Apr 18, 2014

Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes

BioRxiv : the Preprint Server for Biology
Alexandre MelnikovTarjei S Mikkelsen

Abstract

Deep mutational scanning has emerged as a promising tool for mapping sequence-activity relationships in proteins, RNA and DNA. In this approach, diverse variants of a sequence of interest are first ranked according to their activities in a relevant pooled assay, and this ranking is then used to infer the shape of the fitness landscape around the wild-type sequence. Little is currently know, however, about the degree to which such fitness landscapes are dependent on the specific assay conditions from which they are inferred. To explore this issue, we performed deep mutational scanning of APH(3')II, a Tn5 transposon-derived kinase that confers resistance to aminoglycoside antibiotics, in E. coli under selection with each of six structurally diverse antibiotics at a range of inhibitory concentrations. We found that the resulting fitness landscapes showed significant dependence on both antibiotic structure and concentration. This shows that the notion of essential amino acid residues is context-dependent, but also that this dependence can be exploited to guide protein engineering. Specifically, we found that differential analysis of fitness landscapes allowed us to generate synthetic APH(3')II variants with orthogonal substrate spe...Continue Reading

  • References
  • Citations

References

  • We're still populating references for this paper, please check back later.
  • References
  • Citations

Citations

  • This paper may not have been cited yet.

Mentioned in this Paper

In Vivo
Antibiotic throat preparations
Antifungal Antibiotics, Topical
Antibiotics, Gynecological
Pharmacologic Substance
Genes, Jumping
Structure
Antibiotics for systemic use
Phosphotransferases
Analysis

About this Paper

Related Feeds

Antifungals

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Antifungals (ASM)

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

Aminoglycosides (ASM)

Aminoglycoside is a medicinal and bacteriologic category of traditional Gram-negative antibacterial medications that inhibit protein synthesis and contain as a portion of the molecule an amino-modified glycoside. Discover the latest research on aminoglycoside here.

Aminoglycosides

Aminoglycoside is a medicinal and bacteriologic category of traditional Gram-negative antibacterial medications that inhibit protein synthesis and contain as a portion of the molecule an amino-modified glycoside. Discover the latest research on aminoglycoside here.

Related Papers

Sequence-activity relationships guide directed evolution

(opens in new tab)
Nature Biotechnology
Joelle N Pelletier, Robert Lortie

Genomic analysis reveals distinct concentration-dependent evolutionary trajectories for antibiotic resistance in Escherichia coli

(opens in new tab)
DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes
Aalap MogreAswin Sai Narain Seshasayee

Directed Evolution of Proteins Based on Mutational Scanning

(opens in new tab)
Methods in Molecular Biology
Carlos G Acevedo-RochaManfred T Reetz
ContactHelpTerms Privacy Cookies Blog
© 2020 Meta ULC. All rights reserved