Advertisement

3 Biotech

, 9:361 | Cite as

Identification and analysis of RNA editing sites in chloroplast transcripts of kenaf (Hibiscus cannabinus L.)

  • Danfeng TangEmail author
  • Fan Wei
  • Muhammad Haneef Kashif
  • Fazal Munsif
  • Ruiyang ZhouEmail author
Original Article
  • 33 Downloads

Abstract

RNA editing is one of the post-transcriptional modification processes and can lead to changes in sequencing and functioning of corresponding proteins and genetic information. To reveal the composition and characteristic of RNA editing of kenaf chloroplast genome, the RNA editing sites in kenaf chloroplast were predicted and identified using bioinformatics and RT-PCR analysis. The prediction results showed a total of 48 editing sites distributed in 22 genes, all of them were C to U conversion leading to amino acid changes. Further analysis of the position of RNA editing sites revealed that except 11 editing sites located at the first codon base, the other editing sites were found at the second codon base. Then four genes were randomly selected to validate the editing sites. Results showed that it was accurate to study the chloroplast RNA editing sites by bioinformatics method accompanied with cloning sequencing. Furthermore, the protein secondary structure and transmembrane domain of ndhD and atpA that had undergone gene editing also changed after editing. This implied that proteins with structural changes may have an impact on kenaf growth. Meanwhile, the differential editing site was found in chloroplast transcripts in kenaf CMS line and its maintainer line, indicating that chloroplast RNA editing could be associated with kenaf CMS. Therefore, the present study laid a foundation to further reveal the biological functioning of chloroplast RNA editing in CMS and its maintainer lines in kenaf.

Keywords

Kenaf Chloroplast RNA editing RT-PCR 

Notes

Acknowledgements

All the authors are thankful for Guangxi Post-doctoral Special Fund (Y201002061), China Postdoctoral Science Foundation funded project (2018M643379), Natural Science Foundation of Guangxi (2018JJB130096). We also thank professor Ruiyang Zhou for providing materials.

Author contributions

WF, FM and MHK helped perform the experiments and write the manuscript; TDF conducted the experiments and edited the article. TDF and ZRY approved the version to be published.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

13205_2019_1893_MOESM1_ESM.docx (186 kb)
Supplementary material 1 (DOCX 186 kb)

References

  1. Agbaje G (2010) Profitability of kenaf seed production as affected by different agronomic practices. J Food Agric Environ 8(1):229–233Google Scholar
  2. Bock R, Kössel H, Maliga P (1994) Introduction of a heterologous editing site into the tobacco plastid genome: the lack of RNA editing leads to a mutant phenotype. EMBO J 13(19):4623–4628CrossRefGoogle Scholar
  3. Bock DG, Kane NC, Ebert DP, Rieseberg LH (2014) Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke. New Phytol 201(3):1021–1030CrossRefGoogle Scholar
  4. Catalán P, Olmstead RG (2000) Phylogenetic reconstruction of the genusBrachypodium P. Beauv.(Poaceae) from combined sequences of chloroplastndhF gene and nuclear ITS. Plant Syst Evol 220(1-2):1–19CrossRefGoogle Scholar
  5. Chen J, Mo LY, Ruan L, Zhou RY, Wang RG, Fan ZL (2012) Study on the absorption and accumulation characteristics of heavy metals by different hemp and jute. Guangdong Agric Sci 10:25–28Google Scholar
  6. Corneille S, Lutz K, Maliga P (2000) Conservation of RNA editing between rice and maize plastids: are most editing events dispensable? Mol Gen Genet MGG 264(4):419–424CrossRefGoogle Scholar
  7. Cosentino SL, Copani V, Patanè C, Mantineo M, D’Agosta GM (2008) Agronomic, energetic and environmental aspects of biomass energy crops suitable for Italian environments. Ital J Agron 2:81–95CrossRefGoogle Scholar
  8. Covello PS, Gray MW (1989) RNA editing in plant mitochondria. Nature 341(6243):662CrossRefGoogle Scholar
  9. Danalatos N, Archontoulis S (2010) Growth and biomass productivity of kenaf (Hibiscus cannabinus, L.) under different agricultural inputs and management practices in central Greece. Ind Crops Prod 32(3):231–240CrossRefGoogle Scholar
  10. Doyle J (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus 12:13–15Google Scholar
  11. Drescher A, Hupfer H, Nickel C, Albertazzi F, Hohmann U, Herrmann R, Maier R (2002) C-to-U conversion in the intercistronic ndhI/ndhG RNA of plastids from monocot plants: conventional editing in an unconventional small reading frame? Mol Genet Genom 267(2):262–269CrossRefGoogle Scholar
  12. Freyer R, Hoch B, Neckermann K, Maier RM, Kössel H (1993) RNA editing in maize chloroplasts is a processing step independent of splicing and cleavage to monocistronic mRNAs. Plant J 4(4):621–629CrossRefGoogle Scholar
  13. Ge QL, Farhana K, Zhao X, Wang M, Wang S, Song W, Nie XJ (2017) Prediction and identification of the RNA editing sites in chloroplast transcripts of Triticum urartu. Mol Plant Breed 7:2479–2488Google Scholar
  14. Hanson MR, Sutton C, Luis B (1996) Plant organelle gene expression: altered by RNA editing. Trends Plant Sci 1(2):57–64CrossRefGoogle Scholar
  15. He P, Huang S, Xiao G, Zhang Y, Yu J (2016) Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis. BMC Plant Biol 16(1):257CrossRefGoogle Scholar
  16. Hein A, Polsakiewicz M, Knoop V (2016) Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors. BMC Evol Biol 16(1):23CrossRefGoogle Scholar
  17. Heller WP, Hayes ML, Hanson MR (2008) Cross-competition in editing of chloroplast RNA transcripts in vitro implicates sharing of trans-factors between different C targets. J Biol Chem 283(12):7314–7319CrossRefGoogle Scholar
  18. Hirose T, Kusumegi T, Tsudzuki T, Sugiura M (1999) RNA editing sites in tobacco chloroplast transcripts: editing as a possible regulator of chloroplast RNA polymerase activity. Mol Gen Genet MGG 262(3):462–467CrossRefGoogle Scholar
  19. Hoch B, Maier RM, Appel K, Igloi GL, Kössel H (1991) Editing of a chloroplast mRNA by creation of an initiation codon. Nature 353(6340):178CrossRefGoogle Scholar
  20. Jarvis P, Lopez-Juez E (2013) Biogenesis and homeostasis of chloroplasts and other plastids. Nat Rev Mol Cell Biol 14(12):787–802.  https://doi.org/10.1038/nrm3702 CrossRefPubMedGoogle Scholar
  21. Jiang Y, Fan S, Song M, Yu J, Yu S (2012) Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures. Genet Mol Res 11(2):987–1001CrossRefGoogle Scholar
  22. Junior TC, Carraro DM, Benatti MR, Barbosa ACA, Kitajima JP, Carrer H (2004) Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome. Curr Genet 46(6):366–373CrossRefGoogle Scholar
  23. Kugler DE (1988) Kenaf newsprint: realizing commercialization of a new crop after four decades of research and development: a report on the Kenaf Demonstration Project. U.S. Dept. of Agriculture, Cooperative State Research Service, Special Projects and Program Systems, p 13Google Scholar
  24. Liu SY, Feng KW, Bian JX, Wang M, Yang ZK, Nie XJ, Song WN (2015) Prediction and identification of the RNA editing sites in chloroplast transcripts of Triticum dicoccoides. J Triticeae 12:1609–1616Google Scholar
  25. Lopez C, Freyer R, Guera A (1997) Sequence of ndhA gene of barley (Hordeum vulgare L.) plastid (accession nos. Y13729 & Y13730). Transcript editing in Graminean organs. Plant Physiol 115:313CrossRefGoogle Scholar
  26. Maier RM, Hoch B, Zeltz P, Kössel H (1992) Internal editing of the maize chloroplast ndhA transcript restores codons for conserved amino acids. Plant Cell 4(5):609–616PubMedPubMedCentralGoogle Scholar
  27. Maier RM, Neckermann K, Igloi GL, Kössel H (1995) Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol 251(5):614–628CrossRefGoogle Scholar
  28. Mower JP (2009) The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucl Acids Res 37(suppl_2):W253–W259CrossRefGoogle Scholar
  29. Nelson G, Nieschlag H, Wolff I (1962) A search for new fiber crops, V. Pulping studies on kenaf. Tappi 45(10):780–786Google Scholar
  30. Ramesh M (2016) Kenaf (Hibiscus cannabinus L.) fibre based bio-materials: a review on processing and properties. Prog Mater Sci 78–79:1–92.  https://doi.org/10.1016/j.pmatsci.2015.11.001 CrossRefGoogle Scholar
  31. Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG, Maier RM (2002) The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol Biol Evol 19(9):1602–1612CrossRefGoogle Scholar
  32. Shi W, Deng P, Li B, Niu S, Nie X, Wang L, Abdul WB, Song W (2012) Prediction and identification of RNA editing sites in chloroplast transcripts of Brachypodium distachyon. J Triticeae Crops 32(1):28–35Google Scholar
  33. Shikanai T (2006) RNA editing in plant organelles: machinery, physiological function and evolution. Cell Mol Life Sci CMLS 63(6):698–708CrossRefGoogle Scholar
  34. Tang DF, Wei F, Kashif MH, Khan A, Li ZQ, Shi QQ, Jia RX, Xie HY, Zhang L, Li B, Chen P, Zhou RY (2018) Analysis of chloroplast differences in leaves of rice isonuclear alloplasmic lines. Protoplasma 255(3):863–871.  https://doi.org/10.1007/s00709-017-1189-6 CrossRefPubMedGoogle Scholar
  35. Tang DF, Wei F, Qin SX, Aziz K, Muhammad HK, Zhou RY (2019) Polyethylene glycol induced drought stress strongly influences seed germination, root morphology and cytoplasm of different kenaf genotypes. Ind Crops Prod 137:180–186CrossRefGoogle Scholar
  36. Tillich M, Funk HT, Schmitz-Linneweber C, Poltnigg P, Sabater B, Martin M, Maier RM (2005) Editing of plastid RNA in Arabidopsis thaliana ecotypes. Plant J 43(5):708–715CrossRefGoogle Scholar
  37. Touzinsky G, Cunningham R, Bagby M (1980) Papermaking properties of kenaf thermomechanical pulp. Tappi J 63(1):53Google Scholar
  38. Webber CL III, Bledsoe RE (1993) Kenaf: Production, harvesting, processing, and products. New Crops Wiley, New York, pp 416–421Google Scholar
  39. Zhang T (2003) Improvement of kenaf yarn for apparel applications. Louisiana State UniversityGoogle Scholar

Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  1. 1.College of AgricultureGuangxi UniversityNanningChina
  2. 2.Guangxi Botanical Garden of Medicinal PlantsNanningChina

Personalised recommendations