Salinity stress reveals three types of RNA editing sites in mitochondrial Nad7 gene of wild barley both in silico and in qRT-PCR experiments

Ramadan, Ahmed M.; Said, Osama A. M.; Abushady, Asmaa M.

doi:10.1007/s40626-021-00225-x

Cited by 6 publications

(3 citation statements)

References 52 publications

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“…Similar findings also reported in soybean, in which RNA editing efficiency increased due to salt stress ( Rodrigues et al, 2017 ). In other study of NADH dehydrogenase subunit 7 (nad7) in barley, salinity enhanced the RNA editing efficiency ( Ramadan et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress

Rehman

Uzair²,

Chao

et al. 2022

Front. Plant Sci.

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Ribonucleic acid editing (RE) is a post-transcriptional process that altered the genetics of RNA which provide the extra level of gene expression through insertion, deletions, and substitutions. In animals, it converts nucleotide residues C-U. Similarly in plants, the role of RNA editing sites (RES) in rice under alkaline stress is not fully studied. Rice is a staple food for most of the world population. Alkaline stress cause reduction in yield. Here, we explored the effect of alkaline stress on RES in the whole mRNA from rice chloroplast and mitochondria. Ribonucleic acid editing sites in both genomes (3336 RESs) including chloroplast (345 RESs) and mitochondria (2991 RESs) with average RES efficiency ∼55% were predicted. Our findings showed that majority of editing events found in non-synonymous codon changes and change trend in amino acids was hydrophobic. Four types of RNA editing A-G (A-I), C-T (C-U), G-A, and T-C were identified in treated and untreated samples. Overall, RNA editing efficiency was increased in the treated samples. Analysis of Gene Ontology revealed that mapped genes were engaged in many biological functions and molecular processes. We also checked the expression of pentatricopeptide repeat (PPR), organelle zinc-finger (OZI), and multiple organellar RNA editing factors/RNA editing factor interacting proteins genes in control and treatment, results revealed upregulation of PPR and OZ1 genes in treated samples. This induction showed the role of these genes in RNA editing. The current findings report that RNA editing increased under alkaline stress which may contribute in adaptation for rice by changing amino acids in edited genes (88 genes). These findings will provide basis for identification of RES in other crops and also will be useful in alkaline tolerance development in rice.

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Section: Discussionmentioning

confidence: 99%

Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress

Rehman

Uzair²,

Chao

et al. 2022

Front. Plant Sci.

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“…Finally, many future explanations of some events should be clarified, such as how prymidine changes to purines, such as G to C or U to G. Additionally, we should investigate how we can exploit this phenomenon to improve the tolerance of plants to environmental stress after discovering the relationship of RNA editing with endurance to adverse environmental conditions [ 2 , 12 , 13 ].…”

Section: Bioinformatics Approaches To Studying Rna Editingmentioning

confidence: 99%

“…RNA editing can happen in multiple ways, such as the C-to-U, U-to-C, and A-to-I conversions, as well as insertions and deletions of U or G. However, in plants, RNA editing occurs mainly in the mitochondria and plastids. C-to-U-type RNA editing is primarily found [ 8 ]; however, recent studies have investigated new types of editing without suggesting the mechanisms involved in these new types, such as U to G [ 13 ]. Plant organellar RNA editing involves at least three elements: trans-acting factors that bind to cis-acting elements and thereby recruit editing enzymes to induce nucleotide conversion [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

RNA Editing in Chloroplast: Advancements and Opportunities

Mohammed

Ahmad

Ramadan

2022

CIMB

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Many eukaryotic and prokaryotic organisms employ RNA editing (insertion, deletion, or conversion) as a post-transcriptional modification mechanism. RNA editing events are common in these organelles of plants and have gained particular attention due to their role in the development and growth of plants, as well as their ability to cope with abiotic stress. Owing to rapid developments in sequencing technologies and data analysis methods, such editing sites are being accurately predicted, and many factors that influence RNA editing are being discovered. The mechanism and role of the pentatricopeptide repeat protein family of proteins in RNA editing are being uncovered with the growing realization of accessory proteins that might help these proteins. This review will discuss the role and type of RNA editing events in plants with an emphasis on chloroplast RNA editing, involved factors, gaps in knowledge, and future outlooks.

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Prediction of RNA editing sites in maize under salt stress through transcriptomic approaches

Alshaya,

Uzair,

Rehman

et al. 2024

Plant Biotechnol Rep

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Salinity stress reveals three types of RNA editing sites in mitochondrial Nad7 gene of wild barley both in silico and in qRT-PCR experiments

Cited by 6 publications

References 52 publications

Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress

Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress

RNA Editing in Chloroplast: Advancements and Opportunities

Prediction of RNA editing sites in maize under salt stress through transcriptomic approaches

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