Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii

J Exp Bot. 2015 Aug;66(15):4551-66. doi: 10.1093/jxb/erv217. Epub 2015 May 28.


Microalgae-based biofuels are promising sources of alternative energy, but improvements throughout the production process are required to establish them as economically feasible. One of the most influential improvements would be a significant increase in lipid yields, which could be achieved by altering the regulation of lipid biosynthesis and accumulation. Chlamydomonas reinhardtii accumulates oil (triacylglycerols, TAG) in response to nitrogen (N) deprivation. Although a few important regulatory genes have been identified that are involved in controlling this process, a global understanding of the larger regulatory network has not been developed. In order to uncover this network in this species, a combined omics (transcriptomic, proteomic and metabolomic) analysis was applied to cells grown in a time course experiment after a shift from N-replete to N-depleted conditions. Changes in transcript and protein levels of 414 predicted transcription factors (TFs) and transcriptional regulators (TRs) were monitored relative to other genes. The TF and TR genes were thus classified by two separate measures: up-regulated versus down-regulated and early response versus late response relative to two phases of polar lipid synthesis (before and after TAG biosynthesis initiation). Lipidomic and primary metabolite profiling generated compound accumulation levels that were integrated with the transcript dataset and TF profiling to produce a transcriptional regulatory network. Evaluation of this proposed regulatory network led to the identification of several regulatory hubs that control many aspects of cellular metabolism, from N assimilation and metabolism, to central metabolism, photosynthesis and lipid metabolism.

Keywords: Biofuel; Chlamydomonas reinhardtii; RNA-seq; metabolomics; network analysis; proteomics; regulatory hubs; transcription factors; transcriptional regulators..

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algal Proteins / genetics
  • Algal Proteins / metabolism
  • Chlamydomonas reinhardtii / genetics*
  • Chlamydomonas reinhardtii / metabolism
  • Gene Expression Regulation*
  • Gene Regulatory Networks*
  • Genome
  • Lipid Metabolism*
  • Metabolome
  • Nitrogen / deficiency*
  • Proteome
  • Transcriptome


  • Algal Proteins
  • Proteome
  • Nitrogen