RNA EDITING IN Calotropis procera MITOCHONDRIAL NADH-DEHYDROGENASE SUBUNIT 3 GENE
Abstract
Nad3 (NADH-dehydrogenase subunit 3) gene from genomic (accession no. KP171516) and cDNA (accession no. KP171517) was identified in desert plant Calotropis procera using RNA seq and DNA seq data. A number of cytosines are altered to be recognized as uridines in transcripts of the nad3 locus in mitochondria. The nucleotide modifications were found at 11 different nucleotide positions (nucleotide no. 44, 62, 80, 209, 215,230, 247, 266, 275, 317 and 349) within the nad3 coding region. Heterogeneous RNA editing in C. procera nad3 RNA was not detected in this study. These alterations in the mRNA sequence change codon identities to specify 11 amino acids. The alteration in nucleotides leads to codons alteration specifying different amino acids, the common being proline to leuciene (P-L). Other changes were serine to leucine (S-L), serine to phenylalanine (S-F), proline to serine and arginine to tryptophan (R-W). These alterations are common in mitochondrial nad3 gene of most plant species with few differences according to the properties of the amino acids involved.References
Aiton, W. T. (2010). Germplasm Resources Information Network. United States Department of Agriculture, 2001-10-19, Retrieved, 2010-06-26.
Aleel, K. G. (2011). To Thy Proteins Be True: RNA Editing in Plants. Plant Physiology, 156: 453-454.
Anders, S. and W. Huber (2010). Differential expression analysis for sequence count data. Genome Biol., 11: R106
Benne, R., J. Van den Burg, J. P. Brakenhoff, P. Sloof, J. H. Van Boom and M. C. Tromp (1986). Major transcript of the frame shifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell, 46: 819-826.
Bentolila, S., L. E. Elliott and M. R. Hanson (2008). Genetic architecture of mitochondrial editing in Arabidopsis thal1iana. Genetics, 178: 1693-1708.
Boutraa, T. (2010). Growth performance and biomass partitioning of the desert shrub Calotropis procera under water stress conditions. Research Journal of Agriculture and Biological Sciences, 6: 20-26.
Brown, C., T., L. K. Fishwick, B. M. Chokshi, M. A. Cuff, J. M. Jackson, T. Oglesby, A. T. Rioux, E. Rodriguez, G. S. Stupp, A. H. Trupp, J. S. Woollcombe-Clarke, T. N. Wright, W. J. Zaragoza, J. C. Drew, E. W. Triplett and L. Wayne (2011). Whole-genome sequencing and phenotypic analysis of Bacillus subtilis mutants following evolution under conditions of relaxed selection for sporulation. Applied and Environmental Microbiology, 77: 6867-6877.
Castandet, B. and A. Araya (2011). RNA editing in plant organelles. Why make it easy? Biochemistry (Mosc), 76: 924-931.
Chateigner-Boutin, A. L. and I. Small (2007). A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons. Nucleic Acids Res., 35: e114.
Colombo, R., O. Marı´n, S. Iraza´bal and W. Tezara (2007). Relaciones hı´dricas, fotosı´ntesis y anatomı´a foliar de dos especies del ge´nero Calotropis. Interciencia, 32: 791-796.
Copley, R. R., T. Doerks, I. Letunic and P. Bork (2002). Protein domain analysis in the era of complete genomes. FEBS Lett., 513: 129-134.
Farajollahi, S. and S. Maas (2010). Molecular diversity through RNA editing: A balancing act. Trends Genet., 26: 221-230.
Giege´, P. and A. Brennicke (1999). RNA editing in Arabidopsis mitochondria affects 441 C to U changes in ORFs. Proc. Natl. Acad. Sci., USA, 96: 15324-15329.
Hiesel, R., B. Wissinger, W. Schuster and A. Brennicke (1989). RNA editing in plant mitochondria. Science, 246: 1632-1634.
Hollender, C. A., C. Kang, O. Darwish, A. Geretz, B. F. Matthews, J. Slovin, N. Alkharouf and Liu Zhongchi (2014). Floral transcriptomes in woodland Strawberry uncover developing receptacle and anther gene networks. Plant Physiology, 165: 1062-1075.
Hui, Y. and L. Dong (2012). Functional disruption of the pentatrico-peptide protein SLG1 affects mitochondrial RNA editing, plant development, and responses to abiotic stresses in Arabidopsis. The Plant Journal, 70: 432-444.
Kalinati, Y. N., V. D. Kumar and S. S. Reddy (2008). RNA editing in NAD3 and ATP9 transcripts of safflower (Carthamus tinctorius). Int. J. Integr. Biol., 3: 143-149.
Katerina, C., J. Oppelt, L. Radova, K. Musilova, N. Tom, F. Pardy, J. Malcikova, K. Plevova, B. Tichy, Y. Brychtova, M. Doubek, M. Trbusek, J. Mayer, J. Koca, R. Calogero, S. Pospisilova and M. Mraz (2014). Abstract 5198: Identification of microRNAs involved in DNA damage response in malignant B cells and their biological and clinical relevance. Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA.
Khan, R., S. Shahzad, M. I. Choudhary, S. A. Khan and A. Ahmad (2007). Biodiversity of the endophytic fungi isolated from Calotropis procera (Ait.) R. Br. Pakistan J. Botany, 39: 2233-2239.
Lu, B. and M. R. Hanson (1996). Fully edited and partially edited nad9 transcripts differ in size and both are associated with polysomes in potato mitochondria. Nucleic Acids Res., 24: 1369-1374.
Matthew, J. B., R. B. Russell, M. R. Barnes and I. C. Gray (2003). Amino Acid Properties and Consequences of Substitutions. Bioinformatics for Geneticists. John Wiley & Sons, Ltd. ISBNs: 0-470-84393-4 (HB); 0-470-84394-2 (PB).
Nishikura, K. (2006). Editor meets silencer: Crosstalk between RNA editing and RNA interference. Nat. Rev. Mol. Cell Biol., 7: 919-931.
Ramadan, A. M., A. M. Shokry, N. O. Gadalla, S. M. Hassan, S. Edris, M. A. Al-Kordy, O. A. Abuzinadah, J. S. M. Sabir, S. R. Al-Akilli, H. S. M. Al-Zahrani, R. M. Hussein, F. M. El-Domyati and A. Bahieldin (2012). Detection of a MAPK-Like Gene in Calotropis procera Plant from the De Novo Assembled Genome Contigs of the High Throughput Sequencing Dataset. Life Sci. J., 9: 157-166.
Rurek, M., S. Marek, A. Natalia, M. Barbara and A. Halina (2001). Differences in editing of mitochondrial nad3 transcripts from CMS and fertile carrots. Acta Biochimica Polonica, 48: 711-717.
Shokry, A., S. Al-Karim, A. Ramadan, N. Gadallah, Sanaa G. Al Attas, J. S. M. Sabir, Sabah M. Hassan, M. A. Madkour, R. Bressan, M. Mahfouz and A. Bahieldin (2014). Detection of a Usplike gene in Calotropis procera plant from the de novo assembled genome contigs of the high-throughput sequencing dataset. C. R. Biologies, 337: 86-94.
Wolfgang, S., B. Wissinger, M. Unseld and A. Brennicke (1990). Transcripts of the NADH-dehydrogenase subunit 3 gene are differentially edited in Oenothera mitochondria. The EMBO Journal, 9: 263-269.
