Stefan Janecek - Home page

Laboratory of Protein Evolution is engaged in basic research in the field of protein bioinformatics. It is focused on the in silico study of proteins at the molecular level, i.e. to compare the primary and tertiary protein structures and to draw the relationships between the sequence, structure and evolution on one side and function, specificity and stability of the other side. The main aim is - within a collaboration with experimental approaches - protein engineering and design. In the centre of attention, there are enzymes hydrolyzing starch and related oligo- and polysaccharides, mainly from the alpha-amylase families (~30 different enzyme specificities), currently classified in the CAZy system (Carbohydrate-Active Enzymes) into families of glycoside hydrolases GH13, GH57, GH119 and eventually also GH126. The interest is also in functionally and evolutionarily related enzymes from families GH70, GH77 and GH31, as well as in starch binding domains from the so-called CAZy CBM families.

The Head of the Laboratory, Stefan Janecek, has been devoted to the scientific field of the in silico studying of proteins for 25 years continuously, 15 last years being giving his experiences to students as a university teacher at the University of SS Cyril and Methodius in Trnava. Under his supervising, 5 PhD-students have already finished their studies successfully. He has been the founder and main organizer of a series of international symposia about the enzymes from the alpha-amylase family - ALAMYs, held from 2001 traditionally in the Smolenice Castle in Slovakia. In 2016, he established the international open-access scientific journal Amylase. He is also one of curators and co-authors of the web-based encyclopedia for carbohydrate-active enzymes CAZypedia.

Representative scientific achievements could be listed as follows: (i) identification of conserved sequence regions in amylolytic enzyme families GH13 and GH57; (ii) definition of subfamilies of oligo-1,6-glucosidases and neopullulanase in the alpha-amylase family GH13; (iii) revealing a remote homology between the alpha-amylase family GH13 and its related family of alpha-glucosidases GH31; (iv) discovery and characterisation of sequence unique amylomaltase from the family GH77 from borreliae (namely from Borrelia burgdorferi); (v) identification of sequence-structural similarity and evolutionary homology between the alpha-amylase families GH57 and GH119; (vi) describing a close relatedness of family GH13 alpha-amylases from archaeons and plants; (vii) elucidation of evolutionary relationships among individual enzyme specificities in the alpha-amylase families GH13 and GH57; (viii) highlighting the evolutionary history of the mammalian heavy-chain amino acid transporters within the alpha-amylase family GH13; (ix) contributing to the knowledge on relationships among different families of starch-binding domains from various enzymes and proteins; and (x) describing a putative starch-binding domain of the family CBM20 typical for microbial amylolytic enzymes in the mammalian protein genethonin-1.

Amylase
Laboratory of Protein Evolution is engaged in basic research in the field of protein bioinformatics. It is focused on the in silico study of proteins at the molecular level, i.e. to compare the primary and tertiary protein structures and to draw the relationships between the sequence, structure and evolution on one side and function, specificity and stability of the other side. The main aim is - within a collaboration with experimental approaches - protein engineering and design. In the centre of attention, there are enzymes hydrolyzing starch and related oligo- and polysaccharides, mainly from the alpha-amylase families (~30 different enzyme specificities), currently classified in the CAZy system (Carbohydrate-Active Enzymes) into families of glycoside hydrolases GH13, GH57, GH119 and eventually also GH126. The interest is also in functionally and evolutionarily related enzymes from families GH70, GH77 and GH31, as well as in starch binding domains from the so-called CAZy CBM families. The Head of the Laboratory, Stefan Janecek, has been devoted to the scientific field of the in silico studying of proteins for 25 years continuously, 15 last years being giving his experiences to students as a university teacher at the University of SS Cyril and Methodius in Trnava. Under his supervising, 5 PhD-students have already finished their studies successfully. He has been the founder and main organizer of a series of international symposia about the enzymes from the alpha-amylase family - ALAMYs, held from 2001 traditionally in the Smolenice Castle in Slovakia. In 2016, he established the international open-access scientific journal Amylase. He is also one of curators and co-authors of the web-based encyclopedia for carbohydrate-active enzymes CAZypedia. Representative scientific achievements could be listed as follows: (i) identification of conserved sequence regions in amylolytic enzyme families GH13 and GH57; (ii) definition of subfamilies of oligo-1,6-glucosidases and neopullulanase in the alpha-amylase family GH13; (iii) revealing a remote homology between the alpha-amylase family GH13 and its related family of alpha-glucosidases GH31; (iv) discovery and characterisation of sequence unique amylomaltase from the family GH77 from borreliae (namely from Borrelia burgdorferi); (v) identification of sequence-structural similarity and evolutionary homology between the alpha-amylase families GH57 and GH119; (vi) describing a close relatedness of family GH13 alpha-amylases from archaeons and plants; (vii) elucidation of evolutionary relationships among individual enzyme specificities in the alpha-amylase families GH13 and GH57; (viii) highlighting the evolutionary history of the mammalian heavy-chain amino acid transporters within the alpha-amylase family GH13; (ix) contributing to the knowledge on relationships among different families of starch-binding domains from various enzymes and proteins; and (x) describing a putative starch-binding domain of the family CBM20 typical for microbial amylolytic enzymes in the mammalian protein genethonin-1.
Interested in joining the group? Prospective students? Looking for a Bachelor, Master and/or PhD-project...? Feel free to contact at Stefan.Janecek@savba.sk. Write a few lines describing your interest in this type of research work and your motivation. You should be ready to study and work a lot having, however, ambitious scientific aims and, especially, enjoying a highly friendly and generous atmosphere.
Selected publications Full Papers: (29) Janickova Z. & Janecek S. (2021) In silico analysis of fungal and chloride-dependent α-amylases within the family GH13 with identification of possible secondary surface-binding sites. Molecules 26: 5704. (28) Marecek F., Moeller M.S., Svensson B. & Janecek S. (2021) A putative novel starch-binding domain revealed by in silico analysis of the N-terminal domain in bacterial amylomaltases from the family GH77. 3 Biotech 11: 229. (27) Kerenyiova L. & Janecek S. (2020) Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non-catalytic terminal domains. 3 Biotech 10: 420. (26) Kerenyiova L. & Janecek S. (2020) A detailed in silico analysis of the amylolytic family GH126 and its possible relatedness to family GH76. Carbohydr. Res. 494: 108082. (25) Janickova Z. & Janecek S. (2020) Fungal α-amylases from three GH13 subfamilies: their sequence-structural features and evolutionary relationships. Int. J. Biol. Macromol. 159: 763-772. (24) Janecek S. & Zamocka B. (2020) A new GH13 subfamily represented by the α-amylase from the halophilic archaeon Haloarcula hispanica. Extremophiles 24: 207-217. (23) Zhang X., Leemhuis H., Janecek S., Martinovicova M., Pijning T. & van der Maarel M.J.E.C. (2019) Identification of Thermotoga maritima MSB8 GH57 α-amylase AmyC as a glycogen-branching enzyme with high hydrolytic activity. Appl. Microbiol. Biotechnol. 103: 6141-6151. (22) Martinovicova M. & Janecek S. (2018) In silico analysis of the alpha-amylase family GH57: eventual subfamilies reflecting enzyme specificities. 3 Biotech 8: 307. (21) Kuchtova A., Gentry M.S. & Janecek S. (2018) A unique evolution of the carbohydrate-binding module CBM20 in laforin. FEBS Letters 592: 586-598. (20) Janecek S., Majzlova K., Svensson B. & MacGregor E.A. (2017) The starch-binding domain family CBM41 – an in silico analysis of evolutionary relationships. Proteins Struct. Funct. Bioinform. 85: 1480-1492. (19) Mieog J.C., Janecek S. & Ral J.P. (2017) New insight in cereal starch degradation: identification and structural characterization of four alpha-amylases in bread wheat. Amylase 1: 35-49. (18) Sarian F.D., Janecek S., Pijning T., Ihsanawati, Nurachman Z., Radjasa O.K., Dijkhuizen L., Natalia D. & van der Maarel M.J.E.C. (2017) A new group of glycoside hydrolase family 13 alpha-amylases with an aberrant catalytic triad. Sci. Rep. 7: 44230. (17) Kuchtova A. & Janecek S. (2016) Domain evolution in enzymes of the neopullulanase subfamily. Microbiology 162: 2099-2115. (16) Kuchtova A. & Janecek S. (2015) In silico analysis of family GH77 with focus on amylomaltases from borreliae and disproportionating enzymes DPE2 from plants and bacteria. Biochim. Biophys. Acta 1854: 1260-1268. (15) Janecek S., Kuchtova A. & Petrovicova S. (2015) A novel GH13 subfamily of alpha-amylases with a pair of tryptophans in the helix alpha3 of the catalytic TIM-barrel, the LPDlx signature in the conserved sequence region V and a conserved aromatic motif at the C-terminus. Biologia 70: 1284-1294. (14) Janecek S. & Kuchtova A. (2012) In silico identification of catalytic residues and domain fold of the family GH119 sharing the catalytic machinery with the alpha-amylase family GH57. FEBS Lett. 586: 3360-3366. (13) Blesak K. & Janecek S. (2012) Sequence fingerprints of enzyme specificities from the glycoside hydrolase family GH57. Extremophiles 16: 497-506. (12) Janecek S. & Blesak K. (2011) Sequence-structural *features and evolutionary relationships of family GH57 alpha-amylases and their putative alpha-amylase-like homologues. Protein* J. 30: 429-435*. (11) Gabrisko M. & Janecek S. (2009) Looking for the ancestry of the heavy-chain subunits of heteromeric amino acid transporters rBAT and 4F2hc within the GH13 alpha-amylase family. FEBS J. 276: 7265-7278. (10) Godany A., Vidova B. & Janecek S. (2008) The unique glycoside hydrolase family 77 amylomaltase from Borrelia burgdorferi* with only catalytic triad conserved. FEMS Microbiol. Lett. 284: 84-91. (9) Machovic M. & Janecek S. (2006) The evolution of putative starch-binding domains. FEBS Lett. 580: 6349-6356. (8) Zona R., Chang-Pi-Hin F., O’Donohue M.J. & Janecek S. (2004) Bioinformatics of the family 57 glycoside hydrolases and identification of catalytic residues in amylopullulanase from Thermococcus hydrothermalis. Eur. J. Biochem. 271: 2863-2872. (7) Janecek S., Svensson B. & MacGregor E.A. (2003) Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain. Eur. J. Biochem. 270: 635-645. (6) Oslancova A. & Janecek S. (2002) Oligo-1,6-glucosidase and neopullulanase enzyme subfamilies from the alpha-amylase family defined by the fifth conserved sequence region. Cell. Mol. Life Sci. 59: 1945-1959. (5) Janecek S. & Sevcik J. (1999) The evolution of starch-binding domain. FEBS Lett. 456: 119-125. (4) Janecek S., Leveque E., Belarbi A. & Haye B. (1999) Close evolutionary relatedness of alpha-amylases from Archaea and plants. J. Mol. Evol. 48: 421-426. (3) Janecek S., Svensson B. & Henrissat B. (1997) Domain evolution in the alpha-amylase family. J. Mol. Evol. 45: 322-331. (2) Janecek S. (1994) Sequence similarities and evolutionary relationships of microbial, plant and animal alpha-amylases. Eur. J. Biochem. 224: 519-524. (1) Janecek S. (1992) New conserved amino acid region of alpha-amylases in the third loop of their (beta/alpha)₈-barrel domains. Biochem. J. 288: 1069-1070. Review articles: (10) Janecek S. & Svensson B. (2022) How many alpha-amylase GH families are there in the CAZy database? Amylase 6: 1-10. An "Opinion" paper. (9) Janecek S., Marecek F., Svensson B. & MacGregor E.A. (2019) Starch-binding domains as CBM families - history, occurrence,structure, function and evolution. Biotechnol. Adv. 37: 107451. (8) Janecek S. & Gabrisko M. (2016) Remarkable evolutionary relatedness among the enzymes and proteins from the alpha-amylase family. Cell. Mol. Life Sci. 73: 2707-2725. (7) Janecek S., Svensson B. & MacGregor E.A. (2014) Alpha-amylase - an enzyme specificity found in various families of glycoside hydrolases. Cell. Mol. Life Sci. 71: 1149-1170. (6) Janecek S., Svensson B. & MacGregor E.A. (2011) Structural and evolutionary aspects of two families of non-catalytic domains present in starch and glycogen binding proteins from microbes, plants and animals. Enzyme Microb. Technol. 49: 429-440. (5) Christiansen C., Abou Hachem M., Janecek S., Viksoe-Nielsen A., Blennow A. & Svensson B. (2009) The carbohydrate-binding module family 20 – diversity, structure, and function. FEBS J. 276: 5006-5029. (4) Machovic M. & Janecek S. (2006) Starch-binding domains in the post-genome era. Cell. Mol. Life Sci. 63: 2710-2724. (3) Janecek S. (2002) How many conserved sequence regions are there in the alpha-amylase family? Biologia 57 (Suppl. 11): 29-41. (2) MacGregor E.A., Janecek S. & Svensson B. (2001) Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes. Biochim. Biophys. Acta 1546: 1-20. (1) Janecek S. (1997) Alpha-amylase family: molecular biology and evolution. Progr. Biophys. Mol. Biol. 67: 67-97.
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