Green transcription factors: a chlamydomonas overview

Abstract

Transcription factors (TFs) control gene expression by interacting with cis-elements in target gene promoters. Transcription regulators (TRs) assist in controlling gene expression through interaction with TFs, chromatin remodeling, or other mechanisms. Both types of proteins thus constitute master controllers of dynamic transcriptional networks. To uncover such control elements in the photosynthetic green alga Chlamydomonas reinhardtii, we performed a comprehensive analysis of its genome sequence. In total, we identified 234 genes encoding 147 TFs and 87 TRs of approximately 40 families. The set of putative TFs and TRs, including their transcript and protein sequences, domain architectures, and supporting information about putative orthologs, is available at http://plntfdb.bio.uni-potsdam.de/v2.0/. Twelve of 34 plant-specific TF families were found in at least one algal species, indicating their early evolutionary origin. Twenty-two plant-specific TF families and one plant-specific TR family were not observed in algae, suggesting their specific association with developmental or physiological processes characteristic to multicellular plants. We also analyzed the occurrence of proteins that constitute the light-regulated transcriptional network in angiosperms and found putative algal orthologs for most of them. Our analysis provides a solid ground for future experimental studies aiming at deciphering the transcriptional regulatory networks in green algae.

Figure 1.—

Phylogenetic tree of RWP-RK TFs in plants. We identified one PoGO (PoGO 1) conserved in all green plants, which includes the NIT2 TF (CRE 195807), a regulatory factor of genes involved in the nitrate assimilation pathway. Additionally, there are two possible groups of paralogs (PoGP 1 and PoGP 2) of Chlamydomonas genes. Red, C. merolae (CME); violet, O. tauri (OTA); light green, C. reinhardtii (CRE); light blue, P. patens (PPA); green, A. thaliana (ATH); brown, P. trichocarpa (PTR); gray, O. sativa ssp. japonica (OSAJ). The first three letters of the sequence name indicate the species (the first four letters in the case of OSAJ), and the remaining letters or numbers represent the accession code through which the respective sequence can be retrieved from the PlnTFDB (http://plntfdb.bio.uni-potsdam.de/v2.0).