Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Comparative analysis of AGPase proteins and conserved domains in sweetpotato (Ipomoea batatas (L.) Lam.) and its two wild relatives

  • Nie, Hualin (Department of Environmental Horticulture, University of Seoul) ;
  • Kim, Sujung (Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration) ;
  • Kim, Jongbo (Department of Biotechnology, College of Biomedical & Health Sciences, Global Campus. Konkuk University) ;
  • Kwon, Suk-Yoon (Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Sun-Hyung (Department of Environmental Horticulture, University of Seoul)
  • Received : 2022.02.09
  • Accepted : 2022.02.22
  • Published : 2022.03.31
Download PDF
⟨ Previous Next ⟩

Abstract

Conserved domains are defined as recurring units in molecular evolution and are commonly used to interpret the molecular function and biochemical structure of proteins. Herein, the ADP-glucose pyrophosphorylase (AGPase) amino acid sequences of three species of the Ipomoea genus [Ipomoea trifida, I. triloba, and I. batatas (L.) Lam. (sweetpotato)] were identified to investigate their physicochemical and biochemical characteristics. The molecular weight, isoelectric point, instability index, and grand average of hyropathy markedly differed among the three species. The aliphatic index values of sweetpotato AGPase proteins were higher in the small subunit than in the large subunit. The AGPase proteins from sweetpotato were found to contain an LbH_G1P_AT_C domain in the C-terminal region and various domains (NTP_transferase, ADP_Glucose_PP, or Glyco_tranf_GTA) in the N-terminal region. Conversely, most of its two relatives (I. trifida and I. triloba) were found to only contain the NTP_transferase domain in the N-terminal region. These findings suggested that these conserved domains were species-specific and related to the subunit types of AGPase proteins. The study may enable research on the AGPase-related specific characteristics of sweetpotatoes that do not exist in the other two species, such as starch metabolism and tuberization mechanism.

Keywords

References

  1. Ballicora MA, Iglesias AA, Preiss J (2004) ADP-glucose pyrophos phorylase, a regulatory enzyme for bacterial glycogen synthesis. Microbiol Mol Biol Rev 67(2):213-225. https://doi.org/10.1128/mmbr.67.2.213-225.2003
  2. Bjorklund AK, Ekman D, Light S, Frey-Skott J, Elofsson A (2005) Domain Rearrangements in Protein Evolution. J Mol Biol 353(4):911-923. https://doi.org/10.1016/j.jmb.2005.08.067
  3. Crevillen P, Ballicora MA, Merida A, Preiss J, Romero JM (2003) The different large subunit isoforms of Arabidopsis thaliana ADP-glucose pyrophosphorylase confer distinct kinetic and regulatory properties to the heterotetrameric enzyme. J Biol Chem 278(31):28508-28515. https://doi.org/10.1074/jbc.M304280200
  4. Forslund K, Pekkari I, Sonnhammer EL (2011) Domain architecture conservation in orthologs. BMC Bioinformatics 12:326. https://doi.org/10.1186/1471-2105-12-326
  5. Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy Server. In: Walker JM (eds) The proteomics protocols handbook. Humana Press, New Jersey, pp 571-607. https://doi.org/10.1385/1-59259-890-0:571
  6. Guerois R, Serrano L (2001) Protein design based on folding models. Curr Opin Struct Biol 11:101-106. https://doi.org/10.1016/S0959-440X(00)00170-6
  7. Ingolfsson H, Yona G (2008) Protein domain prediction. Methods Mol Biol 426:117-143. https://doi.org/10.1007/978-1-60327-058-8_7
  8. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 35:1547-1549. https://doi.org/10.1093/molbev/msy096
  9. Lee SS, Bae JM, Oh MS, Liu, JR, Harn CH (2000) Isolation and characterization of polymorphic cDNAs partially encoding ADP-glucose pyrophosphorylase (AGPase) large subunit from sweet potato. Mol Cells 10(1):108-112. https://doi.org/10.1007/s10059-000-0108-3
  10. Li BQ, Hu LL, Chen L, Feng KY, Cai YD, Chou KC (2012) Prediction of protein domain with mRMR feature selection and analysis. PLOS ONE 7(6):e39308. https://doi.org/10.1371/journal.pone.0039308
  11. Li L, Preiss J (1992) Characterization of ADP-glucose pyrophosphorylase from a starch-deficient mutant of Arabidopsis thaliana (L). Carbohydr Res 227:227-239. https://doi.org/10.1016/0008-6215(92)85074-A
  12. Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Zhang D, Bryant SH (2012) CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res 41(D1):D348-D352. https://doi.org/10.1093/nar/gks1243
  13. Ren J, Wen L, Gao X, Jin C, Xue Y, Yao X (2009) DOG 1.0: illustrator of protein domain structures. Cell Res 19(2):271-273. https://doi.org/10.1038/cr.2009.6
  14. Roullier C, Duputie A, Wennekes P, Benoit L, Bringas VMF, Rossel G, Tay D, McKey D, Lebot V (2013) Disentangling the origins of cultivated sweet-potato (Ipomoea batatas (L.) Lam.). PLOS ONE 8(5):e62707. https://doi.org/10.1371/journal.pone.0062707
  15. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
  16. Seo SG, Bea SH, Jun BK, Kim ST, Kwon SY, Kim SH (2015) Overexpression of ADP-glucose pyrophosphorylase (IbAGPaseS) affects expression of carbohydrate regulated genes in sweetpotato [Ipomoea batatas (L.) Lam. cv. Yulmi]. Genes Genom 37:595-605. https://doi.org/10.1007/s13258-015-0289-y
  17. Smith-White BJ, Preiss J (1992) Comparison of proteins of ADP-glucose pyrophosphorylase from diverse sources. J Mol Evol 34(5):449-464. https://doi.org/10.1007/BF00162999
  18. Tsubone M, Kubota F, Saitou K, Kadowaki M (2000) Enhancement of tuberous root production and Adenosine 5'-Diphosphate Pyrophosphorylase (AGPase) activity in sweetpotato (Ipomoea batatas Lam.) by exogenous injection of sucrose solution. J Agro Crop Sci 184(3):181-186. https://doi.org/10.1046/j.1439-037x.2000.00396.x
  19. Wang W, Chen D, Liu D, Cheng Y, Zhang X, Song L, Hu M, Dong J, Shen F (2020) Comprehensive analysis of the Gossypium hirsutum L. respiratory burst oxidase homolog (Ghrboh) gene family. BMC Genomics 21:91. https://doi.org/10.1186/s12864-020-6503-6
  20. Welbaum GE (2015) Vegetable production and practices. CAB International, Oxfordshire
  21. Wu S, Lau KH, Cao Q et al (2018) Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nat Commun 9:4580. https://doi.org/10.1038/s41467-018-06983-8
  22. Yatomi M, Kubota F, Saito K, Agata W (1996) Evaluation of root sink ability of sweetpotato (Ipomoea batatas Lam.) cultivars on the basis of enzymatic activity in the starch synthesis pathway. J Agro Crop Sci 177(1):17-23. https://doi.org/10.1111/j.1439-037X.1996.tb00587.x
  23. Zhou Y, Chen Y, Tao X, Cheng X, Wang H (2016) Isolation and characterization of cDNAs and genomic DNAs encoding ADP-glucose pyrophosphorylase large and small subunits from sweetpotato. Mol Genet Genomics 291(2):609-620. https://doi.org/10.1007/s00438-015-1134-3