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Background  The lipid content of microalgae is regarded as an important indicator for biodiesel. Many attempts have been made to increase the lipid content of microalgae through biochemical and genetic engineering. Significant lipid accumulation in microalgae has been achieved using biochemical engineering, such as nitrogen starvation, but the cell growth was severely limited. However, enrichment of lipid content in microalgae by genetic engineering is anticipated. In this study, GmDof4 from soybean ( Glycine max ), a transcription factor affecting the lipid content in  Arabidopsis , was transferred into  Chlorella ellipsoidea . We then investigated the molecular mechanism underlying the enhancement of the lipid content of transformed  C. ellipsoidea .    Results  We constructed a plant expression vector, pGmDof4, and transformed  GmDof4  into  C. ellipsoidea  by electroporation. The resulting expression of  GmDof4  significantly enhanced the lipid content by 46.4 to 52.9%, but did not affect the growth rate of the host cells under mixotrophic culture conditions. Transcriptome profiles indicated that 1,076 transcripts were differentially regulated: of these, 754 genes were significantly upregulated and 322 genes were significantly downregulated in the transgenic strains under mixotrophic culture conditions. There are 22 significantly regulated genes (|log 2  ratio| >1) involved in lipid and fatty acid metabolism. Quantitative real-time PCR and an enzyme activity assay revealed that GmDof4 significantly up-regulated the gene expression and enzyme activity of acetyl-coenzyme A carboxylase, a key enzyme for fatty acid synthesis, in transgenic  C. ellipsoidea  cells.    Conclusions  The hetero-expression of a transcription factor  GmDof4  gene from soybean can significantly increase the lipid content but not affect the growth rate of  C. ellipsoidea  under mixotrophic culture conditions. The increase in lipid content could be attributed to the large number of genes with regulated expression. In particular, the acetyl-coenzyme A carboxylase gene expression and enzyme activity were significantly upregulated in the transgenic cells. Our research provides a new way to increase the lipid content of microalgae by introducing a specific transcription factor to microalgae strains that can be used for the biofuel and food industries.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-014-0128-4) contains supplementary material, which is available to authorized users.

Overexpression of the soybean transcription factor GmDof4 significantly enhances the lipid content of Chlorella ellipsoidea