Role of aliasing and interacting factors in the enhanced production of dehalogenase from Yarrowia lipolytica for degradation of brominated compounds

Aakanksha Vatsal; Chirag Potdar; Smita S. Zinjarde; V. Ravi Kumar; Bhasker D. Kulkarni; Ameeta RaviKumar

Journal of Industrial and Engineering Chemistry, Vol.41, 114-121, September, 2016

DOI10.1016/j.jiec.2016.07.015 Export Citation

Role of aliasing and interacting factors in the enhanced production of dehalogenase from Yarrowia lipolytica for degradation of brominated compounds

Aakanksha Vatsal, Chirag Potdar, Smita S. Zinjarde, V. Ravi Kumar^{1, †}, Bhasker D. Kulkarni¹, and Ameeta RaviKumar^†

Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
¹Chemical Engineering and Process Development Division, National Chemical Laboratory, Pune 411008, India

E-mail:,

Use of persistent organobromines for industrial applications has led to their accumulation in environment. Yarrowia lipolytica NCIM 3589, a tropical marine yeast, degrades and detoxifies bromocompounds by an initial hydrolytic step. By optimizing culture conditions with 1-bromodecane as reference compound, the dehalogenase involved was remarkably enhanced 13-fold (384.13 U/ml) by a hybrid statistical Plackett.Burman and Box.Behnken design of experiments. Studies bring out in a novel way the role of aliasing and other masked interactions in growth media factors. Importantly, the enzyme acted on C3-C16 bromoalkanes and bromoaromatics, thereby generalizing the ‘green chemistry’ applicability of optimized media formulation for biotechnological applications.

Keywords:Dehalogenase;Brominated compound;Medium optimization;Plackett-Burman;Box-Behnken;Yarrowia lipolytica

[References]

Cousins T, Palm A, The Handbook of Environmental Chemistry, vol. 3, Part R, Springer-Verlag, Berlin Heidelberg, 2003 p. 301.
Chaudhry GR, Chapalmadugu S, Microbiol. Rev., 55, 59 (1991)
Streger S, Condee CW, Togna AP, Deflaun MF, Environ. Sci. Technol., 33, 4477 (1999)
Bosma TNP, Harms H, Zehnder AJB, in: Beek B (Ed.), The Handbook of Environmental Chemistry Part K, Biodegradation and Persistence, Springer-Verlag, Berlin, Heidelberg, 2001 p. 164.
Darnerud PO, Environ. Int., 29, 841 (2003)
Allard AS, Nielsen AH, The Handbook of Environmental Chemistry, vol. 3, Part R, Springer-Verlag, Berlin Heidelberg, 2003, pp. 1.
Fetzner S, Lingens F, Microbiol. Rev., 58, 641 (1994)
Stucki G, Thuer M, Environ. Sci. Technol., 29, 2339 (1995)
Prokop Z, Oplustil F, DeFrank J, Damborsky J, Biotechnol. J., 1370 (2006)
Swanson PE, Curr. Opin. Biotechnol., 10, 365 (1999)
Campbell DW, Muller C, Reardon KF, Biotechnol. Lett., 28(12), 883 (2006)
Reardon KF, Campbell DW, Muller C, Eng. Life Sci., 9, 291 (2009)
Bidmanova S, Chaloupkova R, Damborsky J, Prokop Z, Anal. Bioanal. Chem., 398, 1891 (2010)
Los GV, Wood K, Methods Mol. Biol., 356, 195 (2007)
Vatsal A, Zinjarde SS, Kumar AR, Yeast, 28, 721 (2011)
Vatsal A, Zinjarde SS, Kumar AR, Biodegradation, 26, 127 (2015)
Li XY, Liu ZQ, Chi ZM, Bioresour. Technol., 99(14), 6386 (2008)
Ferreira SLC, Bruns RE, Ferreira HS, Matos GD, David JM, Brand GC, da Silva EGP, Portugal LA, dos Reis PS, Souza AS, dos Santos WNL, Anal. Chim. Acta, 597, 179 (2007)
Burkert JFM, Maugeri F, Rodrigues MI, Bioresour. Technol., 91(1), 77 (2004)
Bhavsar K, Kumar VR, Khire JM, J. Ind. Microbiol. Biotechnol., 38, 1407 (2011)
Plackett RL, Burman JP, Biometrika, 33, 305 (1946)
Stowe RA, Mayer RP, Ind. Eng. Chem., 58, 36 (1966)
Kalil SJ, Maugeri F, Rodrigues MI, Process Biochem., 35(6), 539 (2000)
Tyssedal J, Grinde H, Rostad CC, Qual. Reliab. Eng. Int., 22, 651 (2006)
Khuri AI, Mukhopadhyay S, WIREs Comput. Stat., 2, 128 (2010)
Roquemore KG, Technometrics, 18, 419 (1976)
Tiwary E, Gupta R, Bioresour. Technol., 101(15), 6103 (2010)
Iwasaki I, Utsumi S, Ozawa T, Bull. Chem. Soc. Jpn., 25, 226 (1952)
Jesenska A, Sedlacek I, Damborsky J, Appl. Environ. Microbiol., 66, 219 (2000)
Box GEP, Behnken DW, Technometrics, 2, 455 (1960)
Myers RH, Montgomery DC, Alexander-Cook CM, Response Surface Methodology: Process and Product Optimization Using Designed Experiments, third ed., John Wiley & Sons, New Jersey, 2009.
Montgomery DC, Borror CM, Stanley JD, Qual. Eng., 10, 371 (1997)
Hamada M, Wu CJF, J. Qual. Technol., 24, 130 (1992)
Koudelakova T, Chovancova E, Brezovsky J, Monincova M, Fortova A, Jarkovsky J, Damborsky J, Biochem. J., 435, 345 (2011)
Lin CJ, Yang LR, Xu G, Wu JP, Biotechnol. Bioprocess Eng., 16, 923 (2011)
Affholter JA, Swanson PE, Hueylin KL, Richard RA, Recombinant haloaliphatic dehalogenases. US patent Publication number WO1998036080 A1. Application number PCT US1998/002776, 1998.

[1] Cousins T, Palm A, The Handbook of Environmental Chemistry, vol. 3, Part R, Springer-Verlag, Berlin Heidelberg, 2003 p. 301.

[2] Chaudhry GR, Chapalmadugu S, Microbiol. Rev., 55, 59 (1991)

[3] Streger S, Condee CW, Togna AP, Deflaun MF, Environ. Sci. Technol., 33, 4477 (1999)

[4] Bosma TNP, Harms H, Zehnder AJB, in: Beek B (Ed.), The Handbook of Environmental Chemistry Part K, Biodegradation and Persistence, Springer-Verlag, Berlin, Heidelberg, 2001 p. 164.

[5] Darnerud PO, Environ. Int., 29, 841 (2003)

[6] Allard AS, Nielsen AH, The Handbook of Environmental Chemistry, vol. 3, Part R, Springer-Verlag, Berlin Heidelberg, 2003, pp. 1.

[7] Fetzner S, Lingens F, Microbiol. Rev., 58, 641 (1994)

[8] Stucki G, Thuer M, Environ. Sci. Technol., 29, 2339 (1995)

[9] Prokop Z, Oplustil F, DeFrank J, Damborsky J, Biotechnol. J., 1370 (2006)

[10] Swanson PE, Curr. Opin. Biotechnol., 10, 365 (1999)

[11] Campbell DW, Muller C, Reardon KF, Biotechnol. Lett., 28(12), 883 (2006)

[12] Reardon KF, Campbell DW, Muller C, Eng. Life Sci., 9, 291 (2009)

[13] Bidmanova S, Chaloupkova R, Damborsky J, Prokop Z, Anal. Bioanal. Chem., 398, 1891 (2010)

[14] Los GV, Wood K, Methods Mol. Biol., 356, 195 (2007)

[15] Vatsal A, Zinjarde SS, Kumar AR, Yeast, 28, 721 (2011)

[16] Vatsal A, Zinjarde SS, Kumar AR, Biodegradation, 26, 127 (2015)

[17] Li XY, Liu ZQ, Chi ZM, Bioresour. Technol., 99(14), 6386 (2008)

[18] Ferreira SLC, Bruns RE, Ferreira HS, Matos GD, David JM, Brand GC, da Silva EGP, Portugal LA, dos Reis PS, Souza AS, dos Santos WNL, Anal. Chim. Acta, 597, 179 (2007)

[19] Burkert JFM, Maugeri F, Rodrigues MI, Bioresour. Technol., 91(1), 77 (2004)

[20] Bhavsar K, Kumar VR, Khire JM, J. Ind. Microbiol. Biotechnol., 38, 1407 (2011)

[21] Plackett RL, Burman JP, Biometrika, 33, 305 (1946)

[22] Stowe RA, Mayer RP, Ind. Eng. Chem., 58, 36 (1966)

[23] Kalil SJ, Maugeri F, Rodrigues MI, Process Biochem., 35(6), 539 (2000)

[24] Tyssedal J, Grinde H, Rostad CC, Qual. Reliab. Eng. Int., 22, 651 (2006)

[25] Khuri AI, Mukhopadhyay S, WIREs Comput. Stat., 2, 128 (2010)

[26] Roquemore KG, Technometrics, 18, 419 (1976)

[27] Tiwary E, Gupta R, Bioresour. Technol., 101(15), 6103 (2010)

[28] Iwasaki I, Utsumi S, Ozawa T, Bull. Chem. Soc. Jpn., 25, 226 (1952)

[29] Jesenska A, Sedlacek I, Damborsky J, Appl. Environ. Microbiol., 66, 219 (2000)

[30] Box GEP, Behnken DW, Technometrics, 2, 455 (1960)

[31] Myers RH, Montgomery DC, Alexander-Cook CM, Response Surface Methodology: Process and Product Optimization Using Designed Experiments, third ed., John Wiley & Sons, New Jersey, 2009.

[32] Montgomery DC, Borror CM, Stanley JD, Qual. Eng., 10, 371 (1997)

[33] Hamada M, Wu CJF, J. Qual. Technol., 24, 130 (1992)

[34] Koudelakova T, Chovancova E, Brezovsky J, Monincova M, Fortova A, Jarkovsky J, Damborsky J, Biochem. J., 435, 345 (2011)

[35] Lin CJ, Yang LR, Xu G, Wu JP, Biotechnol. Bioprocess Eng., 16, 923 (2011)

[36] Affholter JA, Swanson PE, Hueylin KL, Richard RA, Recombinant haloaliphatic dehalogenases. US patent Publication number WO1998036080 A1. Application number PCT US1998/002776, 1998.