Three subfamilies of fungal GH13 alpha-amylases - their evolutionary relatedness and ancestry

Authors: Zuzana Janíčková 1,2    Štefan Janeček 1,2   
1 Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, SK-84551 Bratislava, Slovakia    2 Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, J. Herdu 2, SK-91701 Trnava, Slovakia   
Year: 2019
Section: Cellular metabolism, physiology, molecular biology and genetics
Abstract No.: 1856
ISBN: 978-80-972360-4-5

Among the glycoside hydrolase (GH) CAZy classification, the α-amylase family GH13 ranks among the largest GH families[1]. In 2006, the α-amylase family GH13 was divided into 35 subfamilies by CAZy curators[2]; the current number of GH13 subfamilies being 42[1]. Originally, fungal α-amylases were classified in the subfamily GH13_1[3] but recently, such enzymes were identified as close homologues of the rather actinobacterial subfamily GH13_32[4]. Members of the subfamily GH13_1 are typical extracellular α-amylases produced by molds and yeasts with the Taka-amylase A, i.e. the α-amylase from Aspergillus oryzae, as the main representative. On the other hand, the subfamily GH13_32 was considered for a long time to be a typical subfamily of bacterial α-amylases, originating mainly from actinobacteria and exhibiting a close relatedness to chloride-dependent animal α-amylases from subfamilies GH13_15 and GH13_24[3,5]. Some intracellular α-amylases of fungal origin, involved in the synthesis of cell wall α-1,3-glucan, have been classified also in the subfamily GH13_5 that originally covered bacterial liquefying α-amylases[3].

The main goals of the present study therefore were: (i) to perform a detailed bioinformatics analysis of fungal α-amylases that exist in three sequentially different forms (subfamilies GH13_1, GH13_5 and GH13_32); (ii) to update the knowledge on their unique sequence-structural features; and (iii) to contribute to the evolutionary picture of the α-amylase family GH13. In addition, the study was aimed at identifying new fungal α-amylases that could represent intermediates between studied subfamilies in an effort to contribute to correct annotation of hypothetical proteins obtained from genome sequencing projects.

The present study thus delivers the in silico analysis of fungal α-amylases from subfamilies GH13_1 and GH13_32 including those from GH13_5. Four sequence logos were calculated based on CSRs identified in all α-amylases. While the first sequence logo covers all the three GH13 subfamilies, the three additional logos of the three individual subfamilies indicate the features discriminating the subfamilies from each other[3]. With regard to evolutionary relationships, fungal α-amylases from the subfamily GH13_32 seem to be evolutionarily more closely related to those from the subfamily GH13_5 than to their counterparts from the subfamily GH13_1. The α-amylases from the subfamily GH13_1 originating from Rhizophlyctis rosea, Neolecta irregularis and Schizosaccharomyces pombe occupy an intermediary position in the tree indicating a remarkable evolutionary relatedness to their counterparts from subfamilies GH13_5 and GH13_32. The evolutionary tree shows also the three α-amylases from a single fungus Pholiota microspora (PnAmy1, PnAmy2 and PnAmy3) present in subfamilies GH13_1, GH13_5 and GH13_32, respectively.

This work was supported by grant No. 2/0146/17 from the Slovak Grant Agency VEGA.
[1]Lombard V., Ramulu H.G., Drula E., Coutinho P.M., Henrissat B. (2014). Nucleic Acids Res., 42, D490-D495.
[2]Stam M.R., Danchin E.G., Rancurel C., Coutinho P.M., Henrissat B. (2006). Protein Eng. Design Select., 19, 555-562.
[3]Janecek S., Svensson B., MacGregor E.A. (2014). Cell. Mol. Life Sci., 71, 1149-1170.
[4]Da Lage J.L, Binder M., Hua-Van A., Janecek S., Casane D. (2013). BMC Evol. Biol., 13, 40.
[5]Da Lage, J.L., Feller, G., Janecek, S. (2004). Cell. Mol. Life Sci., 61, 97–109.