Directed evolution of the substrate specificity of biotin ligase

Wei Cheng Lu, Matthew Levy, Rodney Kincaid, Andrew D. Ellington

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

We have developed selection scheme for directing the evolution of Escherichia coli biotin protein ligase (BPL) via in vitro compartmentalization, and have used this scheme to alter the substrate specificity of the ligase towards the utilization of the biotin analogue desthiobiotin. In this scheme, a peptide substrate (BAP) was conjugated to a DNA library encoding BirA, emulsified such that there was a single template per compartment, and protein variants were transcribed and translated in vitro. Those variants that could efficiently desthiobiotinylate their corresponding peptide:DNA conjugate were subsequently captured and amplified. Following just six rounds of selection and amplification several variants that demonstrated higher activity with desthiobiotin were identified. The best variants from Round 6, BirA6-40 and BirA6-47, showed 17-fold and 10-fold higher activity, respectively, their abilities to use desthiobiotin as a substrate. While selected enzymes contained a number of substitutions, a single mutation, M157T, proved sufficient to provide much greater activity with desthiobiotin. Further characterization of BirA6-40 and the single substitution variant BirAM157T revealed that they had twoto threefold higher kcat values for desthiobiotin. These variants had also lost much of their ability to utilize biotin, resulting in orthogonal enzymes that in conjunction with streptavidin variants that can utilize desthiobiotin may prove to be of great use in developing additional, robust conjugation handles for a variety of biological and biotechnological applications.

Original languageEnglish (US)
Pages (from-to)1071-1081
Number of pages11
JournalBiotechnology and Bioengineering
Volume111
Issue number6
DOIs
StatePublished - 2014

Fingerprint

Ligases
Biotin
Substrate Specificity
Peptides
DNA
Substitution reactions
Substrates
Enzymes
Proteins
Escherichia coli
Amplification
Streptavidin
Escherichia coli Proteins
Gene Library
desthiobiotin
Mutation

Keywords

  • Biotin
  • Biotin protein ligase
  • Desthiobiotin
  • Emulsion
  • In vitro compartmentalization

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Medicine(all)

Cite this

Directed evolution of the substrate specificity of biotin ligase. / Lu, Wei Cheng; Levy, Matthew; Kincaid, Rodney; Ellington, Andrew D.

In: Biotechnology and Bioengineering, Vol. 111, No. 6, 2014, p. 1071-1081.

Research output: Contribution to journalArticle

Lu, WC, Levy, M, Kincaid, R & Ellington, AD 2014, 'Directed evolution of the substrate specificity of biotin ligase', Biotechnology and Bioengineering, vol. 111, no. 6, pp. 1071-1081. https://doi.org/10.1002/bit.25176
Lu, Wei Cheng ; Levy, Matthew ; Kincaid, Rodney ; Ellington, Andrew D. / Directed evolution of the substrate specificity of biotin ligase. In: Biotechnology and Bioengineering. 2014 ; Vol. 111, No. 6. pp. 1071-1081.
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