Skip to main content
SpringerLink
Log in

Cloning and Expression Analysis of Eight Upland Cotton Pentatricopeptide Repeat Family Genes

  • Published:
Applied Biochemistry and Biotechnology Aims and scope Submit manuscript

Abstract

The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in plants. Most PPR genes are localized in mitochondria and chloroplasts functioning in regulation of plant growth and development, fertility restoration for cytoplasmic male sterility (CMS), and stress defense. In this study, using in silico cloning and PCR amplification with degenerate primers based on Arabidopsis PPR genes, we cloned eight new full-length PPR genes encoding protein sequences ranging from 458 to 875 amino acids, with 8 to 16 repetitive PPR elements in upland cotton and all of them lack introns. Expression analysis revealed that eight PPR genes were differently expressed in roots, stems, leaves, and floral buds. As for GhI12, its expression in floral buds at days 3–5 was significantly higher in line 777R (restorer line) than in line 777A (CMS line). Further tests with real-time PCR showed that GhI12 expression peaked at day 3 in 777R, followed by a gradual decline, while its expression fluctuated in 777A, peaking at day 5 and day 13. In addition, Gh155c17 and GhI12 were upregulated under salt stress. This is the first report of upland cotton PPR genes involved in salt stress response.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Lurin, C., Andrés, C., Aubourg, S., Bellaoui, M., Bitton, F., Bruyère, C., et al. (2004). Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. The Plant Cell, 16, 2089–2103.

    Article  CAS  Google Scholar 

  2. Small, I. D., & Peeters, N. (2000). The PPR motif—a TPR-related motif prevalent in plant organellar proteins. Trends in Biochemical Sciences, 25(2), 454–471.

    Article  Google Scholar 

  3. Ikeda, T. M., & Gray, M. W. (1999). Characterization of a DNA-binding protein implicated in transcription in wheat mitochondria. pTAC2, −6, and −12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression. Molecular and Cellular Biology, 19, 8113–8122.

    Article  CAS  Google Scholar 

  4. Pfalz, J., Liere, K., Kandlbinder, A., Dietz, K. J., & Oelmüller, R. (2006). pTAC2, −6, and −12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression. The Plant Cell, 18, 176–197.

    Article  CAS  Google Scholar 

  5. Pusnik, M., Small, I., Read, L. K., Fabbro, T., & Schneider, A. (2007). Pentatricopeptide repeat proteins in Trypanosoma bruceifunction in mitochondrial ribosomes. Molecular and Cellular Biology, 27, 6876–6888.

    Article  CAS  Google Scholar 

  6. Fan, M., Jin, L. P., Liu, Q. C., & Qu, D. Y. (2008). Cloning of SoDIPPR gene of pentatricopeptide repeat (PPR) protein family in potato and analysis of expression characteristics under drought conditions. Scientia Agricultura Sinica, 41(8), 2249–2257.

    CAS  Google Scholar 

  7. Liu, Y. J., Xiu, Z. H., Meeley, R., & Tan, B. C. (2013). Empty pericarp5 encodes a pentatricopeptide repeat protein that is required for mitochondrial RNA editing and seed development in maize. The Plant Cell, 25(3), 868–883.

    Article  CAS  Google Scholar 

  8. O’Toole, N., Hattori, M., Andres, C., Iida, K., Lurin, C., Schmitz-Linneweber, C., et al. (2008). On the expansion of the pentatricopeptide repeat gene family in plants. Molecular Biology and Evolution, 25, 1120–1128.

    Article  Google Scholar 

  9. Umbach, A. L., Fiorani, F., & Siedow, J. N. (2005). Characterization of transformed Arabidopsis with altered alternative oxidase levels and analysis of effects on reactive oxygen species in tissue. Plant Physiology, 139, 1806–1820.

    Article  CAS  Google Scholar 

  10. Baxter, C. J., Redestig, H., Schauer, N., Repsilber, D., Patil, K. R., Nielsen, J., et al. (2007). The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Physiology, 143, 312–325.

    Article  CAS  Google Scholar 

  11. Yan, S. P., Zhang, Q. Y., Tang, Z. C., Su, W. A., & Sun, W. N. (2006). Comparative proteomic analysis provides new insights into chilling stress responses in rice. Molecular & Cellular Proteomics, 5, 484–496.

    Article  CAS  Google Scholar 

  12. Baldwin, J. C., & Dombrowski, J. E. (2006). Evaluation of Loliumtemulentumas a model grass species for the study of salinity stress by PCR-based subtractive suppression hybridization analysis. Plant Science, 171, 459–469.

    Article  CAS  Google Scholar 

  13. Ma, S., Gong, Q., & Bohnert, H. J. (2006). Dissecting salt stress pathways. Journal of Experimental Botany, 57, 1097–1107.

    Article  CAS  Google Scholar 

  14. Yang, L., Zhu, H., Guo, W., & Zhang, T. (2010). Molecular cloning and characterization of five genes encoding pentatricopeptide repeat proteins from upland cotton (Gossypiumhirsutum L.). Molecular Biology Reports, 37, 801–808.

    Article  CAS  Google Scholar 

  15. Zhou, K., Ye, W. W., Wang, J. J., Wang, D. L., Fan, B. X., & Wang, S. (2011). Cloning and salt-tolerance analysis of Gene Plastid Transcriptionally Active (GhPTAC) from Gossypiumhirsutum L. Acta Agronomica Sinica, 37(9), 1551–1558 Published in Chinese.

    Article  CAS  Google Scholar 

  16. Saha, D., Prasad, A. M., & Srinivasan, R. (2007). Pentatricopeptide repeat proteins and their emerging roles in plants. Plant Physiology and Biochemistry, 45, 521–534.16.

    Article  CAS  Google Scholar 

  17. Livak, K. J., & Schmittgen, T. D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25, 402–408.

    Article  CAS  Google Scholar 

  18. Andrés, C., Lurin, C., & Small, I. D. (2007). The multifarious roles of PPR proteins in plant mitochondrial gene expression. Physiologia Plantarum, 129, 14–22.

    Article  Google Scholar 

  19. Desloire, S., Gherbi, H., Laloui, W., Marhadour, S., Clouet, V., Cattolico, L., et al. (2003). Identification of the fertility restoration locus, Rfo, in radish, as a member of the pentatricopeptide-repeat protein family. EMBO Reports, 4, 588–594.

    Article  CAS  Google Scholar 

  20. Bentolila, S., Alfonso, A. A., & Hanson, M. R. (2002). A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proceedings of the National Academy of Sciences, 99, 10887–10892.

    Article  CAS  Google Scholar 

  21. Wang, Z., Zou, Y., Li, X., Zhang, Q., Chen, L., Wu, H., et al. (2006). Cytoplasmic male sterility of rice with boro II cytoplasm is caused by a cytotoxic peptide and is restored by two related PPR motif genes via distinct modes of mRNA silencing. The Plant Cell, 18, 676–687.

    Article  CAS  Google Scholar 

  22. Brown, G. G., Formanová, N., Jin, H., Wargachuk, R., Dendy, C., Patil, P., et al. (2003). The radish Rfo restorer gene of Ogura cytoplasmic male sterility encodes a protein with multiple pentatricopeptide repeats. The Plant Journal, 35, 262–272.

    Article  CAS  Google Scholar 

  23. Akagi, H., Nakamura, A., Yokozeki-Misono, Y., Inagaki, A., Takahashi, H., Mori, K., et al. (2004). Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein. Theoretical and Applied Genetics, 108, 1449–1457.

    Article  CAS  Google Scholar 

  24. Klein, R. R., Klein, P. E., Mullet, J. E., Minx, P., Rooney, W. L., & Schertz, K. F. (2005). Fertility restorer locus Rf1 of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the colinear region of rice chromosome 12. Theoretical and Applied Genetics, 111, 994–1012.

    Article  CAS  Google Scholar 

  25. Koizuka, N., Imai, R., Fujimoto, H., Hayakawa, T., Kimura, Y., Kohno-Murase, J., et al. (2003). Genetic characterization of a pentatricopeptide repeat protein gene, orf687, that restores fertility in the cytoplasmic male-sterile Kosena radish. The Plant Journal, 34, 407–415.

    Article  CAS  Google Scholar 

  26. Wu, J., Cao, X., Guo, L., Qi, T., Wang, H., Tang, H., et al. (2014). Development of a candidate gene marker for Rf 1 based on a PPR gene in cytoplasmic male sterile CMS-D2 upland cotton. Molecular Breeding, 34, 231–240.

    Article  Google Scholar 

  27. Wang, X. (1998). Cytological observation of microsporogenesis and RAPD analysis of mitochondrial DNAs for cytoplasmic male-sterile cotton line. Scientia Agricultura Sinica, 31(2), 70–75.

    CAS  Google Scholar 

  28. Hashimoto, M., Endo, T., Peltier, G., Tasaka, M., & Shikanai, T. (2003). A nucleus-encoded factor, CRR2, is essential for the expression of chloroplast ndhB in Arabidopsis. The Plant Journal, 36, 541–549.

    Article  CAS  Google Scholar 

  29. Kotera, E., Tasaka, M., & Shikanai, T. (2005). A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature, 433, 326–330.

    Article  CAS  Google Scholar 

  30. Kocábek, T., Řepková, J., Dudová, M., Hoyerová, K., & Vrba, L. (2006). Isolation and characterization of a novel semi-lethal Arabidopsis thaliana mutant of gene for pentatricopeptide (PPR) repeat-containing protein. Genetica, 128, 395–407.

    Article  Google Scholar 

  31. Tuteja, N., Singh, M. B., Misra, M. K., Bhalla, P. L., & Tuteja, R. (2001). Molecular mechanisms of DNA damage and repair: progress in plants. Critical Reviews in Biochemistry and Molecular Biology, 36, 337–397.

    Article  CAS  Google Scholar 

  32. Koussevitzky, S., Nott, A., Mockler, T. C., Hong, F., Sachetto-Martins, G., Surpin, M., et al. (2007). Signals from chloroplasts converge to regulate nuclear gene expression. Science, 316, 715–719.

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was financially supported by National Natural Science Foundation of China (31240011), the Youth Scientific Research Foundation of Shandong Academy of Agricultural Sciences (2014QNM05), and Shandong Province Natural Science Foundation (BS2011NY09).

Author information

Authors and Affiliations

  1. Cotton Research Centre, Shandong Academy of Agricultural Sciences, 250100, Jinan, People’s Republic of China

    Zongfu Han, Fanjin Kong, Yongsheng Deng, Zongwen Wang, Guifang Shen, Jinghui Wang, Bing Duan & Ruzhong Li

  2. School of Biological Science and Technology, University of Jinan, Jinan, 250022, People’s Republic of China

    Yuxiang Qin

Authors
  1. Zongfu Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuxiang Qin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fanjin Kong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yongsheng Deng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zongwen Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Guifang Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jinghui Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Bing Duan
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Ruzhong Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ruzhong Li.

Additional information

Zongfu Han and Yuxiang Qin contributed equally to the work.

Electronic supplementary material

Supplemental Fig. 1

Melting curves of GHI12 and Ubi. (DOCX 104 kb)

Supplemental table 1

Primer pairs used in gene cloning (DOCX 14 kb)

Supplemental table 2

Primer pairs for gene expression analysis (DOCX 11 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Han, Z., Qin, Y., Kong, F. et al. Cloning and Expression Analysis of Eight Upland Cotton Pentatricopeptide Repeat Family Genes. Appl Biochem Biotechnol 180, 1243–1255 (2016). https://doi.org/10.1007/s12010-016-2164-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12010-016-2164-y

Keywords

Search

Navigation