Reconstructing Dynamic Promoter Activity Profiles from Reporter Gene Data

Soumya Kannan, Thomas Sams, Jérôme Maury, Christopher T Workman*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

347 Downloads (Pure)

Abstract

Accurate characterization of promoter activity is important when designing expression systems for systems biology and metabolic engineering applications. Promoters that respond to changes in the environment enable the dynamic control of gene expression without the necessity of inducer compounds, for example. However, the dynamic nature of these processes poses challenges for estimating promoter activity. Most experimental approaches utilize reporter gene expression to estimate promoter activity. Typically the reporter gene encodes a fluorescent protein that is used to infer a constant promoter activity despite the fact that the observed output may be dynamic and is a number of steps away from the transcription process. In fact, some promoters that are often thought of as constitutive can show changes in activity when growth conditions change. For these reasons, we have developed a system of ordinary differential equations for estimating dynamic promoter activity for promoters that change their activity in response to the environment that is robust to noise and changes in growth rate. Our approach, inference of dynamic promoter activity (PromAct), improves on existing methods by more accurately inferring known promoter activity profiles. This method is also capable of estimating the correct scale of promoter activity and can be applied to quantitative data sets to estimate quantitative rates.
Original languageEnglish
JournalA C S Synthetic Biology
ISSN2161-5063
DOIs
Publication statusPublished - 2018

Bibliographical note

This is an open access article published under a Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.

Keywords

  • Dynamic model
  • Fluorescent proteins
  • Growth profiling
  • Ordinary differential equations
  • Promoter activity

Cite this