Skip to main content

Enzyme Technology, Functional Proteomics, and Systems Biology Toward Unraveling Molecular Basis for Functionality and Interactions in Biotechnological Processes

  • Chapter
Frontier Discoveries and Innovations in Interdisciplinary Microbiology

Abstract

Metagenomics provides the opportunity to uncover many unculturable extremophilic microorganisms, which represent majority of the planet’s biological diversity and are being utilized in industries to further furnish industrial process and products. This strategy has resulted in the isolation of novel biocatalysts and bioactive molecules. Here in this chapter, we will review various strategies for manipulating enzyme attributes like its activity, stability, inhibition, designing novel substrates, and substrate-specific binding. We have also recapitulated the idea of functional proteomics and systems biology approach in protein engineering.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Adrio JL, Demain AL (2014) Microbial enzymes: tools for biotechnological processes. Biomolecules 4:117–139

    Article  PubMed Central  PubMed  Google Scholar 

  • Akutsu T, Miyano S, Kuhara S (2000) Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics 16:727–734

    Article  CAS  PubMed  Google Scholar 

  • Bornholdt S (2008) Boolean network models of cellular regulation: prospects and limitations. J R Soc Interface 5:S85–S94

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Deb K, Pratap A, Agarwal S, Meyarivan T (2002) A fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE Tran Evol Comput 6(2):182–197

    Article  Google Scholar 

  • Dumon C, Varvak A, Wall MA, Flint JE, Lewis RJ, Lakey JH, Morland C, Luginbühl P, Healey S, Todaro T, DeSantis G, Sun M, Gessert LP, Tan X, Weiner DP, Gilbert HJ (2008) Engineering hyperthermostability into a GH11 Xylanase is mediated by subtle changes to protein structure. J Biol Chem 283:22557–22564

    Article  CAS  PubMed  Google Scholar 

  • Fujii R, Nakagawa Y, Hiratake J, Sogabe A, Sakata K (2005) Directed evolution of Pseudomonas aeruginosa lipase for improved amide-hydrolyzing activity. Protein Eng Des Sel 18:93–101

    Article  CAS  PubMed  Google Scholar 

  • Gupta R, Beg QK, Lorenz P (2002) Bacterial alkaline proteases: molecular approaches and industrial applications. Appl Microbiol Biotechnol 59(1):15–32

    Article  CAS  PubMed  Google Scholar 

  • Hirose O, Yoshida R, Imoto S, Yamaguchi R, Higuchi T et al (2008) Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics 24:932–942

    Article  CAS  PubMed  Google Scholar 

  • Houde A, Kademi A, Leblanc D (2004) Lipases and their industrial applications: an overview. Appl Biochem Biotechnol 118(1–3):155–170

    Article  CAS  PubMed  Google Scholar 

  • Jones A, Lamsa M, Frandsen TP, Spendler T, Harris P, Sloma A, Xu F, Nielsen JB, Cherry JR (2008) Directed evolution of a maltogenic α-amylase from Bacillus sp. TS-25. J Biotechnol 134:325–333

    Article  CAS  PubMed  Google Scholar 

  • Karthik MV, Satya Deepak MV, Shukla P (2012a) Explication of interactions between HMGCR isoform 2 and various statins through in silico modeling and docking. Comput Biol Med 42(2):156–163. doi:10.1016/j

    Article  CAS  PubMed  Google Scholar 

  • Karthik MVK, Syed H, Goswami T, Shukla P (2012b) Model and molecular docking substrate stabilization of Microsporum canis keratinase. Online J Bioinform 13(1):33–40

    Google Scholar 

  • Li S, Yang X, Yang S, Zhu M, Wang X (2012) Technology prospecting on enzymes: application, marketing and engineering. Comput Struct Biotechnol J 2(3):1–11

    Google Scholar 

  • Miyazaki K, Wintrode PL, Grayling RA, Rubingh DN, Arnold FH (2000) Directed evolution study of temperature adaptation in a psychrophilic enzyme. J Mol Biol 297:1015–1026

    Article  CAS  PubMed  Google Scholar 

  • Mollania N, Khajeh K, Ranjbar B, Hosseinkhani S (2011) Enhancement of a bacterial laccase thermostability through directed mutagenesis of a surface loop. Enzyme Microb Technol 49:446–452

    Article  CAS  PubMed  Google Scholar 

  • Needham C, Bradford J, Bulpitt AJ, Westhead D (2007) A primer on learning in Bayesian networks for computational biology. PLoS Comput Biol 3, e129

    Article  PubMed Central  PubMed  Google Scholar 

  • Raue A, Schilling M, Bachmann J, Matteson A, Schelke M, Kaschek D, Hug S, Kreutz C, Harms BD, Theis FJ, Klingmüller U, Timmer J (2013) Lessons learned from quantitative dynamical modeling in systems biology. PLoS One. doi:10.1371/journal.pone.0074335

    PubMed  Google Scholar 

  • Shimamura T, Imoto S, Yamaguchi R, Fujita A, Nagasaki M et al (2009) Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst Biol 3:41–54

    Article  PubMed Central  PubMed  Google Scholar 

  • Shmulevich I, Dougherty ER, Kim S, Zhang W (2002) Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18:261–274

    Article  CAS  PubMed  Google Scholar 

  • Singh PK, Shukla P (2012) Molecular modeling and docking of microbial inulinases towards perceptive enzyme-substrate interactions. Indian J Microbiol 52(3):373–380

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Singh PK, Shukla P (2014) Systems biology as an approach for deciphering microbial interactions. Brief Funct Genomics. doi:10.1093/bfgp/elu023

    PubMed  Google Scholar 

  • Steuer R, Kurths J, Daub CO, Weise J, Selbig J (2002) The mutual information: detecting and evaluating dependencies between variables. Bioinformatics 18:S231–S240

    Article  PubMed  Google Scholar 

  • Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302:249–255

    Article  CAS  PubMed  Google Scholar 

  • Teplyakov AV, van der Laan JM, Lammers AA, Kelders H, Kalk KH, Misset O, Mulleners LJ, Dijkstra BW (1995) Protein engineering of the high-alkaline serine protease PB92 from Bacillus alcalophilus: functional and structural consequences of mutation at the S4 substrate binding pocket. Protein Eng 5(5):413–420

    Article  Google Scholar 

  • Tobe S, Shimogaki H, Ohdera M, Asai Y, Oba K, Iwama M, Irie M (2006) Expression of Bacillus protease (Protease BYA) from Bacillus sp. Y in Bacillus subtilis and enhancement of its specific activity by site-directed mutagenesis-improvement in productivity of detergent enzyme. Biol Pharm Bull 29:26–33

    Article  CAS  PubMed  Google Scholar 

  • Vijayvargiya S, Shukla P (2012) A niched Pareto genetic algorithm for finding variable length regulatory motifs in DNA sequences. 3Biotech (Springer) 2(2):141–148

    Google Scholar 

  • Zou M, Conzen S (2005) A new dynamic Bayesian network approach for identifying gene regulatory networks from time course microarray data. Bioinformatics 21:71–79

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors acknowledge the support from SERB, Department of Science and Technology (DST), Government of India (DST Fast Track Grant. No. SR/FT/LS-31/2012), and University Grants Commission (UGC), New Delhi, India (Grant No. 42-457/2013(SR)). Mehak Baweja duly acknowledges the University Research Scholarship (URS) from M.D. University, Rohtak, India.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Pratyoosh Shukla .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer India

About this chapter

Cite this chapter

Baweja, M., Singh, P.K., Shukla, P. (2016). Enzyme Technology, Functional Proteomics, and Systems Biology Toward Unraveling Molecular Basis for Functionality and Interactions in Biotechnological Processes. In: Shukla, P. (eds) Frontier Discoveries and Innovations in Interdisciplinary Microbiology. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2610-9_13

Download citation

Publish with us

Policies and ethics