N. tabacum leaf. Results The results showed that TMV reduced the m6A level. Moreover, protein sequence alignments revealed partial homology among human ALKBH5, Arabidopsis (NP_001031793), and Nicotiana sylvestris (XP_009800010). The gene expression level of the potential demethylase XM_009801708 increased at 14 and 21 days in N. tabacum infected with TMV, whereas all of the potential methylases decreased. Conclusions The reversible m6A modification in N. tabacum mRNA might represent a novel epigenetic mechanism involved in TMV

Binding constants of Southern rice black-streaked dwarf virus Coat Protein with ferulic acid derivatives

The data present binding constants between ferulic acid derivatives and the Coat Protein (P10) by fluorescence titration in this article, which is hosted in the research article entitled “Interaction Research on an Antiviral Molecule that Targets the Coat Protein of Southern rice black-streaked dwarf virus’’ (Ran et al., 2017) [1]. The data include fluorescence quenching spectrum, Stern–Volmer quenching constants, and binding parameters. In this article, a more comprehensive data interpretation and analysis is explained

Additional file 1: of N 6 -methyl-adenosine level in Nicotiana tabacum is associated with tobacco mosaic virus

Figure S1. Calibration curves for the quantification of A in mRNA. The amounts of A ranged from 0.1–2.5 μmol. Figure S2. Calibration curves for the quantification of C in mRNA. The amounts of C ranged from 0.5–25 μmol. Figure S3. Calibration curves for the quantification of G in RNA. The amounts of G ranged from 0.25–12.5 μmol. Figure S4. Calibration curves for the quantification of U in RNA. The amounts of U ranged from 5 to 250 μmol. Figure S5. Calibration curves for the quantification of m6A in RNA. The amounts of m6A ranged from 0.005–0.250 μmol. Figure S6. Representative UHPLC-HR-MS/MS results for the quantification of A in N. tabacum K326 with selected-ion chromatograms. Figure S7. Representative UHPLC-HR-MS/MS results for the quantification of C in N. tabacum K326 with selected-ion chromatograms. Figure S8. Representative UHPLC-HR-MS/MS results for the quantification of U in N. tabacum K326 with selected-ion chromatograms. Table S1. Primer sequences for RT-qPCR analysis. (PDF 1250 kb

Evaluation of Rice Resistance to Southern Rice Black-Streaked Dwarf Virus and Rice Ragged Stunt Virus through Combined Field Tests, Quantitative Real-Time PCR, and Proteome Analysis

Diseases caused by southern rice black-streaked dwarf virus (SRBSDV) and rice ragged stunt virus (RRSV) considerably decrease grain yield. Therefore, determining rice cultivars with high resistance to SRBSDV and RRSV is necessary. In this study, rice cultivars with high resistance to SRBSDV and RRSV were evaluated through field trials in Shidian and Mangshi county, Yunnan province, China. SYBR Green I-based quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to quantitatively detect virus gene expression levels in different rice varieties. The following parameters were applied to evaluate rice resistance: acre yield (A.Y.), incidence of infected plants (I.I.P.), virus load (V.L.), disease index (D.I.), and insect quantity (I.Q.) per 100 clusters. Zhongzheyou1 (Z1) and Liangyou2186 (L2186) were considered the most suitable varieties with integrated higher A.Y., lower I.I.P., V.L., D.I. and I.Q. features. In order to investigate the mechanism of rice resistance, comparative label-free shotgun liquid chromatography tandem-mass spectrometry (LC-MS/MS) proteomic approaches were applied to comprehensively describe the proteomics of rice varieties’ SRBSDV tolerance. Systemic acquired resistance (SAR)-related proteins in Z1 and L2186 may result in the superior resistance of these varieties compared with Fengyouxiangzhan (FYXZ)