Natural changes in light interact with circadian regulation at promoters to control gene expression in cyanobacteria

Abstract
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Abstract

The circadian clock interacts with other regulatory pathways to tune physiology to predictable daily changes and unexpected environmental fluctuations. However, the complexity of circadian clocks in higher organisms has prevented a clear understanding of how natural environmental conditions affect circadian clocks and their physiological outputs. Here, we dissect the interaction between circadian regulation and responses to fluctuating light in the cyanobacterium Synechococcus elongatus. We demonstrate that natural changes in light intensity substantially affect the expression of hundreds of circadian-clock-controlled genes, many of which are involved in key steps of metabolism. These changes in expression arise from circadian and light-responsive control of RNA polymerase recruitment to promoters by a network of transcription factors including RpaA and RpaB. Using phenomenological modeling constrained by our data, we reveal simple principles that underlie the small number of stereotyped responses of dusk circadian genes to changes in light.

Data availability

The following data sets were generated

(2017) Natural changes in light interact with circadian regulation at promoters to control gene expression in cyanobacteria
GSE104204.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104204

The following previously published data sets were used

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Author details

Joseph Robert Piechura

Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0001-5349-4567
Kapil Amarnath

FAS Center for Systems Biology, Harvard University, Cambridge, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-2589-9684
Erin K O'Shea

Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States

For correspondence
osheae@hhmi.org

Competing interests
Erin K O'Shea, President of Howard Hughes Medical Institute, one of the three founding funders of eLife.

"This ORCID iD identifies the author of this article:" 0000-0002-2649-1018

Funding

Howard Hughes Medical Institute

Erin K O'Shea

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.