Skip to main content
SpringerLink
Log in

Comparative and evolutionary analysis of α-amylase gene across monocots and dicots

  • Original Article
  • Published:
Functional & Integrative Genomics Aims and scope Submit manuscript

Abstract

α-amylase is an important enzyme involved in starch degradation to provide energy to the germinating seedling. The present study was conducted to reveal structural and functional evolution of this gene among higher plants. Discounting polyploidy, most plant species showed only a single copy of the gene making multiple isoforms in different tissues and developmental stages. Genomic length of the gene ranged from 1472 bp in wheat to 2369 bp in soybean, and the size variation was mainly due to differences in the number and size of introns. In spite of this variation, the intron phase distribution and insertion sites were mostly conserved. The predicted protein size ranged from 414 amino acid (aa) in soybean to 449aa in Brachypodium. Overall, the protein sequence similarity among orthologs ranged from 56.4 to 97.4 %. Key motifs and domains along with their relative distances were conserved among plants although several species, genera, and class specific motifs were identified. The glycosyl hydrolase superfamily domain length varied from 342aa in soybean to 384aa in maize and sorghum while length of the C-terminal β-sheet domain was highly conserved with 61aa in all monocots and Arabidopsis but was 59aa in soybean and Medicago. Compared to rice, 3D structure of the proteins showed 89.8 to 91.3 % similarity among the monocots and 72.7 to 75.8 % among the dicots. Sequence and relative location of the five key aa required for the ligand binding were highly conserved in all species except rice.

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
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Baulcombe DC, Buffard D (1983) Gibberellic-acid-regulated expression of α-amylase and six other genes in wheat aleurone layers. Planta 157:493–501

    Article  CAS  PubMed  Google Scholar 

  • Beck E, Ziegler P (1989) Biosynthesis and degradation of starch in higher plants. Ann Rev Plant Physiol 40:95–117

  • Biasini et al. (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucl Acids Res 42:(W1):W252-W258

  • Callis J, Ho TH (1983) Multiple molecular forms of the gibberellin-induced from the aleurone layers of barley seeds. Arch Biochem Biophys 1:224–234

    Article  Google Scholar 

  • Cheng CR, Oldach K, Mrva K, Mares D (2014) Analysis of high pI α-Amy-1 gene family members expressed in late maturity α-amylase in wheat (Triticum aestivum L). Mol Breed 33:519–529. doi:101007/s11032-01309968-z

  • Chrispeels MJ, Varner JE (1967) Gibberellic acid-enhanced synthesis and release of α-amylase and ribonuclease by isolated barley aleurone layers. Plant Physiol 42:398–406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2:1511–1519

  • Dhaliwal AK, Mohan A, Gill KS (2014) Comparative analysis of ABCB1 reveals novel structural and functional conservation between monocots and dicots. Front Plant Sci 5:1–10

  • Daussant J, Renard HA (1987) Development of different α-amylase isozymes, having high and low isoelectric points, during early stages of kernel development in wheat. J Cereal Sci 5:13–21

  • Emebiri LC, Oliver JR, Mrva K, Mares D (2010) Association mapping of late maturity α-amylase (LMA) activity in a collection of synthetic hexaploid wheat. Mol Breed 26:39–49

    Article  CAS  Google Scholar 

  • Farber GK, Petsko GA (1990) The evolution of α/β barrel enzymes. Trends Biochem Sci 15:228–234

  • Harvey BMR, Oaks A (1974) The hydrolysis of endosperm protein in Zea mays. Plant Physiol 53:453–457

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Henrissat B (1991) A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J 280:309–316

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Higgins TJV, Jacobsen JV, Zwar JA (1982) Gibberellic acid and abscisic acid modulate protein synthesis and mRNA levels in barley aleurone layers. Plant Mol Biol 1:191–215

    Article  CAS  PubMed  Google Scholar 

  • Janecek S (1992) New conserved amino acid region of α-amylases in the third loop of their (β/α) 8-barrel domains. Biochem J 288:1069–1070

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Janecek S (1994) Parallel B/α-barrels of α-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase versus the barrel of β-amylase: evolutionary distance is a reflection of unrelated sequences. FEBS Lett 353:119–123

    Article  CAS  PubMed  Google Scholar 

  • Janecek S (2002) How many conserved sequence regions are there in the α-amylase family? Biologia 57:29–41

  • Janecek S (2009) Amylolytic enzymes-focus on the alpha-amylases from the Archaea and plants. Nova Biotechnolgia 9:5–25

    Google Scholar 

  • Janecek S, Svenssen B, Henrissat B (1997) Domain evolution in the α-amylase family. J Mol Evol 45:322–331

    Article  CAS  PubMed  Google Scholar 

  • Karrer EE, Litts JC, Rodriguez RL (1991) Differential expression of alpha amylase genes in germinating rice and barley seeds. Plant Mol Biol 16:797-805.

  • Kaur S, Dhugga KS, Gill K, Singh J (2016) Novel structural and functional motifs in cellulose synthase (CesA) genes of bread wheat (Triticum aestivum, L.). PLoS ONE 11(1):e0147046. doi:10.1371/journal.pone.0147046

    Article  PubMed  PubMed Central  Google Scholar 

  • Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE (2015) The Phyre2 web portal for protein modelling, prediction and analysis. Nat Protoc 10:845–858

  • Kuriki T, Imanaka T (1999) The concept of the alpha-amylase family: structural similarity and common catalytic mechanism. J Biosci Bioeng 87:557–565

  • Lanahan MB, Ho TH, Rogers SW, Rogers JC (1992) A gibberellin response complex in cereal alpha-amylase gene promoters. Plant Cell 4:203–211

    CAS  PubMed  PubMed Central  Google Scholar 

  • Larkin et al (2007) Clustal W and clustal X version 2.0. Bioinformatics 23:2947–2948

  • Luthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83–85

    Article  CAS  PubMed  Google Scholar 

  • MacGregor EA (1988) α-amylase structure and activity. J Prot Chem 7:399-415

  • MacGregor EA (1993) Relationship between structure and activity in α-amylase family of starch-metabolizing enzymes. Starch-Starke 45:232–237

  • MacGregor AE, Janecek S, Svensson B (2001) Relationship of sequence and structure to specifiity in the alpha-amylase family of enzymes. Biochim Biophys Acta 1546:1-20

  • Matsuura Y, Kusonoki M, Harada W, Kakaudo M (1984) Structure and possible catalytic residues of taka-amylase. J Biochem 95:697–702

  • Mundy J, Yamaguchi-Shinozaki K, Chua NH (1990) Nuclear proteins bind conserved elements in the abscisic acid-responsive promoter of a rice Rab gene. Proc Natl Acad Sci U S A 87:1406–1410

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Murata T, Akazawa T, Fukuchi S (1968) Enzymic mechanism of starch breakdown in germinating rice seeds I; an analytical study. Plant Physiol 43:1899–1905

  • Nakajima R, Tadayuki I, Alba S (1986) Comparison of amino acid sequences of eleven different α-amylases. Appl Microbiol Biotech 23:355–360

  • Neill SD, Kumagai MH, Majumdar A, Huang N, Sutliff TD, Rodriguez RL (1990) The amylase genes in Oryza sativa: characterization of cDNA clones and mRNA expression during seed germination. Mol Genet Genomics 202:235–244

  • Rogozin IB, Sverdlov AV, Babenko VN, Koonin EV (2005) Analysis of evolution of exon-intron structure of eukaryotic genes. Brief Bioinform 6:118–134

    Article  CAS  PubMed  Google Scholar 

  • Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690

  • Spratt BG, Pardee AB (1975) Penicillin-binding proteins and cell shape in E. coli. Nature 254:516–517

    Article  CAS  PubMed  Google Scholar 

  • Staerz UD, Kanagawa O, Bevan MJ (1985) Hybrid antibodies can target sites for attack by T cells. Lett Nature 314:628–631

  • Svensson B (1994) Protein engineering in the alpha-amylase family: catalytic mechanism, substrate specificity, and stability. Plant Mol Biol 25:141–157

    Article  CAS  PubMed  Google Scholar 

  • Swain RR, Dekker EE (1966) Seed germination studies ii. Pathways for starch degradation seedlings. Biochim Biophys Acta 122:87–100

    Article  CAS  PubMed  Google Scholar 

  • Takata H, Kuriki T, Okada S, Takesada Y, Lizuka M, Minamiura N, Imanaka T (1992) Action of neopullulanase: neopullulanase catalyzes both hydrolysis and transglycosylation at alpha (1–4) and alpha (1–6)-glucosidic linkages. J Bio Chem 267:18447–18452

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

  • Wass MN, Kelley LA, Sterberg MJE (2010) 3D LigandSite: predicting ligand binding site using similar structures. Nucl Acid Res 38:W469-W473

  • Ye Y, Godzik A (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19:11246–11255

  • Yomo H, Varner JE (1973) Control of the formation of amylases and proteases in the cotyledons of germinating peas. Plant Physiol 51:708–713

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was supported by the USDA National Institute of Food and Agriculture, Hatch (project number WNP00449), and United States Agency for International Development Feed the Future Innovation Lab-Climate Resilient Wheat (Grant number AID-OAA-A-13-00008).

Author information

Authors and Affiliations

  1. Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India

    Sorabh Sethi, Johar S. Saini, Navreet K. Brar, Shabda Verma & Navraj K. Sarao

  2. Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA

    Amita Mohan & Kulvinder S. Gill

Authors
  1. Sorabh Sethi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Johar S. Saini
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Amita Mohan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Navreet K. Brar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shabda Verma
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Navraj K. Sarao
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Kulvinder S. Gill
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Johar S. Saini.

Electronic supplementary materials

Below is the link to the electronic supplementary material.

Supplemental Table 1

Percent nucleotide similarity of OsAmy coding sequence (CDS) with ortholog in monocot and dicot species. (DOCX 15 kb)

Supplemental Table 2

Percent similarity of OsAmy with predicted protein in orthologs of monocot and dicot species along with their corresponding protein lengths. (DOCX 39 kb)

Supplemental Table 3

Length of GHS Domain and C-terminal β-sheet domain in monocot and dicot species. (DOCX 38 kb)

Supplemental Table 4

3D structure quality assessment parameters of α-amylase among monocots and dicots using SWISS-MODEL and SAVES server. (DOCX 58 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sethi, S., Saini, J.S., Mohan, A. et al. Comparative and evolutionary analysis of α-amylase gene across monocots and dicots. Funct Integr Genomics 16, 545–555 (2016). https://doi.org/10.1007/s10142-016-0505-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10142-016-0505-0

Keywords

Search

Navigation