Activation of the Carbon Concentrating Mechanism by CO2 Deprivation Coincides with Massive Transcriptional Restructuring in Chlamydomonas reinhardtii

Authors

Andrew J. Brueggeman, University of Nebraska-Lincoln
Dayananda S. Gangadharaiah, University of Nebraska-Lincoln
Matyas F. Cserhati, University of Nebraska-LincolnFollow
David Casero, University of California, Los Angeles
Donald P. Weeks, University of Nebraska–Lincoln,Follow
Istvan Ladunga, University of Nebraska at LincolnFollow

ORCID IDs

Istvan Ladunga

Date of this Version

5-2012

Citation

The Plant Cell, Vol. 24: 1860–1875, May 2012; doi: 10.1105/tpc.111.093435

Comments

Copyright (c) 2012 American Society of Plant Biologists. Used by permission.

Abstract

A CO₂-concentrating mechanism (CCM) is essential for the growth of most eukaryotic algae under ambient (392 ppm) and very low (ppm) CO₂ concentrations. In this study, we used replicated deep mRNA sequencing and regulatory network reconstruction to capture a remarkable scope of changes in gene expression that occurs when Chlamydomonas reinhardtii cells are shifted from high to very low levels of CO₂ (£100 ppm). CCM induction 30 to 180 min post-CO₂ deprivation coincides with statistically significant changes in the expression of an astonishing 38% (5884) of the 15,501 nonoverlapping C. reinhardtii genes. Of these genes, 1088 genes were induced and 3828 genes were downregulated by a log₂ factor of 2. The latter indicate a global reduction in photosynthesis, protein synthesis, and energy-related biochemical pathways. The magnitude of transcriptional rearrangement and its major patterns are robust as analyzed by three different statistical methods. De novo DNA motif discovery revealed new putative binding sites for Myeloid oncogene family transcription factors potentially involved in activating low CO₂–induced genes. The (CA)n repeat (9 ≤ n ≤ 25) is present in 29% of upregulated genes but almost absent from promoters of downregulated genes. These discoveries open many avenues for new research.

Includes supplemental materials.