Determining the structural amino acid attributes which are important in both protein thermostability and alkalophilicity: a case study on xylanase
Languages of publication
Xylanases are used in the recycling of biomass and have other industrial applications including pulp bleaching. These enzymes are also applied in the baking industry and for the manufacture of animal feed. Such technologies as, for example, pulp bleaching entail high temperatures and high pHs. As a result, there is great demand from industry for thermostable and halostable forms of xylanase. Due to the relatively high variation in the thermo- and halo-stability of xylanases, feature selection was employed as a model to discover the important attributes of their amino acid sequences affecting the thermo- and halo-stability of the enzyme. A data set containing the amino acid sequences of xylanases with different thermo- and halostabilities was collected. Seventy-four amino acid attributes were obtained for each enzyme sequence. After running a feature selection algorithm for each of the thermo- and halostablity variables, features were classified as either important, unimportant or marginal. The results showed a significant correlation between structural amino acid attitudes and stability in harsh temperatures or alkaline conditions. Features such as lysine, glutamic acid, and positively/negatively charged residues showed a positive correlation with both the thermostability and alkalophilicity attributes of the protein. For the first time, we found attributes which were important for both stability at high temperatures as well as in alkaline conditions by mining sequence-derived amino acid attributes using data mining.
- Anderson D.E., Becktel W.J., Dahlquist F.W.(1990) pH-induced denaturation of proteins: a single salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme. Biochemistry29: 2403-2408.
- Arase A., YomoT., UrabeI., HataY., KatsubeY., OkadaH. (1993) Stabilization of xylanase by random mutagenesis. FEBS Lett. 316: 123-127.
- Ashrafi E., AlemzadehA., EbrahimiM., EbrahimieE., DadkhodaeiN. (2011) Amino acid features of P1B-ATPase heavy metal transporters enabling small numbers of organisms to cope with heavy metal pollution. Bioinformatics Biol. Ins. 5: 5-9.
- Bakhtiarizadeh M.R., Moradi-Shahrbabak M., Ebrahimi M., Ebrahimie E. (2014) Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology. J. Theor Biol. 356: 213-222.
- Bijanzadeh E., EmamY., EbrahimieE. (2010) Determining the most important features contributing to wheat grain yield using supervised feature selection model. Austral. J. Crop Sci. 4: 402-407.
- Chen Y.-L., Tang T.-Y., ChengK.-J. (2001) Directed evolution to produce an alkalophilic variant from a Neocallimastix patriciarum xylanase. Can. J. Microbiol. 47: 1088-1094.
- Cheng H.-L., WangP.-M., ChenY.-C., YangS.-S., ChenY.-C. (2008) Cloning, characterization and phylogenetic relationships of a endoxylanase-encoding gene from Streptomyces thermonitrificans NTU-88. Bioresour. Technol. 99: 227-231.
- Collins T., GerdayC., FellerG. (2006) Xylanases, xylanase families and extremophilic xylanases. Fems Microbiol. Rev. 29: 3-23.
- Decelle B., TsangA., StormsR.K. (2004) Cloning, functional expression and characterization of three Phanerochaete chrysosporium endo-1, 4-ß-xylanases. Curr. Genet. 46: 166-175.
- Ebrahimi M., Aghagolzadeh P., Shamabadi N., Tahmasebi A., Alsharifi M., Adelson D.L., Hemmatzadeh F., Ebrahimie E. (2014) Understanding the undelaying mechanism of HA-subtyping in the level of physic-chemical characteristics of protein. PloS one 9: e96984.
- Ebrahimi M., Ebrahimie E. (2010) Sequence-based prediction of enzyme thermostability through bioinformatics algorithms. Curr. Bioinform. 5: 195-203.
- Ebrahimi M., Ebrahimie E., Shamabadi N., Ebrahimi M. (2010) Are there any differences between features of proteins expressed in malignant and benign breast cancers? J. Res. Med. Sci. 15: 299-309.
- Ebrahimi E., EbrahimiM., SarvestaniN.R., EbrahimiM. (2011) Protein attributes contribute to halo-stability, bioinformatics approach. Saline Syst. 7: 1-14.
- Krämer N., SchäferJ., BoulesteixA.-L. (2009) Regularized estimation of large-scale gene association networks using graphical Gaussian models. BMC Bioinform. 10: 384.
- Kulkarni N., ShendyeA., RaoM. (2006) Molecular and biotechnological aspects of xylanases. FEMS Microbiol. Rev. 23: 411-456.
- Lakizadeh A., Agha-GolzadehP., EbrahimiM., EbrahimieE., EbrahimiM. (2011) Engineering thermostable enzymes. Adv. Stud. Biol. 3: 63-78.
- Liu H., MotodaH., SetionoR., ZhaoZ. (2010) Feature selection: An ever evolving frontier in data mining. Proc. The Fourth Workshop on Feature Selection in Data Mining, pp. 4-13.
- Manikandan K., BhardwajA., GuptaN., LokanathN.K, GhoshA., ReddyV.S., RamakumarS. (2009) Crystal structures of native and xylosaccharide bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG27: Structural insights into alkalophilicity and implications for adaptation to polyextreme conditions. Protein Sci. 15: 1951-1960.
- Miyazaki K., TakenouchiM., KondoH., NoroN., SuzukiM., TsudaS. (2006) Thermal stabilization of Bacillus subtilis family-11 xylanase by directed evolution. J. Biol. Chem. 281: 10236-10242.
- Natesh R., BhanumoorthyP., VithayathilP., SekarK., RamakumarS., ViswamitraM. (1999) Crystal structure at 1.8 Å resolution and proposed amino acid sequence of a thermostable xylanase from Thermoascus aurantiacus. J. Mol. Biol. 288: 999-1012.
- Russell A.J., FershtA.R. (1987)Rational modification of enzyme catalysis by engineering surface charge. Nature328: 496.
- Shekoofa A., EmamY., EbrahimiM., EbrahimieE. (2011) Application of supervised feature selection methods to define the most important traits affecting maximum kernel water content in maize. Austral. J. Crop Sci. 5: 162-168.
- Shirai T., SuzukiA., YamaneT., AshidaT., KobayashiT., HitomiJ., ItoS. (1997) High-resolution crystal structure of M-protease: phylogeny aided analysis of the high-alkaline adaptation mechanism. Protein Eng. 10: 627-634.
- Shoham Y., SchwartzZ., KhasinA., GatO., ZosimZ., RosenbergE. (1992) Delignification of wood pulp by a thermostable xylanase from Bacillus stearothermophilus strain T-6. Biodegradation 3: 207-218.
- Xie H., FlintJ., VardakouM., LakeyJ.H., LewisR.J., GilbertH.J., DumonC. (2006) Probing the structural basis for the difference in thermostability displayed by family 10 xylanases. J. Mol. Biol. 360: 157-167.
- Zinati Z., ZamansaniF., KayvanjooA.H., EbrahimiM., EbrahimiM., EbrahimieE., Mohammadi DehcheshmehM. (2014) New layers in understanding and predicting α-linolenic acid content in plants using amino acid characteristics of omega-3 fatty acid desaturase. Comput. Biol. Med. 54: 14-23.
Publication order reference