Targeted insertional mutagenesis libraries for deep domain insertion profiling

Willow Coyote-Maestas, David Nedrud, Steffan Okorafor, Yungui He, Daniel Schmidt

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Domain recombination is a key principle in protein evolution and protein engineering, but inserting a donor domain into every position of a target protein is not easily experimentally accessible. Most contemporary domain insertion profiling approaches rely on DNA transposons, which are constrained by sequence bias. Here, we establish Saturated Programmable Insertion Engineering (SPINE), an unbiased, comprehensive, and targeted domain insertion library generation technique using oligo library synthesis and multi-step Golden Gate cloning. Through benchmarking to MuA transposon-mediated library generation on four ion channel genes, we demonstrate that SPINE-generated libraries are enriched for in-frame insertions, have drastically reduced sequence bias as well as near-complete and highly-redundant coverage. Unlike transposon-mediated domain insertion that was severely biased and sparse for some genes, SPINE generated high-quality libraries for all genes tested. Using the Inward Rectifier K+ channel Kir2.1, we validate the practical utility of SPINE by constructing and comparing domain insertion permissibility maps. SPINE is the first technology to enable saturated domain insertion profiling. SPINE could help explore the relationship between domain insertions and protein function, and how this relationship is shaped by evolutionary forces and can be engineered for biomedical applications.

Original languageEnglish (US)
Article numbergkz1110
JournalNucleic acids research
Volume48
Issue number2
DOIs
StatePublished - Jan 24 2020

Bibliographical note

Funding Information:
National Institutes of Health [MH109038 to D.S.]; W.C.-M. is supported by a National Science Foundation Graduate Research Fellowship and a Howard Hughes Medical Institute James H. Gilliam, Jr. Fellowship for Advanced Study. Funding for open access charge: Regents of the University of Minnesota, Twin Cities. Conflict of interest statement. None declared.

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

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