Deciphering the enigma of RNA editing in the ATP1_alpha subunit of ATP synthase in Triticum aestivum

Abstract

There is evidence that RNA editing is related to plant cellular stress as well as electron transport organelles, such as mitochondria. The mitochondrial atp1 gene encodes the alpha-subunit of Atp synthase. Control as well as two periods of drought stress treatments were analyzed in the cDNAs generated from the mitochondrial atp1 gene of two cultivars of Triticum aestivum [Giza 168 (G168) and Gemmiza 10 (GM10)]. Following RNA-seq data assembly, atp1 cDNAs from the control (acc. no. OQ129415), 2-hour (acc. no. OQ129416), and 12-hour (acc. no. OQ129417) time points of the T. aestivum cultivar G168 were obtained. Control (acc. no. OQ129419), 2-hour (acc. no. OQ129420), and 12-hour (acc. no. OQ129421) samples all included reconstructed atp1 transcripts from Gemmiza 10. Atp1 transcripts were assembled using the wheat atp1 gene (acc. no. NC_036024). RNA-seq raw data was utilized to identify 11 RNA editing sites in atp1 in the tolerant cultivar Giza168 and 6 in the sensitive cultivar Gemmiza10. The significant difference in RNA editing observed between control and drought stress conditions in sites led to synonymous amino acids. This led to no change in tertiary structure between tolerant and sensitive cultivars. But the change was focused between produced protein and its correspondence sequence on DNA.

Keywords: Mitochondrial atp1 gene; RNA editing; Tertiary structure; Triticum aestivum.

Fig. 1

Efficiency and distinction using data from total RNA-seq, G168 atp1 RNA editing was compared to the control. (C or T) nucleotide position, (Phe) phenylalanine, (Pro) proline, (Thr) threonine, (Ser) serine, and (Leu) leucine. Three biological replicates' means and standard deviations (black bars) are used to express the data. ** denotes a significant distinction between the treatments. P < 0.01.

Fig. 2

Efficiency and distinction using data from total RNA-seq, GM10 atp1 RNA editing was compared to the control. (C or T) nucleotide position, (Phe) phenylalanine, (Pro) proline, (Thr) threonine, (Ser) serine, and (Leu) leucine. Three biological replicates' means and standard deviations (black bars) are used to express the data. ** denotes a significant distinction between the treatments. P < 0.01.

Fig. 3

Triticum aestivum cultivar G168 editing sites were confirmed by qRT-PCR in three different drought conditions (control, two hours after exposure to drought, and twelve hours after exposure to drought). Three biological replicates' means and standard deviations (black bars) are used to express the data. ** denotes a significant distinction between the treatments. P < 0.01.

Fig. 4

Triticum aestivum cultivar GM10 editing sites were confirmed by qRT-PCR in three different drought conditions (control, two hours after exposure to drought, and twelve hours after exposure to drought). Three biological replicates' means and standard deviations (black bars) are used to express the data. ** denotes a significant distinction between the treatments. P < 0.01.

Fig. 5

Change secondary structure regions in cultivar G168 atpase subunit 1 before and after RNA editing due to drought treatment as well as correspondence sequence at DNA. Alpha helix (blue) and beta sheet (brown).

Fig. 6

Change secondary structure regions in cultivar Gemmiza 10 (GM 10) atpase subunit 1 before and after RNA editing e to drought treatment as well as correspondence sequence at DNA. Alpha helix (blue) and beta sheet (brown).

Fig. 7

RNA editing sites of ATP1. A. The protein sequence alignment between all treatments and the predicted ATP1 wild type (ATP1_WT) in G168. A total five edits were introduced during the stress. B. the ATP1_complex in light purple while the ATP1 subunit in olive green. C. RNA editing sites of ATP1. C. The protein sequence alignment between all treatments and the predicted ATP1 wild type (ATP1_WT) in GM10. D. The ATP1_complex in light purple while the ATP1 subunit in salmon.

Fig. 8

RNA editing sites of ATP1 at different drought treatment. A. Represents all the PDB models of ATP1 wild type (ATP1_WT), ATP1 control (ATP1_C), ATP1 2 h (ATP1_2H) and ATP1 12 h (ATP1_12H) in G168. B. Represents all PDB models of ATP1 wild type (ATP1_WT), ATP1 control (ATP1_C), ATP1 2 h (ATP1_2H) and ATP1 12 h (ATP1_12H) in GM10.

Fig. 9

Conservation of RNA editing sites of ATP1 in both G168 and GM10. Residues with high conservation scores are colored purple, while residues with low conservation scores are colored green. Amino acid residues 324, 393, and 431 have relatively low conservation scores, while residues 497 and 500 have high conservation scores.