Protein engineering of selected residues from conserved sequence regions of a novel Anoxybacillus α-amylase

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Ranjani, Velayudhan ^a   Janeček, Štefan ^b,c   Chai, Kian Piaw ^a   Shahir, Shafinaz ^a   Rahman, Raja Noor Zaliha Raja Abdul ^d   Chan, Kok Gan ^e   Goh, Kian Mau ^a  

^a UNIVERSITI TEKNOLOGI MALAYSIA   (Malaysia)

^b INSTITUTE OF CHEMISTRY   (Slovakia)

^c UNIVERSITY OF SS CYRIL AND METHODIUS   (Slovakia)

^d UNIVERSITY PUTRA MALAYSIA   (Malaysia)

^e UNIVERSITY OF MALAYA   (Malaysia)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLASE; BACTERIAL PROTEIN; MALTOSE; RECOMBINANT PROTEIN; STARCH;

AMINO ACID SEQUENCE; ANOXYBACILLUS; BACILLUS; CHEMISTRY; ENZYME STABILITY; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS; GEOBACILLUS; KINETICS; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PH; PROTEIN ENGINEERING; SITE DIRECTED MUTAGENESIS;

ALPHA-AMYLASES; AMINO ACID SEQUENCE; ANOXYBACILLUS; BACILLUS; BACTERIAL PROTEINS; CONSERVED SEQUENCE; ENZYME STABILITY; ESCHERICHIA COLI; GEOBACILLUS; HYDROGEN-ION CONCENTRATION; KINETICS; MALTOSE; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN ENGINEERING; RECOMBINANT PROTEINS; STARCH;

EID: 84905180510     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep05850     Document Type: Article

References (50)

1. Cantarel, B. L. et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233-D238, doi:10.1093/nar/gkn663 (2009)
2. Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M. &Henrissat, B. The Carbohydrate-Active EnZymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490-D495, doi:10.1093/nar/gkt1178 (2014)
3. Janeček,S., Svensson, B. &MacGregor, E. A. a-Amylase: an enzyme specificity found in various families of glycoside hydrolases. Cell. Mol. Life Sci. 71, 1149-1170, doi:10.1007/s00018-013-1388-z (2014)
4. Svensson, B. Protein engineering in the a-amylase family: catalytic mechanism, substrate specificity, and stability. Plant Mol. Biol. 25, 141-157, doi:10.1007/ bf00023233 (1994)
5. Janeček,S. a-amylase family: molecular biology and evolution. Prog. Biophys.Mol. Biol. 67, 67-97, doi:10.1016/S0079-6107(97)00015-1 (1997)
6. Kuriki, T.&Imanaka, T. The concept of the a-amylase family: structural similarity and common catalytic mechanism. J. Biosci. Bioeng. 87, 557-565, doi:10.1016/ S1389-1723(99)80114-5 (1999)
7. MacGregor, E. A., Janeček,S. &Svensson, B. Relationship of sequence and structure to specificity in the a-amylase family of enzymes. Biochim. Biophys. Acta, Protein Struct. Mol. Enzymol. 1546, 1-20, doi:10.1016/S0167- 4838(00)00302-2 (2001)
8. Stam, M. R., Danchin, E. G. J., Rancurel, C., Coutinho, P. M. &Henrissat, B. Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of a-amylase-related proteins. Protein Eng. Des. Sel. 19, 555-562, doi:10.1093/protein/gzl044 (2006)
9. Oslancová, A. &Janeček,S. Oligo-1,6-glucosidase and neopullulanase enzyme subfamilies from the a-amylase family defined by the fifth conserved sequence region. Cell. Mol. Life Sci. 59, 1945-1959, doi:10.1007/pl00012517 (2002)
10. Majzlová, K., Pukajová, Z. &Janeček,S. Tracing the evolution of the a-amylase subfamily GH13-36 covering the amylolytic enzymes intermediate between oligo-1,6-glucosidases and neopullulanases. Carbohydr. Res. 367, 48-57, doi:10.1016/j.carres.2012.11.022 (2013)
11. Puspasari, F. et al. Raw starch-degrading a-amylase from Bacillus aquimaris MKSC 6.2: isolation and expression of the gene, bioinformatics and biochemical characterization of the recombinant enzyme. J. Appl. Microbiol. 114, 108-120, doi:10.1111/jam.12025 (2013)
12. Koropatkin, N. M., Cameron, E. A. &Martens, E. C. How glycan metabolism shapes the human gut microbiota. Nat. Rev. Microbiol. 10, 323-335, doi:10.1038/ nrmicro2746 (2012)
13. Lévěque, E., Janeček,S., Haye, B. &Belarbi, A. Thermophilic archaeal amylolytic enzymes. Enzyme Microb. Technol. 26, 3-14, doi:10.1016/S0141-0229(99)00142- 8 (2000)
14. van derMaarel,M. J. E. C., van der Veen, B., Uitdehaag, J. C. M., Leemhuis, H. &Dijkhuizen, L. Properties and applications of starch-converting enzymes of the aamylase family. J. Biotechnol. 94, 137-155, doi:10.1016/S0168-1656(01)00407-2 (2002)
15. Tawil, G., Vikso-Nielsen, A., Rolland-Sabaté, A., Colonna, P. &Buléon, A. Hydrolysis of concentrated raw starch: a new very efficient a-amylase from Anoxybacillus flavothermus. Carbohydr. Polym. 87, 46-52, doi:10.1016/ j.carbpol.2011.07.005 (2012)
16. Matpan Bekler, F. &Güven, K. Isolation and production of thermostable aamylase from thermophilic Anoxybacillus sp. KP1 from Diyadin hot spring in Aǧri, Turkey. Biologia 69, 419-427, doi:10.2478/s11756-014- 0343-2 (2014)
17. Agüloǧlu Fincan, S., Enez, B.,Özdemir, S. &Matpan Bekler, F. Purification and characterization of thermostable a-amylase from thermophilic Anoxybacillus flavithermus. Carbohydr. Polym. 102, 144-150, doi:10.1016/j.carbpol.2013.10.048 (2014)
18. Chai, Y. Y., Rahman, R. N. Z. R. A., Illias, R. M. &Goh, K. M. Cloning and characterization of two new thermostable and alkalitolerant a-amylases from the Anoxybacillus species that produce high levels of maltose. J. Ind. Microbiol. Biotechnol. 39, 731-741, doi:10.1007/s10295-011-1074-9 (2012)
19. Kahar, U., Chan, K.-G., Salleh, M., Hii, S. &Goh, K. M. A high molecular-mass Anoxybacillus sp. SK3-4 amylopullulanase: characterization and its relationship in carbohydrate utilization. Int. J. Mol. Sci. 14, 11302-11318, doi:10.3390/ ijms140611302 (2013)
20. Mehta, D. &Satyanarayana, T. Domain C of thermostable a-amylase of Geobacillus thermoleovorans mediates raw starch adsorption. Appl. Microbiol. Biotechnol. 1-17, doi:10.1007/s00253-013-5459-8 (2014)
21. Mok, S.-C., Teh, A.-H., Saito, J. A., Najimudin, N. &Alam,M. Crystal structure of a compact a-amylase from Geobacillus thermoleovorans. Enzyme Microb. Technol. 53, 46-54, doi:10.1016/j.enzmictec.2013.03.009 (2013)
22. Finore, I. et al. Purification, biochemical characterization and gene sequencing of a thermostable raw starch digesting a-amylase from Geobacillus thermoleovorans subsp. stromboliensis subsp. nov. World J. Microbiol. Biotechnol. 27, 2425-2433, doi:10.1007/s11274-011-0715-5 (2011)
23. Janeček,S. How many conserved sequence regions are there in the a-amylase family? Biologia - Section Cellular and Molecular Biology 57 (Suppl. 11, ), 29-41 (2002)
24. Janeček,S., Lévěque, E., Belarbi, A.&Haye, B. Close evolutionary relatedness of aamylases from Archaea and plants. J. Mol. Evol. 48, 421-426, doi:10.1007/ PL00006486 (1999)
25. Li, C. et al.Close relationship of a novel Flavobacteriaceae a-amylase with archaeal a-amylases and good potentials for industrial applications. Biotechnol. Biofuels 7, 18, doi:10.1186/1754-6834-7-18 (2014)
26. Nielsen, J. E. et al. Electrostatics in the active site of an a-amylase. Eur. J. Biochem. 264, 816-824, doi:10.1046/j.1432-1327.1999.00664.x (1999)
27. Wind, R. D., Uitdehaag, J. C. M., Buitelaar, R. M., Dijkstra, B. W. &Dijkhuizen, L. Engineering of cyclodextrin product specificity and pH optima of the thermostable cyclodextrin glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1. J. Biol. Chem. 273, 5771-5779 (1998)
28. Chai, Y. Y., Kahar, U. M., Salleh, M. M., Illias, R. M. &Goh, K. M. Isolation and characterization of pullulan-degrading Anoxybacillus species isolated from Malaysian hot springs. Environ. Technol. 33, 1231-1238, doi:10.1080/ 09593330.2011.618935 (2011)
29. Goh, K. M. et al. Analysis of Anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism. PLoS ONE 9, e90549, doi:10.1371/journal.pone.0090549 (2014)
30. Wind, R. D., Buitelaar, R. M., Eggink, G., Huizing, H. J. &Dijkhuizen, L. Characterization of a new Bacillus stearothermophilus isolate: a highly thermostable a-amylase-producing strain. Appl. Microbiol. Biotechnol. 41, 155-162, doi:10.1007/bf00186953 (1994)
31. Matsuura, Y., Kusunoki, M., Harada, W. &Kakudo, M. Structure and possible catalytic residues of Taka-amylase A. J. Biochem. 95, 697-702 (1984)
32. Ivanova, V. N., Dobreva, E. P. &Emanuilova, E. I. Purification and characterization of a thermostable a-amylase from Bacillus licheniformis. J. Biotechnol. 28, 277-289, doi:10.1016/0168-1656(93)90176-N (1993)
33. Kim, J.-S. et al. Crystal structure of a maltogenic amylase provides insights into a catalytic versatility. J. Biol. Chem. 274, 26279-26286 (1999)
34. Cha,H.-J. et al.Molecular and enzymatic characterization of amaltogenic amylase that hydrolyzes and transglycosylates acarbose. Eur. J. Biochem. 253, 251-262, doi:10.1046/j.1432-1327.1998.2530251.x (1998)
35. Dauter, Z. et al. X-ray structure of Novamyl, the five-domain ''maltogenic'' aamylase from Bacillus stearothermophilus: maltose and acarbose complexes at 1.7A resolution. Biochemistry 38, 8385-8392, doi:10.1021/bi990256l (1999)
36. Puspasari, F. et al. Characteristics of raw starch degrading a-amylase from Bacillus aquimaris MKSC 6.2 associated with soft coral Sinularia sp. Starch - Stärke 63, 461-467, doi:10.1002/star.201000127 (2011)
37. Goh, K. M.,Mahadi, N. M., Hassan, O., Abdul Rahman, R. N. Z. R. &Illias, R. M. The effects of reaction conditions on the production of c-cyclodextrin from tapioca starch by using a novel recombinant engineered CGTase. J. Mol. Catal. BEnzym. 49, 118-126, doi:10.1016/j.molcatb.2007.09.011 (2007)
38. Goh, K. M., Mahadi, N. M., Hassan, O., Rahman, R. N. Z. R. A. &Illias, R. M. A predominant b-CGTase G1 engineered to elucidate the relationship between protein structure and product specificity. J. Mol. Catal. B-Enzym. 57, 270-277, doi:10.1016/j.molcatb.2008.09.016 (2009)
39. Han, R. et al. Recent advances in discovery, heterologous expression, and molecular engineering of cyclodextrin glycosyltransferase for versatile applications. Biotechnol. Adv. 32, 415-428, doi:10.1016/j.biotechadv.2013.12.004 (2014)
40. Chen, Y.-H. et al.Mutational analysis of the proposed calcium-binding aspartates of a truncated a-amylase from Bacillus sp. strain TS-23. Ann. Microbiol. 60, 307-315, doi:10.1007/s13213-010-0042-3 (2010)
41. Liu, Y., Shen, W., Shi, G.-Y. &Wang, Z.-X. Role of the calcium-binding residues Asp231, Asp233, and Asp438 in a-amylase of Bacillus amyloliquefaciens as revealed by mutational analysis. Curr. Microbiol. 60, 162-166, doi:10.1007/ s00284-009-9517-5 (2010)
42. Chang,C.-T. et al. Identification of essential histidine residues in a recombinant aamylase of thermophilic and alkaliphilic Bacillus sp. strain TS-23. Extremophiles 7, 505-509, doi:10.1007/s00792-003-0341-8 (2003)
43. Priyadharshini, R. &Gunasekaran, P. Site-directed mutagenesis of the calciumbinding site of a-amylase of Bacillus licheniformis. Biotechnol. Lett. 29, 1493-1499, doi:10.1007/s10529-007-9428-0 (2007)
44. Benson, D. A. et al. GenBank. Nucleic Acids Res. 42, D32-D37, doi:10.1093/nar/ gkt1030 (2014)
45. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. &Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410, doi:10.1016/S0022- 2836(05)80360-2 (1990)
46. Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539-544, doi:10.1038/ msb.2011.75 (2011)
47. Crooks, G. E., Hon, G., Chandonia, J. M. &Brenner, S. E. WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190, doi:10.1101/gr.849004 (2004)
48. Arnold, K., Bordoli, L., Kopp, J. &Schwede, T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22, 195-201, doi:10.1093/bioinformatics/bti770 (2006)
49. Pronk, S. et al.GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845-854, doi:10.1093/ bioinformatics/btt055 (2013)
50. Muniandy, K. et al. Application of statistical experimental design for optimization of novel a-amylase production by Anoxybacillus species. J. Biol. Sci. 13, 605-613, doi:10.3923/jbs.2013.605.613 (2013)