Skip to main content
SpringerLink
Log in

Genome-wide identification, classification, and expression analysis of the phytocyanin gene family in Phalaenopsis equestris

  • Original paper
  • Published:
Biologia Plantarum

Abstract

Phytocyanins (PCs) are ancient blue copper-binding proteins in plants that bind to single type I copper atoms and function as electron transporters. PCs play an important role in plant development and stress resistance. Many PCs are considered to be chimeric arabinogalactan proteins (AGPs). Previously, 38, 62, and 84 PC genes were identified in Arabidopsis thaliana, Oryza sativa, and Brassica rapa, respectively. In this study, we identified 30 putative PC genes in the orchid Phalaenopsis equestris through comprehensive bioinformatics analysis. Based on phylogeny and motif constitution, the P. equestris phytocyanins (PePCs) were divided into five subclasses: 10 early nodulin-like proteins, 10 uclacyanin-like proteins, five stellacyanin-like proteins, four plantacyanin-like proteins, and one unknown protein. Structural and glycosylation predictions suggested that 16 PePCs were glycosylphosphatidylinositol-anchored proteins localized to the plasma membrane, 22 PePCs contain N-glycosylation sites, and 14 are chimeric AGPs. Phylogenetic analysis indicated that each subfamily was derived from a common ancestor before the divergence of monocot and dicot lineages and that the expansion of the PC subfamilies occurred after the divergence of orchids and Arabidopsis. The number of exons in PC genes was conserved. Expression analysis in four tissues revealed that nine PC genes were highly expressed in flowers, stems, and roots, suggesting that these genes play important roles in growth and development in P. equestris. The results of this study lay the foundation for further analysis of the functions of this gene family in plants.

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

Similar content being viewed by others

Abbreviations

AG:

arabinogalactan

AGPs:

arabinogalactan proteins

ALR:

arabinogalactan-like region

BCPs:

blue copper-binding proteins

BLASTP :

protein basic local alignment search tool

ENODLs:

early nodulin-like proteins

GAS:

glycosylphosphatidylinositol-anchor signal

GPI:

glycosylphosphatidylinositol

HRGPs:

hydroxyproline-rich glycoproteins

PCs:

phytocyanins

PCLD:

plastocyanin-like domain

PLAs:

phytocyanin-like arabinogalactan proteins

PLCs:

plantacyanins

PLCLs:

plantacyanin-like proteins

RPKM:

reads per kilobase per million mapped reads

SCs:

stellacyanins

SCLs:

stellacyanin-like proteins

SP:

signal peptide

UCs:

uclacyanins

UCLs:

uclacyanin-like proteins

References

  • Borner, G.H.H., Lilley, K.S., Stevens, T.J., Dupree, P.: Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis: a proteomic and genomic analysis. — Plant Physiol. 132: 568–577, 2003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cao, J., Li X., Lv, Y.Q., Ding, L.: Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays. — Front. Plant Sci. 6: 515, 2015.

    Article  PubMed  PubMed Central  Google Scholar 

  • Chatterjee, S., Mayor, S.: The GPI-anchor and protein sorting. — Cell. Mol. Life Sci. 58: 1969–1987, 2001.

    Article  CAS  PubMed  Google Scholar 

  • De Rienzo, F., Gabdoulline, R.R., Menziani, M.C., Wade, R.C.: Blue copper proteins: a comparative analysis of their molecular interaction properties. — Protein Sci. 9: 1439–1454, 2000.

    Article  PubMed  PubMed Central  Google Scholar 

  • Deng, W., Wang, Y., Liu, Z., Cheng, H., Xue, Y.: HemI: a toolkit for illustrating heatmaps. — PLoS ONE 9: e111988, 2014.

    Article  Google Scholar 

  • Diab, A.A., Teulat-Merah, B., This, D., Ozturk, N.Z., Benscher, D., Sorrells, M.E.: Identification of drought-inducible genes and differentially expressed sequence tags in barley. — Theor. appl. Genet. 109: 1417–1425, 2004.

    Article  CAS  PubMed  Google Scholar 

  • Dong, J., Kim, S.T., Lord, E.M.: Plantacyanins plays a role in reproduction in Arabidopsis. — Plant Physiol. 138: 778–789, 2005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Estévez, J.M., Kieliszewski, M.J., Khitrov, N., Somervile, C.: Characterization of synthetic hydroxyproline-rich proteoglycans with arabinogalactan protein and extensin motifs in Arabidopsis. — Plant Physiol. 142: 458–470, 2006.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ezaki, B., Gardner, R.C., Ezaki, Y., Matsumoto, H.: Expression of aluminum-induced genes in transgenic Arabidopsis plants can ameliorate aluminum stress and/or oxidative stress. — Plant Physiol. 122: 657–665, 2000.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ezaki, B., Sasaki, K., Matsumoto, H., Nakashima, S.: Functions of two genes in aluminium (Al) stress resistance: repression of oxidative damage by the AtBCB gene and promotion of efflux of Al ions by the NtGDI1 gene. — J. exp. Bot. 56: 2661–2671, 2005.

    Article  CAS  PubMed  Google Scholar 

  • Fedorova, M., Van de Mortel, J., Matsumoto, P.A., Cho, J., Town, C.D., VandenBosch, K.A., Gantt, J.S., Vance, C.P.: Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula. — Plant Physiol. 130: 519–537, 2002.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garrett, T.P.J., Clingeleffer, D.J., Guss, J.M., Rogers, S.J., Freeman, H.C.: The crystal structure of poplar apoplastocyanin at 1.8 Å resolution. The geometry of the copper-binding site is created by the polypeptide. — J. biol. Chem. 259: 1822–1825, 1984.

    Google Scholar 

  • Gaspar, Y., Johnson, K.L., McKenna, J.A., Bacic, A., Schultz, C.J.: The complex structures of arabinogalactan proteins and the journey towards understanding function. — Plant mol. Biol. 47: 161–176, 2001.

    Article  CAS  PubMed  Google Scholar 

  • Greene, E.A., Erard, M., Dedieu, A., Barke, D.G.B.: MtENOD16 and 20 are members of a family of phytocyanin-related early nodulins. — Plant mol. Biol. 36: 775–783, 1998.

    Article  CAS  PubMed  Google Scholar 

  • Guo, A.Y., Zhu, Q.H., Chen, X., Luo, J.C.: GSDS: a gene structure display server. — Yi Chuan 29: 1023–1026, 2007.

    Article  CAS  PubMed  Google Scholar 

  • Harrison, M.J.: Development of the arbuscular mycorrhizal symbiosis. — Curr. Opin. Plant Biol. 1: 360–365, 1998.

    Article  CAS  PubMed  Google Scholar 

  • Hart, P.J., Nersissian, A.M., Herrmann, T.G., Nalbandyan, R.M., Valentine, J.S., Eisenberg, D.: A missing link in cupredoxins-crystal structure of cucumber stellacyanin at 1.6 Å resolution. — Protein Sci. 5: 2175–2183, 1996.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kreps, J.A., Wu, Y., Chang, H.S., Zhu, T., Wang, X., Harper, J.F.: Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. — Plant Physiol. 130: 2129–2141, 2002.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lamport, D.T.A.: Hydroxyproline-O-glycosidic linkage of the primary cell wall extensin. — Nature 216: 1322–1324, 1965.

    Article  Google Scholar 

  • Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Vallentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J., Higgins, D.G.: Clustal W and Clustal X version 2.0. — Bioinformatics 23: 2947–2948, 2007.

    Article  CAS  PubMed  Google Scholar 

  • Li, J., Gao, G.Z., Zhang, T.Y.: The phytocyanin genes in Chinese cabbage (Brasssica rapa L.): genome-wide identifiction, classification and expression analysis. — Mol. Genet. Genomics 288: 1–20, 2013.

    Article  CAS  PubMed  Google Scholar 

  • Ma, H.L., Zhao, J.: Genome-wide identification, classification, and expression analysis of the arabinogalactan protein gene family in rice (Oryza sativa L.). — J. exp. Bot. 61: 2647–2668, 2010.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma, H.L., Zhao, H.M., Liu, Z., Zhao, J.: The phytocyanin gene family in rice (Oryza sativa L.): genome-wide identification, classification and transcriptional analysis. — PLoS ONE 6: e25184, 2011.

    Article  Google Scholar 

  • Majewska-Sawka, A., Nothnagel, E.A.: The multiple roles of arabinogalactan proteins in plant development. — Plant Physiol. 122: 3–9, 2000.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mann, K., Schafer, W., Thoenes, U., Messerchmidt, A., Mehrabian, Z.B., Nalbandyan, R.M.: The amino acid sequence of a type I copper protein with an unusual serineand hydroxyproline-rich C-terminal domain isolated from cucumber peelings. — Feder. eur. biochem. Soc. Lett. 314: 220–223, 1992.

    Article  CAS  Google Scholar 

  • Mashiguchi, K., Yamaguchi, I., Suzuki, Y.: Isolation and identification of glycosylphosphatidylinositol-anchored arabinogalactan proteins and novel β-glucosyl Yariv-reactive proteins from seeds of rice (Oryza sativa). — Plant Cell Physiol. 45: 1817–1829, 2004.

    Article  CAS  PubMed  Google Scholar 

  • Mashiguchi, K., Asami, T., Suzuki, Y.: Genome-wide identification, structure and expression studies, and mutant collection of 22 early nodulin-like protein genes in Arabidopsis. — Biosci. Biotechnol. Biochem. 73: 2452–2459, 2009.

    Article  CAS  PubMed  Google Scholar 

  • Nersissian, A.M., Immoos, C., Hill, M.G., Hart, P.J., Williams, G., Herrmann, R.G., Valentine, J.C.: Uclacyanins, stellacyanins, and plantacyanins are distinct subfamilies of phytocyanins: plant specific mononuclear blue copper proteins. — Protein Sci. 7: 1915–1929, 1998.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ozturk, Z.N., Talamé, V., Deyholos, M., Michalowski, C.B., Galbraith, D.W., Gozukirmizi, N., Tuberosa, R., Bohnert, H.J.: Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley. — Plant mol. Biol. 48: 551–573, 2002.

    Article  CAS  Google Scholar 

  • Perotto, S., Rodda, Ma., Benetti, A., Sillo, F., Ercole, E., Rodda, Mi., Girlanda, M., Murat, C., Balestrini, R.: Gene expression in mycorrhizal orchid protocorms suggests a friendly plant-fungus relationship. — Planta 239: 1337–1349, 2014.

    Article  CAS  PubMed  Google Scholar 

  • Petersen, T.N., Brunak, S., Von Heijine, G., Nielsen, H.: Signal P 4.0: discriminating signal peptides from transmembrane regions. — Nature Methods 8: 785–786, 2011.

    Article  CAS  PubMed  Google Scholar 

  • Richards, K.D., Schott, E.J., Sharma, Y.K., Davis, K.R., Gardner, R.C.: Aluminum induces oxidative stress genes in Arabidopsis thaliana. — Plant Physiol. 116: 409–418, 1998.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ruan, X.M., Luo, F., Li, D.D., Zhang, J., Liu, Z.H., Xu, W.L., Huang, G.Q., Li, X.B.: Cotton BCP genes encoding putative blue copper-binding proteins are functionally expressed in fiber development and involved in response to high-salinity and heavy metal stresses. — Physiol. Plant. 141: 71–83, 2011.

    Article  CAS  PubMed  Google Scholar 

  • Rydén, L.G., Hunt, L.T.: Evolution of protein complexity: the blue copper-containing oxidases and related proteins. — J. mol. Evol. 36: 41–66, 1993.

    Article  PubMed  Google Scholar 

  • Schultz, C., Gilson, P., Oxley, D., Youl, J., Bacic, A.: GPI-anchors on arabinogalactan-proteins: implications for signaling in plants. — Trends Plant Sci. 3: 426–431, 1998.

    Article  Google Scholar 

  • Schultz, C.J., Ferguson, K.L., Lahnstein, J., Bacic, A.: Post-translational modifications of arabinogalactan-peptides of Arabidopsis thaliana. — J. biol. Chem. 278: 45503–45511, 2004.

    Article  Google Scholar 

  • Schultz, C.J., Rumsewicz, M.P., Johnson, K.L., Jones, B.J., Gaspar, Y.M., Bacic, A.: Using genomic resources to guide research directions. The arabinogalactan protein gene family as a test case. — Plant Physiol. 129: 1448–1463, 2002.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Seifert, G.J., Roberts, K.: The biology of arabinogalactan proteins. — Annu. Rev. Plant Biol. 58: 137–161, 2007.

    Article  CAS  PubMed  Google Scholar 

  • Showalter, A.M.: Arabinogalactan-proteins: structure, expression and function. — Cell. mol. Life Sci. 58: 1399–1417, 2001.

    Article  CAS  PubMed  Google Scholar 

  • Showalter, A.M., Keppler, B., Lichtenberg, J., Gu, D.Z., Welch, L.R.: A bioinformatics approach to the identification, classification, and analysis of hydroxyproline-rich glycoproteins. — Plant Physiol. 153: 485–513, 2010.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shpak, E., Barbar, E., Leykam, J.F., Kieliszewski, M.J.: Contiguous hydroxyproline residues direct hydroxyproline arabinosylation in Nicotiana tabacum. — J. biol. Chem. 276: 11272–11278, 2001.

    Article  CAS  PubMed  Google Scholar 

  • Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumer, K.: MEGA6: molecular evolutionary genetics analysis version 6.0. — Biol. Evol. 30: 2725–2729, 2013.

    Article  CAS  Google Scholar 

  • Tan, L., Leykam, J.F., Kieliszewski, M.J.: Glycosylation motifs that direct arabinogalactan addition to arabinogalactan proteins. — Plant Physiol. 132: 1362–1369, 2003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tan, L., Showalter, A.M., Egelund, J., Hernandez-Sanchez, A., Doblin, M.S., Bacic, A.: Arabinogalactan-proteins and the research challenges for these enigmatic plant cell surface proteoglycans. — Front. Plant Sci. 3: 140, 2012.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van Driessche, G., Dennison, C., Sykes, A.G., Van Beeumen, J.: Heterogeneity of the covalent structure of the blue copper protein umecyanin from horse-radish roots. — Protein Sci. 4: 209–227, 1995.

    Article  PubMed  PubMed Central  Google Scholar 

  • Wu, H., Shen, Y., Hu, Y., Tan, S., Lin, Z.: A phytocyanin-related early nodulin-like gene, BcBCP1, cloned from Boea crassifolia enhances osmotic tolerance in transgenic tobacco. — J. Plant Physiol. 168: 935–943, 2011.

    Article  CAS  PubMed  Google Scholar 

  • Yoshizaki, M., Furumoto, T., Hata, S., Shinozaki, M., Izui, K.: Characterization of a novel gene encoding a phytocyanin-related protein in morning glory (Pharbitis nil). — Biochem. biophys. Res. Commun. 268: 466–470, 2000.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, P.R. China

    L. Xu, X. J. Wang, T. Wang & L. B. Li

  2. College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, P.R. China

    L. Xu

Authors
  1. L. Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. X. J. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. T. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. L. B. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to L. B. Li.

Additional information

Acknowledgments: This work was supported by grants from the Ministry of Science and Technology (No. 2012BAD01B0702 and No. 2013AA102607).

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Xu, L., Wang, X.J., Wang, T. et al. Genome-wide identification, classification, and expression analysis of the phytocyanin gene family in Phalaenopsis equestris . Biol Plant 61, 445–452 (2017). https://doi.org/10.1007/s10535-017-0716-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10535-017-0716-9

Additional key words

Search

Navigation